[med-svn] [openbugs] 01/01: Imported Upstream version 3.2.3
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Fri Jun 6 04:40:40 UTC 2014
This is an automated email from the git hooks/post-receive script.
bob.dybian-guest pushed a commit to branch master
in repository openbugs.
commit 0ae4596ed14b5e9cb15e9bb6d7698aaaee7e5890
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Fri Jun 6 06:30:35 2014 +0200
Imported Upstream version 3.2.3
---
AUTHORS | 8 +
COPYING | 42 +
ChangeLog | 5 +
INSTALL | 370 ++
Makefile.am | 1 +
Makefile.in | 676 +++
NEWS | 27 +
README | 64 +
aclocal.m4 | 971 ++++
autom4te.cache/output.0 | 4564 ++++++++++++++++++
autom4te.cache/output.1 | 4564 ++++++++++++++++++
autom4te.cache/requests | 144 +
autom4te.cache/traces.0 | 776 +++
autom4te.cache/traces.1 | 335 ++
bin/OpenBUGS | 172 +
configure | 4564 ++++++++++++++++++
configure.ac | 12 +
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doc/Examples/Cervix.html | 1 +
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doc/Examples/Cervixinits1.txt | 1 +
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doc/Examples/DataCloning.html | 1 +
doc/Examples/Dogs.html | 1 +
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doc/Examples/Dugongs.html | 1 +
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doc/Examples/Fire.html | 1 +
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doc/Examples/Firedata.txt | 499 ++
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doc/Examples/FunShapesinits1.html | 1 +
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doc/Reliability/Manuals/Distributions.html | 1 +
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doc/testscript.txt | 13 +
install-sh | 527 +++
lib/libOpenBUGS.so | Bin 0 -> 3090092 bytes
missing | 331 ++
src/Makefile.am | 37 +
src/Makefile.in | 342 ++
src/OpenBUGS.h | 14 +
src/OpenBUGSCli.c | 17 +
1559 files changed, 32452 insertions(+)
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 0000000..64fae2c
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1,8 @@
+OpenBUGS was developed by Andrew Thomas, Dave Lunn, David Spiegelhalter and Nicky Best.
+
+Nathan Coulter, Neal Thomas and Chris Jackson also contributed to the Linux port.
+
+This Linux source package for OpenBUGS is maintained by Chris Jackson
+<chris.jackson at mrc-bsu.cam.ac.uk>
+
+For further information, see http://openbugs.info
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..64bb42a
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,42 @@
+COPYRIGHT
+---------
+
+OpenBUGS is copyright
+
+(c) 2010-2011 OpenBUGS Project Management Group
+(c) 1990-1996 Medical Research Council, UK
+(c) 1996-2010 MRC (UK) and Imperial College, UK
+
+OpenBUGS may be modified and redistributed under the terms of the GPL
+version 3: http://www.gnu.org/licenses/gpl.html
+
+OpenBUGS also includes modified and unmodified components from
+"BlackBox Component Builder" (BlackBox) and from "Component Pascal
+Source Code Beautifier" (CpcBeautifier).
+
+Full and unmodified versions of these software can be obtained from
+BlackBox: http://www.oberon.ch/blackbox.html
+CpcBeautifier: http://www.zinnamturm.eu/downloadsAC.htm
+
+
+DEVELOPMENT
+-----------
+
+The source code for the OpenBUGS shared library libOpenBUGS.so is
+provided in the Windows package for OpenBUGS, available for download from
+
+http://www.openbugs.info
+
+The source is written in the Blackbox Component Pascal language, and
+provided as Blackbox compound document (.odc) files. These can be
+opened in the Windows version of OpenBUGS, but to compile them the
+Blackbox development environment is required, available from
+
+http://oberon.ch/blackbox.html
+
+Blackbox is only available for Windows, and no Linux development tools
+exist. The Linux shared library is cross-compiled on Windows. For
+further information about developing OpenBUGS, see the files in the
+Developer subdirectory of the Windows installation.
+
+See each individual source file (.odc) for an exact license statement.
diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 0000000..b92a019
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,5 @@
+See NEWS for changes to source package for Linux, and
+
+ http://openbugs.net/w/WhatsNew
+
+for changes in OpenBUGS itself.
diff --git a/INSTALL b/INSTALL
new file mode 100644
index 0000000..a1e89e1
--- /dev/null
+++ b/INSTALL
@@ -0,0 +1,370 @@
+Installation Instructions
+*************************
+
+Copyright (C) 1994-1996, 1999-2002, 2004-2011 Free Software Foundation,
+Inc.
+
+ Copying and distribution of this file, with or without modification,
+are permitted in any medium without royalty provided the copyright
+notice and this notice are preserved. This file is offered as-is,
+without warranty of any kind.
+
+Basic Installation
+==================
+
+ Briefly, the shell commands `./configure; make; make install' should
+configure, build, and install this package. The following
+more-detailed instructions are generic; see the `README' file for
+instructions specific to this package. Some packages provide this
+`INSTALL' file but do not implement all of the features documented
+below. The lack of an optional feature in a given package is not
+necessarily a bug. More recommendations for GNU packages can be found
+in *note Makefile Conventions: (standards)Makefile Conventions.
+
+ The `configure' shell script attempts to guess correct values for
+various system-dependent variables used during compilation. It uses
+those values to create a `Makefile' in each directory of the package.
+It may also create one or more `.h' files containing system-dependent
+definitions. Finally, it creates a shell script `config.status' that
+you can run in the future to recreate the current configuration, and a
+file `config.log' containing compiler output (useful mainly for
+debugging `configure').
+
+ It can also use an optional file (typically called `config.cache'
+and enabled with `--cache-file=config.cache' or simply `-C') that saves
+the results of its tests to speed up reconfiguring. Caching is
+disabled by default to prevent problems with accidental use of stale
+cache files.
+
+ If you need to do unusual things to compile the package, please try
+to figure out how `configure' could check whether to do them, and mail
+diffs or instructions to the address given in the `README' so they can
+be considered for the next release. If you are using the cache, and at
+some point `config.cache' contains results you don't want to keep, you
+may remove or edit it.
+
+ The file `configure.ac' (or `configure.in') is used to create
+`configure' by a program called `autoconf'. You need `configure.ac' if
+you want to change it or regenerate `configure' using a newer version
+of `autoconf'.
+
+ The simplest way to compile this package is:
+
+ 1. `cd' to the directory containing the package's source code and type
+ `./configure' to configure the package for your system.
+
+ Running `configure' might take a while. While running, it prints
+ some messages telling which features it is checking for.
+
+ 2. Type `make' to compile the package.
+
+ 3. Optionally, type `make check' to run any self-tests that come with
+ the package, generally using the just-built uninstalled binaries.
+
+ 4. Type `make install' to install the programs and any data files and
+ documentation. When installing into a prefix owned by root, it is
+ recommended that the package be configured and built as a regular
+ user, and only the `make install' phase executed with root
+ privileges.
+
+ 5. Optionally, type `make installcheck' to repeat any self-tests, but
+ this time using the binaries in their final installed location.
+ This target does not install anything. Running this target as a
+ regular user, particularly if the prior `make install' required
+ root privileges, verifies that the installation completed
+ correctly.
+
+ 6. You can remove the program binaries and object files from the
+ source code directory by typing `make clean'. To also remove the
+ files that `configure' created (so you can compile the package for
+ a different kind of computer), type `make distclean'. There is
+ also a `make maintainer-clean' target, but that is intended mainly
+ for the package's developers. If you use it, you may have to get
+ all sorts of other programs in order to regenerate files that came
+ with the distribution.
+
+ 7. Often, you can also type `make uninstall' to remove the installed
+ files again. In practice, not all packages have tested that
+ uninstallation works correctly, even though it is required by the
+ GNU Coding Standards.
+
+ 8. Some packages, particularly those that use Automake, provide `make
+ distcheck', which can by used by developers to test that all other
+ targets like `make install' and `make uninstall' work correctly.
+ This target is generally not run by end users.
+
+Compilers and Options
+=====================
+
+ Some systems require unusual options for compilation or linking that
+the `configure' script does not know about. Run `./configure --help'
+for details on some of the pertinent environment variables.
+
+ You can give `configure' initial values for configuration parameters
+by setting variables in the command line or in the environment. Here
+is an example:
+
+ ./configure CC=c99 CFLAGS=-g LIBS=-lposix
+
+ *Note Defining Variables::, for more details.
+
+Compiling For Multiple Architectures
+====================================
+
+ You can compile the package for more than one kind of computer at the
+same time, by placing the object files for each architecture in their
+own directory. To do this, you can use GNU `make'. `cd' to the
+directory where you want the object files and executables to go and run
+the `configure' script. `configure' automatically checks for the
+source code in the directory that `configure' is in and in `..'. This
+is known as a "VPATH" build.
+
+ With a non-GNU `make', it is safer to compile the package for one
+architecture at a time in the source code directory. After you have
+installed the package for one architecture, use `make distclean' before
+reconfiguring for another architecture.
+
+ On MacOS X 10.5 and later systems, you can create libraries and
+executables that work on multiple system types--known as "fat" or
+"universal" binaries--by specifying multiple `-arch' options to the
+compiler but only a single `-arch' option to the preprocessor. Like
+this:
+
+ ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+ CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+ CPP="gcc -E" CXXCPP="g++ -E"
+
+ This is not guaranteed to produce working output in all cases, you
+may have to build one architecture at a time and combine the results
+using the `lipo' tool if you have problems.
+
+Installation Names
+==================
+
+ By default, `make install' installs the package's commands under
+`/usr/local/bin', include files under `/usr/local/include', etc. You
+can specify an installation prefix other than `/usr/local' by giving
+`configure' the option `--prefix=PREFIX', where PREFIX must be an
+absolute file name.
+
+ You can specify separate installation prefixes for
+architecture-specific files and architecture-independent files. If you
+pass the option `--exec-prefix=PREFIX' to `configure', the package uses
+PREFIX as the prefix for installing programs and libraries.
+Documentation and other data files still use the regular prefix.
+
+ In addition, if you use an unusual directory layout you can give
+options like `--bindir=DIR' to specify different values for particular
+kinds of files. Run `configure --help' for a list of the directories
+you can set and what kinds of files go in them. In general, the
+default for these options is expressed in terms of `${prefix}', so that
+specifying just `--prefix' will affect all of the other directory
+specifications that were not explicitly provided.
+
+ The most portable way to affect installation locations is to pass the
+correct locations to `configure'; however, many packages provide one or
+both of the following shortcuts of passing variable assignments to the
+`make install' command line to change installation locations without
+having to reconfigure or recompile.
+
+ The first method involves providing an override variable for each
+affected directory. For example, `make install
+prefix=/alternate/directory' will choose an alternate location for all
+directory configuration variables that were expressed in terms of
+`${prefix}'. Any directories that were specified during `configure',
+but not in terms of `${prefix}', must each be overridden at install
+time for the entire installation to be relocated. The approach of
+makefile variable overrides for each directory variable is required by
+the GNU Coding Standards, and ideally causes no recompilation.
+However, some platforms have known limitations with the semantics of
+shared libraries that end up requiring recompilation when using this
+method, particularly noticeable in packages that use GNU Libtool.
+
+ The second method involves providing the `DESTDIR' variable. For
+example, `make install DESTDIR=/alternate/directory' will prepend
+`/alternate/directory' before all installation names. The approach of
+`DESTDIR' overrides is not required by the GNU Coding Standards, and
+does not work on platforms that have drive letters. On the other hand,
+it does better at avoiding recompilation issues, and works well even
+when some directory options were not specified in terms of `${prefix}'
+at `configure' time.
+
+Optional Features
+=================
+
+ If the package supports it, you can cause programs to be installed
+with an extra prefix or suffix on their names by giving `configure' the
+option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
+
+ Some packages pay attention to `--enable-FEATURE' options to
+`configure', where FEATURE indicates an optional part of the package.
+They may also pay attention to `--with-PACKAGE' options, where PACKAGE
+is something like `gnu-as' or `x' (for the X Window System). The
+`README' should mention any `--enable-' and `--with-' options that the
+package recognizes.
+
+ For packages that use the X Window System, `configure' can usually
+find the X include and library files automatically, but if it doesn't,
+you can use the `configure' options `--x-includes=DIR' and
+`--x-libraries=DIR' to specify their locations.
+
+ Some packages offer the ability to configure how verbose the
+execution of `make' will be. For these packages, running `./configure
+--enable-silent-rules' sets the default to minimal output, which can be
+overridden with `make V=1'; while running `./configure
+--disable-silent-rules' sets the default to verbose, which can be
+overridden with `make V=0'.
+
+Particular systems
+==================
+
+ On HP-UX, the default C compiler is not ANSI C compatible. If GNU
+CC is not installed, it is recommended to use the following options in
+order to use an ANSI C compiler:
+
+ ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
+
+and if that doesn't work, install pre-built binaries of GCC for HP-UX.
+
+ HP-UX `make' updates targets which have the same time stamps as
+their prerequisites, which makes it generally unusable when shipped
+generated files such as `configure' are involved. Use GNU `make'
+instead.
+
+ On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
+parse its `<wchar.h>' header file. The option `-nodtk' can be used as
+a workaround. If GNU CC is not installed, it is therefore recommended
+to try
+
+ ./configure CC="cc"
+
+and if that doesn't work, try
+
+ ./configure CC="cc -nodtk"
+
+ On Solaris, don't put `/usr/ucb' early in your `PATH'. This
+directory contains several dysfunctional programs; working variants of
+these programs are available in `/usr/bin'. So, if you need `/usr/ucb'
+in your `PATH', put it _after_ `/usr/bin'.
+
+ On Haiku, software installed for all users goes in `/boot/common',
+not `/usr/local'. It is recommended to use the following options:
+
+ ./configure --prefix=/boot/common
+
+Specifying the System Type
+==========================
+
+ There may be some features `configure' cannot figure out
+automatically, but needs to determine by the type of machine the package
+will run on. Usually, assuming the package is built to be run on the
+_same_ architectures, `configure' can figure that out, but if it prints
+a message saying it cannot guess the machine type, give it the
+`--build=TYPE' option. TYPE can either be a short name for the system
+type, such as `sun4', or a canonical name which has the form:
+
+ CPU-COMPANY-SYSTEM
+
+where SYSTEM can have one of these forms:
+
+ OS
+ KERNEL-OS
+
+ See the file `config.sub' for the possible values of each field. If
+`config.sub' isn't included in this package, then this package doesn't
+need to know the machine type.
+
+ If you are _building_ compiler tools for cross-compiling, you should
+use the option `--target=TYPE' to select the type of system they will
+produce code for.
+
+ If you want to _use_ a cross compiler, that generates code for a
+platform different from the build platform, you should specify the
+"host" platform (i.e., that on which the generated programs will
+eventually be run) with `--host=TYPE'.
+
+Sharing Defaults
+================
+
+ If you want to set default values for `configure' scripts to share,
+you can create a site shell script called `config.site' that gives
+default values for variables like `CC', `cache_file', and `prefix'.
+`configure' looks for `PREFIX/share/config.site' if it exists, then
+`PREFIX/etc/config.site' if it exists. Or, you can set the
+`CONFIG_SITE' environment variable to the location of the site script.
+A warning: not all `configure' scripts look for a site script.
+
+Defining Variables
+==================
+
+ Variables not defined in a site shell script can be set in the
+environment passed to `configure'. However, some packages may run
+configure again during the build, and the customized values of these
+variables may be lost. In order to avoid this problem, you should set
+them in the `configure' command line, using `VAR=value'. For example:
+
+ ./configure CC=/usr/local2/bin/gcc
+
+causes the specified `gcc' to be used as the C compiler (unless it is
+overridden in the site shell script).
+
+Unfortunately, this technique does not work for `CONFIG_SHELL' due to
+an Autoconf bug. Until the bug is fixed you can use this workaround:
+
+ CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
+
+`configure' Invocation
+======================
+
+ `configure' recognizes the following options to control how it
+operates.
+
+`--help'
+`-h'
+ Print a summary of all of the options to `configure', and exit.
+
+`--help=short'
+`--help=recursive'
+ Print a summary of the options unique to this package's
+ `configure', and exit. The `short' variant lists options used
+ only in the top level, while the `recursive' variant lists options
+ also present in any nested packages.
+
+`--version'
+`-V'
+ Print the version of Autoconf used to generate the `configure'
+ script, and exit.
+
+`--cache-file=FILE'
+ Enable the cache: use and save the results of the tests in FILE,
+ traditionally `config.cache'. FILE defaults to `/dev/null' to
+ disable caching.
+
+`--config-cache'
+`-C'
+ Alias for `--cache-file=config.cache'.
+
+`--quiet'
+`--silent'
+`-q'
+ Do not print messages saying which checks are being made. To
+ suppress all normal output, redirect it to `/dev/null' (any error
+ messages will still be shown).
+
+`--srcdir=DIR'
+ Look for the package's source code in directory DIR. Usually
+ `configure' can determine that directory automatically.
+
+`--prefix=DIR'
+ Use DIR as the installation prefix. *note Installation Names::
+ for more details, including other options available for fine-tuning
+ the installation locations.
+
+`--no-create'
+`-n'
+ Run the configure checks, but stop before creating any output
+ files.
+
+`configure' also accepts some other, not widely useful, options. Run
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diff --git a/NEWS b/NEWS
new file mode 100644
index 0000000..cf1d9e3
--- /dev/null
+++ b/NEWS
@@ -0,0 +1,27 @@
+CHANGES TO OpenBUGS ITSELF
+--------------------------
+
+For a list of the changes in recent versions of OpenBUGS, see
+
+http://openbugs.net/w/WhatsNew
+
+
+CHANGES TO THE LINUX PACKAGE
+----------------------------
+
+Version 3.2.1 (2011-03-21)
+--------------------------
+First release of the official Linux source package for OpenBUGS
+
+
+Version 3.2.2 (2012-07)
+-----------------------
+Install binary, library and files directly into $(prefix)/bin,
+$(prefix)/lib, and $(prefix)/share/doc/openbugs, rather than the old
+method of symlinking to files installed in $(prefix)/lib/OpenBUGS.
+
+
+Version 3.2.3 (2014-03)
+--------------------------
+$(DESTDIR) no longer omitted when creating doc dir in Makefile. Thanks
+to Paul Johnson.
diff --git a/README b/README
new file mode 100644
index 0000000..81e99da
--- /dev/null
+++ b/README
@@ -0,0 +1,64 @@
+OpenBUGS is a software package for performing Bayesian analysis and
+simulation using Markov Chain Monte Carlo.
+
+
+
+INSTALLATION
+------------
+
+To install OpenBUGS on a standard Linux system :
+
+./configure
+make
+sudo make install
+
+The "sudo" is included since "make install" requires root
+(administrative) privileges by default. If you don't have
+administrative access, you can get around this by installing in a
+location other than /usr/local, for example /home/chris/usr :
+
+./configure --prefix=/home/chris/usr
+make
+make install
+
+
+
+DOCUMENTATION
+-------------
+
+The full documentation for the OpenBUGS modelling language is
+installed as HTML, by default in
+
+/usr/local/lib/OpenBUGS/doc/Manuals/Contents.html
+
+For help on invoking the Linux command-line program, see
+
+man OpenBUGS
+
+For further information about OpenBUGS, see http://openbugs.info
+
+
+
+DEVELOPMENT
+-----------
+
+For information on development with the OpenBUGS source code, see
+the OpenBUGS Developer Manual, installed by default in
+
+/usr/local/lib/OpenBUGS/doc/Developer/Manual.html
+
+The source code for the OpenBUGS shared library libOpenBUGS.so is
+provided in the Windows package for OpenBUGS, available for download from
+
+http://www.openbugs.net
+
+The source is written in the Blackbox Component Pascal language, and
+provided as Blackbox compound document (.odc) files. These can be
+opened in the Windows version of OpenBUGS, but to compile them the
+Blackbox development environment is required, available from
+
+http://oberon.ch/blackbox.html
+
+Blackbox is only available for Windows, and no Linux development tools
+exist. The ELF format shared library used by the Linux version of
+OpenBUGS is compiled and linked on Windows.
diff --git a/aclocal.m4 b/aclocal.m4
new file mode 100644
index 0000000..da06da5
--- /dev/null
+++ b/aclocal.m4
@@ -0,0 +1,971 @@
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+# serial 1
+
+# AM_PROG_INSTALL_STRIP
+# ---------------------
+# One issue with vendor `install' (even GNU) is that you can't
+# specify the program used to strip binaries. This is especially
+# annoying in cross-compiling environments, where the build's strip
+# is unlikely to handle the host's binaries.
+# Fortunately install-sh will honor a STRIPPROG variable, so we
+# always use install-sh in `make install-strip', and initialize
+# STRIPPROG with the value of the STRIP variable (set by the user).
+AC_DEFUN([AM_PROG_INSTALL_STRIP],
+[AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+dnl Don't test for $cross_compiling = yes, because it might be `maybe'.
+if test "$cross_compiling" != no; then
+ AC_CHECK_TOOL([STRIP], [strip], :)
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+AC_SUBST([INSTALL_STRIP_PROGRAM])])
+
+# Copyright (C) 2006, 2008, 2010 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 3
+
+# _AM_SUBST_NOTMAKE(VARIABLE)
+# ---------------------------
+# Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in.
+# This macro is traced by Automake.
+AC_DEFUN([_AM_SUBST_NOTMAKE])
+
+# AM_SUBST_NOTMAKE(VARIABLE)
+# --------------------------
+# Public sister of _AM_SUBST_NOTMAKE.
+AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
+
+# Check how to create a tarball. -*- Autoconf -*-
+
+# Copyright (C) 2004, 2005, 2012 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 2
+
+# _AM_PROG_TAR(FORMAT)
+# --------------------
+# Check how to create a tarball in format FORMAT.
+# FORMAT should be one of `v7', `ustar', or `pax'.
+#
+# Substitute a variable $(am__tar) that is a command
+# writing to stdout a FORMAT-tarball containing the directory
+# $tardir.
+# tardir=directory && $(am__tar) > result.tar
+#
+# Substitute a variable $(am__untar) that extract such
+# a tarball read from stdin.
+# $(am__untar) < result.tar
+AC_DEFUN([_AM_PROG_TAR],
+[# Always define AMTAR for backward compatibility. Yes, it's still used
+# in the wild :-( We should find a proper way to deprecate it ...
+AC_SUBST([AMTAR], ['$${TAR-tar}'])
+m4_if([$1], [v7],
+ [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
+ [m4_case([$1], [ustar],, [pax],,
+ [m4_fatal([Unknown tar format])])
+AC_MSG_CHECKING([how to create a $1 tar archive])
+# Loop over all known methods to create a tar archive until one works.
+_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
+_am_tools=${am_cv_prog_tar_$1-$_am_tools}
+# Do not fold the above two line into one, because Tru64 sh and
+# Solaris sh will not grok spaces in the rhs of `-'.
+for _am_tool in $_am_tools
+do
+ case $_am_tool in
+ gnutar)
+ for _am_tar in tar gnutar gtar;
+ do
+ AM_RUN_LOG([$_am_tar --version]) && break
+ done
+ am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
+ am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
+ am__untar="$_am_tar -xf -"
+ ;;
+ plaintar)
+ # Must skip GNU tar: if it does not support --format= it doesn't create
+ # ustar tarball either.
+ (tar --version) >/dev/null 2>&1 && continue
+ am__tar='tar chf - "$$tardir"'
+ am__tar_='tar chf - "$tardir"'
+ am__untar='tar xf -'
+ ;;
+ pax)
+ am__tar='pax -L -x $1 -w "$$tardir"'
+ am__tar_='pax -L -x $1 -w "$tardir"'
+ am__untar='pax -r'
+ ;;
+ cpio)
+ am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
+ am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
+ am__untar='cpio -i -H $1 -d'
+ ;;
+ none)
+ am__tar=false
+ am__tar_=false
+ am__untar=false
+ ;;
+ esac
+
+ # If the value was cached, stop now. We just wanted to have am__tar
+ # and am__untar set.
+ test -n "${am_cv_prog_tar_$1}" && break
+
+ # tar/untar a dummy directory, and stop if the command works
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ echo GrepMe > conftest.dir/file
+ AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+ rm -rf conftest.dir
+ if test -s conftest.tar; then
+ AM_RUN_LOG([$am__untar <conftest.tar])
+ grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
+ fi
+done
+rm -rf conftest.dir
+
+AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
+AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+AC_SUBST([am__tar])
+AC_SUBST([am__untar])
+]) # _AM_PROG_TAR
+
diff --git a/autom4te.cache/output.0 b/autom4te.cache/output.0
new file mode 100644
index 0000000..d8319a1
--- /dev/null
+++ b/autom4te.cache/output.0
@@ -0,0 +1,4564 @@
+@%:@! /bin/sh
+@%:@ Guess values for system-dependent variables and create Makefiles.
+@%:@ Generated by GNU Autoconf 2.68 for OpenBUGS 0.1.
+@%:@
+@%:@
+@%:@ Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+@%:@ 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
+@%:@ Foundation, Inc.
+@%:@
+@%:@
+@%:@ This configure script is free software; the Free Software Foundation
+@%:@ gives unlimited permission to copy, distribute and modify it.
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in @%:@(
+ *posix*) :
+ set -o posix ;; @%:@(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in @%:@(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+as_myself=
+case $0 in @%:@((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test "x$CONFIG_SHELL" = x; then
+ as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
+else
+ case \`(set -o) 2>/dev/null\` in @%:@(
+ *posix*) :
+ set -o posix ;; @%:@(
+ *) :
+ ;;
+esac
+fi
+"
+ as_required="as_fn_return () { (exit \$1); }
+as_fn_success () { as_fn_return 0; }
+as_fn_failure () { as_fn_return 1; }
+as_fn_ret_success () { return 0; }
+as_fn_ret_failure () { return 1; }
+
+exitcode=0
+as_fn_success || { exitcode=1; echo as_fn_success failed.; }
+as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
+as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
+as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
+if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
+
+else
+ exitcode=1; echo positional parameters were not saved.
+fi
+test x\$exitcode = x0 || exit 1"
+ as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
+ as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
+ eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
+ test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1"
+ if (eval "$as_required") 2>/dev/null; then :
+ as_have_required=yes
+else
+ as_have_required=no
+fi
+ if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
+
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+as_found=false
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ as_found=:
+ case $as_dir in @%:@(
+ /*)
+ for as_base in sh bash ksh sh5; do
+ # Try only shells that exist, to save several forks.
+ as_shell=$as_dir/$as_base
+ if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ CONFIG_SHELL=$as_shell as_have_required=yes
+ if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ break 2
+fi
+fi
+ done;;
+ esac
+ as_found=false
+done
+$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
+ CONFIG_SHELL=$SHELL as_have_required=yes
+fi; }
+IFS=$as_save_IFS
+
+
+ if test "x$CONFIG_SHELL" != x; then :
+ # We cannot yet assume a decent shell, so we have to provide a
+ # neutralization value for shells without unset; and this also
+ # works around shells that cannot unset nonexistent variables.
+ # Preserve -v and -x to the replacement shell.
+ BASH_ENV=/dev/null
+ ENV=/dev/null
+ (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+ export CONFIG_SHELL
+ case $- in @%:@ ((((
+ *v*x* | *x*v* ) as_opts=-vx ;;
+ *v* ) as_opts=-v ;;
+ *x* ) as_opts=-x ;;
+ * ) as_opts= ;;
+ esac
+ exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"}
+fi
+
+ if test x$as_have_required = xno; then :
+ $as_echo "$0: This script requires a shell more modern than all"
+ $as_echo "$0: the shells that I found on your system."
+ if test x${ZSH_VERSION+set} = xset ; then
+ $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
+ $as_echo "$0: be upgraded to zsh 4.3.4 or later."
+ else
+ $as_echo "$0: Please tell bug-autoconf at gnu.org about your system,
+$0: including any error possibly output before this
+$0: message. Then install a modern shell, or manually run
+$0: the script under such a shell if you do have one."
+ fi
+ exit 1
+fi
+fi
+fi
+SHELL=${CONFIG_SHELL-/bin/sh}
+export SHELL
+# Unset more variables known to interfere with behavior of common tools.
+CLICOLOR_FORCE= GREP_OPTIONS=
+unset CLICOLOR_FORCE GREP_OPTIONS
+
+## --------------------- ##
+## M4sh Shell Functions. ##
+## --------------------- ##
+@%:@ as_fn_unset VAR
+@%:@ ---------------
+@%:@ Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+
+@%:@ as_fn_set_status STATUS
+@%:@ -----------------------
+@%:@ Set @S|@? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} @%:@ as_fn_set_status
+
+@%:@ as_fn_exit STATUS
+@%:@ -----------------
+@%:@ Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} @%:@ as_fn_exit
+
+@%:@ as_fn_mkdir_p
+@%:@ -------------
+@%:@ Create "@S|@as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} @%:@ as_fn_mkdir_p
+@%:@ as_fn_append VAR VALUE
+@%:@ ----------------------
+@%:@ Append the text in VALUE to the end of the definition contained in VAR. Take
+@%:@ advantage of any shell optimizations that allow amortized linear growth over
+@%:@ repeated appends, instead of the typical quadratic growth present in naive
+@%:@ implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+@%:@ as_fn_arith ARG...
+@%:@ ------------------
+@%:@ Perform arithmetic evaluation on the ARGs, and store the result in the
+@%:@ global @S|@as_val. Take advantage of shells that can avoid forks. The arguments
+@%:@ must be portable across @S|@(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+@%:@ as_fn_error STATUS ERROR [LINENO LOG_FD]
+@%:@ ----------------------------------------
+@%:@ Output "`basename @S|@0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+@%:@ provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+@%:@ script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} @%:@ as_fn_error
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+
+ as_lineno_1=$LINENO as_lineno_1a=$LINENO
+ as_lineno_2=$LINENO as_lineno_2a=$LINENO
+ eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
+ test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
+ # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-)
+ sed -n '
+ p
+ /[$]LINENO/=
+ ' <$as_myself |
+ sed '
+ s/[$]LINENO.*/&-/
+ t lineno
+ b
+ :lineno
+ N
+ :loop
+ s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+ t loop
+ s/-\n.*//
+ ' >$as_me.lineno &&
+ chmod +x "$as_me.lineno" ||
+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
+
+ # Don't try to exec as it changes $[0], causing all sort of problems
+ # (the dirname of $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensitive to this).
+ . "./$as_me.lineno"
+ # Exit status is that of the last command.
+ exit
+}
+
+ECHO_C= ECHO_N= ECHO_T=
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+if test -r "$cache_file"; then
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+ # actually), so we avoid doing that. DJGPP emulates it as a regular file.
+ if test /dev/null != "$cache_file" && test -f "$cache_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
+$as_echo "$as_me: loading cache $cache_file" >&6;}
+ case $cache_file in
+ [\\/]* | ?:[\\/]* ) . "$cache_file";;
+ *) . "./$cache_file";;
+ esac
+ fi
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
+$as_echo "$as_me: creating cache $cache_file" >&6;}
+ >$cache_file
+fi
+
+# Check that the precious variables saved in the cache have kept the same
+# value.
+ac_cache_corrupted=false
+for ac_var in $ac_precious_vars; do
+ eval ac_old_set=\$ac_cv_env_${ac_var}_set
+ eval ac_new_set=\$ac_env_${ac_var}_set
+ eval ac_old_val=\$ac_cv_env_${ac_var}_value
+ eval ac_new_val=\$ac_env_${ac_var}_value
+ case $ac_old_set,$ac_new_set in
+ set,)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,set)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,);;
+ *)
+ if test "x$ac_old_val" != "x$ac_new_val"; then
+ # differences in whitespace do not lead to failure.
+ ac_old_val_w=`echo x $ac_old_val`
+ ac_new_val_w=`echo x $ac_new_val`
+ if test "$ac_old_val_w" != "$ac_new_val_w"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5
+$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
+ ac_cache_corrupted=:
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
+$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;}
+ eval $ac_var=\$ac_old_val
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5
+$as_echo "$as_me: former value: \`$ac_old_val'" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5
+$as_echo "$as_me: current value: \`$ac_new_val'" >&2;}
+ fi;;
+ esac
+ # Pass precious variables to config.status.
+ if test "$ac_new_set" = set; then
+ case $ac_new_val in
+ *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
+ *) ac_arg=$ac_var=$ac_new_val ;;
+ esac
+ case " $ac_configure_args " in
+ *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
+ *) as_fn_append ac_configure_args " '$ac_arg'" ;;
+ esac
+ fi
+done
+if $ac_cache_corrupted; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
+$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
+ as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+fi
+## -------------------- ##
+## Main body of script. ##
+## -------------------- ##
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+
+
+am__api_version='1.11'
+
+ac_aux_dir=
+for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
+ if test -f "$ac_dir/install-sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install-sh -c"
+ break
+ elif test -f "$ac_dir/install.sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install.sh -c"
+ break
+ elif test -f "$ac_dir/shtool"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/shtool install -c"
+ break
+ fi
+done
+if test -z "$ac_aux_dir"; then
+ as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5
+fi
+
+# These three variables are undocumented and unsupported,
+# and are intended to be withdrawn in a future Autoconf release.
+# They can cause serious problems if a builder's source tree is in a directory
+# whose full name contains unusual characters.
+ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var.
+ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
+ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
+
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+# Reject install programs that cannot install multiple files.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
+$as_echo_n "checking for a BSD-compatible install... " >&6; }
+if test -z "$INSTALL"; then
+if ${ac_cv_path_install+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in @%:@((
+ ./ | .// | /[cC]/* | \
+ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+ ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \
+ /usr/ucb/* ) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+ if test $ac_prog = install &&
+ grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ elif test $ac_prog = install &&
+ grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # program-specific install script used by HP pwplus--don't use.
+ :
+ else
+ rm -rf conftest.one conftest.two conftest.dir
+ echo one > conftest.one
+ echo two > conftest.two
+ mkdir conftest.dir
+ if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
+ test -s conftest.one && test -s conftest.two &&
+ test -s conftest.dir/conftest.one &&
+ test -s conftest.dir/conftest.two
+ then
+ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+ break 3
+ fi
+ fi
+ fi
+ done
+ done
+ ;;
+esac
+
+ done
+IFS=$as_save_IFS
+
+rm -rf conftest.one conftest.two conftest.dir
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL=$ac_cv_path_install
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ INSTALL=$ac_install_sh
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5
+$as_echo "$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
+$as_echo_n "checking whether build environment is sane... " >&6; }
+# Just in case
+sleep 1
+echo timestamp > conftest.file
+# Reject unsafe characters in $srcdir or the absolute working directory
+# name. Accept space and tab only in the latter.
+am_lf='
+'
+case `pwd` in
+ *[\\\"\#\$\&\'\`$am_lf]*)
+ as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5;;
+esac
+case $srcdir in
+ *[\\\"\#\$\&\'\`$am_lf\ \ ]*)
+ as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;;
+esac
+
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments. Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+ if test "$*" = "X"; then
+ # -L didn't work.
+ set X `ls -t "$srcdir/configure" conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$*" != "X $srcdir/configure conftest.file" \
+ && test "$*" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
+alias in your environment" "$LINENO" 5
+ fi
+
+ test "$2" = conftest.file
+ )
+then
+ # Ok.
+ :
+else
+ as_fn_error $? "newly created file is older than distributed files!
+Check your system clock" "$LINENO" 5
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+test "$program_prefix" != NONE &&
+ program_transform_name="s&^&$program_prefix&;$program_transform_name"
+# Use a double $ so make ignores it.
+test "$program_suffix" != NONE &&
+ program_transform_name="s&\$&$program_suffix&;$program_transform_name"
+# Double any \ or $.
+# By default was `s,x,x', remove it if useless.
+ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
+program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
+
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+
+if test x"${MISSING+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+ *)
+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
+ esac
+fi
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+ am_missing_run="$MISSING --run "
+else
+ am_missing_run=
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5
+$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
+fi
+
+if test x"${install_sh}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+if test "$cross_compiling" != no; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_STRIP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_STRIP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5
+$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
+if test -z "$MKDIR_P"; then
+ if ${ac_cv_path_mkdir+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in mkdir gmkdir; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
+ case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
+ 'mkdir (GNU coreutils) '* | \
+ 'mkdir (coreutils) '* | \
+ 'mkdir (fileutils) '4.1*)
+ ac_cv_path_mkdir=$as_dir/$ac_prog$ac_exec_ext
+ break 3;;
+ esac
+ done
+ done
+ done
+IFS=$as_save_IFS
+
+fi
+
+ test -d ./--version && rmdir ./--version
+ if test "${ac_cv_path_mkdir+set}" = set; then
+ MKDIR_P="$ac_cv_path_mkdir -p"
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for MKDIR_P within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ MKDIR_P="$ac_install_sh -d"
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
+$as_echo "$MKDIR_P" >&6; }
+
+mkdir_p="$MKDIR_P"
+case $mkdir_p in
+ [\\/$]* | ?:[\\/]*) ;;
+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
+esac
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_AWK+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AWK="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+$as_echo "$AWK" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$AWK" && break
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
+set x ${MAKE-make}
+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if eval \${ac_cv_prog_make_${ac_make}_set+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+ @echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+ *@@@%%%=?*=@@@%%%*)
+ eval ac_cv_prog_make_${ac_make}_set=yes;;
+ *)
+ eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ SET_MAKE=
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+ am__leading_dot=.
+else
+ am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+
+if test "`cd $srcdir && pwd`" != "`pwd`"; then
+ # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
+ # is not polluted with repeated "-I."
+ am__isrc=' -I$(srcdir)'
+ # test to see if srcdir already configured
+ if test -f $srcdir/config.status; then
+ as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
+ fi
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+ if (cygpath --version) >/dev/null 2>/dev/null; then
+ CYGPATH_W='cygpath -w'
+ else
+ CYGPATH_W=echo
+ fi
+fi
+
+
+# Define the identity of the package.
+ PACKAGE='openbugs'
+ VERSION='0.1'
+
+
+cat >>confdefs.h <<_ACEOF
+@%:@define PACKAGE "$PACKAGE"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+@%:@define VERSION "$VERSION"
+_ACEOF
+
+# Some tools Automake needs.
+
+ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
+
+
+AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}
+
+
+AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
+
+
+AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
+
+
+MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
+
+# We need awk for the "check" target. The system "awk" is bad on
+# some platforms.
+# Always define AMTAR for backward compatibility. Yes, it's still used
+# in the wild :-( We should find a proper way to deprecate it ...
+AMTAR='$${TAR-tar}'
+
+am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
+
+
+
+
+
+
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_CC"; then
+ ac_ct_CC=$CC
+ # Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+else
+ CC="$ac_cv_prog_CC"
+fi
+
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ fi
+fi
+if test -z "$CC"; then
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+ ac_prog_rejected=yes
+ continue
+ fi
+ ac_cv_prog_CC="cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+if test $ac_prog_rejected = yes; then
+ # We found a bogon in the path, so make sure we never use it.
+ set dummy $ac_cv_prog_CC
+ shift
+ if test $@%:@ != 0; then
+ # We chose a different compiler from the bogus one.
+ # However, it has the same basename, so the bogon will be chosen
+ # first if we set CC to just the basename; use the full file name.
+ shift
+ ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+ fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in cl.exe
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CC" && break
+ done
+fi
+if test -z "$CC"; then
+ ac_ct_CC=$CC
+ for ac_prog in cl.exe
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CC" && break
+done
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+fi
+
+fi
+
+
+test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "no acceptable C compiler found in \$PATH
+See \`config.log' for more details" "$LINENO" 5; }
+
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
+# Try to create an executable without -o first, disregard a.out.
+# It will help us diagnose broken compilers, and finding out an intuition
+# of exeext.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5
+$as_echo_n "checking whether the C compiler works... " >&6; }
+ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
+
+# The possible output files:
+ac_files="a.out conftest.exe conftest a.exe a_out.exe b.out conftest.*"
+
+ac_rmfiles=
+for ac_file in $ac_files
+do
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ * ) ac_rmfiles="$ac_rmfiles $ac_file";;
+ esac
+done
+rm -f $ac_rmfiles
+
+if { { ac_try="$ac_link_default"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link_default") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
+# So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
+# in a Makefile. We should not override ac_cv_exeext if it was cached,
+# so that the user can short-circuit this test for compilers unknown to
+# Autoconf.
+for ac_file in $ac_files ''
+do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj )
+ ;;
+ [ab].out )
+ # We found the default executable, but exeext='' is most
+ # certainly right.
+ break;;
+ *.* )
+ if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
+ then :; else
+ ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ fi
+ # We set ac_cv_exeext here because the later test for it is not
+ # safe: cross compilers may not add the suffix if given an `-o'
+ # argument, so we may need to know it at that point already.
+ # Even if this section looks crufty: it has the advantage of
+ # actually working.
+ break;;
+ * )
+ break;;
+ esac
+done
+test "$ac_cv_exeext" = no && ac_cv_exeext=
+
+else
+ ac_file=''
+fi
+if test -z "$ac_file"; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error 77 "C compiler cannot create executables
+See \`config.log' for more details" "$LINENO" 5; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5
+$as_echo_n "checking for C compiler default output file name... " >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
+$as_echo "$ac_file" >&6; }
+ac_exeext=$ac_cv_exeext
+
+rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
+$as_echo_n "checking for suffix of executables... " >&6; }
+if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # If both `conftest.exe' and `conftest' are `present' (well, observable)
+# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will
+# work properly (i.e., refer to `conftest.exe'), while it won't with
+# `rm'.
+for ac_file in conftest.exe conftest conftest.*; do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ break;;
+ * ) break;;
+ esac
+done
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details" "$LINENO" 5; }
+fi
+rm -f conftest conftest$ac_cv_exeext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
+$as_echo "$ac_cv_exeext" >&6; }
+
+rm -f conftest.$ac_ext
+EXEEXT=$ac_cv_exeext
+ac_exeext=$EXEEXT
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+@%:@include <stdio.h>
+int
+main ()
+{
+FILE *f = fopen ("conftest.out", "w");
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files="$ac_clean_files conftest.out"
+# Check that the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+if test "$cross_compiling" != yes; then
+ { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ if { ac_try='./conftest$ac_cv_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then
+ cross_compiling=no
+ else
+ if test "$cross_compiling" = maybe; then
+ cross_compiling=yes
+ else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details" "$LINENO" 5; }
+ fi
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
+$as_echo "$cross_compiling" >&6; }
+
+rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
+$as_echo_n "checking for suffix of object files... " >&6; }
+if ${ac_cv_objext+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.o conftest.obj
+if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ for ac_file in conftest.o conftest.obj conftest.*; do
+ test -f "$ac_file" || continue;
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
+ *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
+ break;;
+ esac
+done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of object files: cannot compile
+See \`config.log' for more details" "$LINENO" 5; }
+fi
+rm -f conftest.$ac_cv_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5
+$as_echo "$ac_cv_objext" >&6; }
+OBJEXT=$ac_cv_objext
+ac_objext=$OBJEXT
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
+$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
+if ${ac_cv_c_compiler_gnu+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
+$as_echo "$ac_cv_c_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GCC=yes
+else
+ GCC=
+fi
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
+$as_echo_n "checking whether $CC accepts -g... " >&6; }
+if ${ac_cv_prog_cc_g+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_c_werror_flag=$ac_c_werror_flag
+ ac_c_werror_flag=yes
+ ac_cv_prog_cc_g=no
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+else
+ CFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+else
+ ac_c_werror_flag=$ac_save_c_werror_flag
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_c_werror_flag=$ac_save_c_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
+$as_echo "$ac_cv_prog_cc_g" >&6; }
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
+$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
+if ${ac_cv_prog_cc_c89+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_prog_cc_c89=no
+ac_save_CC=$CC
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdarg.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+ char **p;
+ int i;
+{
+ return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+ char *s;
+ va_list v;
+ va_start (v,p);
+ s = g (p, va_arg (v,int));
+ va_end (v);
+ return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
+ function prototypes and stuff, but not '\xHH' hex character constants.
+ These don't provoke an error unfortunately, instead are silently treated
+ as 'x'. The following induces an error, until -std is added to get
+ proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
+ array size at least. It's necessary to write '\x00'==0 to get something
+ that's true only with -std. */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
+ inside strings and character constants. */
+#define FOO(x) 'x'
+int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+ ;
+ return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+ CC="$ac_save_CC $ac_arg"
+ if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_c89=$ac_arg
+fi
+rm -f core conftest.err conftest.$ac_objext
+ test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+ x)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
+$as_echo "none needed" >&6; } ;;
+ xno)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
+$as_echo "unsupported" >&6; } ;;
+ *)
+ CC="$CC $ac_cv_prog_cc_c89"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+if test "x$ac_cv_prog_cc_c89" != xno; then :
+
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+DEPDIR="${am__leading_dot}deps"
+
+ac_config_commands="$ac_config_commands depfiles"
+
+
+am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+ @echo this is the am__doit target
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5
+$as_echo_n "checking for style of include used by $am_make... " >&6; }
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# Ignore all kinds of additional output from `make'.
+case `$am_make -s -f confmf 2> /dev/null` in #(
+*the\ am__doit\ target*)
+ am__include=include
+ am__quote=
+ _am_result=GNU
+ ;;
+esac
+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+ echo '.include "confinc"' > confmf
+ case `$am_make -s -f confmf 2> /dev/null` in #(
+ *the\ am__doit\ target*)
+ am__include=.include
+ am__quote="\""
+ _am_result=BSD
+ ;;
+ esac
+fi
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5
+$as_echo "$_am_result" >&6; }
+rm -f confinc confmf
+
+@%:@ Check whether --enable-dependency-tracking was given.
+if test "${enable_dependency_tracking+set}" = set; then :
+ enableval=$enable_dependency_tracking;
+fi
+
+if test "x$enable_dependency_tracking" != xno; then
+ am_depcomp="$ac_aux_dir/depcomp"
+ AMDEPBACKSLASH='\'
+ am__nodep='_no'
+fi
+ if test "x$enable_dependency_tracking" != xno; then
+ AMDEP_TRUE=
+ AMDEP_FALSE='#'
+else
+ AMDEP_TRUE='#'
+ AMDEP_FALSE=
+fi
+
+
+
+depcc="$CC" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if ${am_cv_CC_dependencies_compiler_type+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CC_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvc7 | msvc7msys | msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CC_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+ am__fastdepCC_TRUE=
+ am__fastdepCC_FALSE='#'
+else
+ am__fastdepCC_TRUE='#'
+ am__fastdepCC_FALSE=
+fi
+
+
+
+ac_config_files="$ac_config_files Makefile src/Makefile"
+
+
+cat >confcache <<\_ACEOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs, see configure's option --config-cache.
+# It is not useful on other systems. If it contains results you don't
+# want to keep, you may remove or edit it.
+#
+# config.status only pays attention to the cache file if you give it
+# the --recheck option to rerun configure.
+#
+# `ac_cv_env_foo' variables (set or unset) will be overridden when
+# loading this file, other *unset* `ac_cv_foo' will be assigned the
+# following values.
+
+_ACEOF
+
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, we kill variables containing newlines.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+(
+ for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+
+ (set) 2>&1 |
+ case $as_nl`(ac_space=' '; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ # `set' does not quote correctly, so add quotes: double-quote
+ # substitution turns \\\\ into \\, and sed turns \\ into \.
+ sed -n \
+ "s/'/'\\\\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
+ ;; #(
+ *)
+ # `set' quotes correctly as required by POSIX, so do not add quotes.
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+) |
+ sed '
+ /^ac_cv_env_/b end
+ t clear
+ :clear
+ s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
+ t end
+ s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
+ :end' >>confcache
+if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
+ if test -w "$cache_file"; then
+ if test "x$cache_file" != "x/dev/null"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
+$as_echo "$as_me: updating cache $cache_file" >&6;}
+ if test ! -f "$cache_file" || test -h "$cache_file"; then
+ cat confcache >"$cache_file"
+ else
+ case $cache_file in #(
+ */* | ?:*)
+ mv -f confcache "$cache_file"$$ &&
+ mv -f "$cache_file"$$ "$cache_file" ;; #(
+ *)
+ mv -f confcache "$cache_file" ;;
+ esac
+ fi
+ fi
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
+$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
+ fi
+fi
+rm -f confcache
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+# Transform confdefs.h into DEFS.
+# Protect against shell expansion while executing Makefile rules.
+# Protect against Makefile macro expansion.
+#
+# If the first sed substitution is executed (which looks for macros that
+# take arguments), then branch to the quote section. Otherwise,
+# look for a macro that doesn't take arguments.
+ac_script='
+:mline
+/\\$/{
+ N
+ s,\\\n,,
+ b mline
+}
+t clear
+:clear
+s/^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*([^)]*)\)[ ]*\(.*\)/-D\1=\2/g
+t quote
+s/^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)/-D\1=\2/g
+t quote
+b any
+:quote
+s/[ `~#$^&*(){}\\|;'\''"<>?]/\\&/g
+s/\[/\\&/g
+s/\]/\\&/g
+s/\$/$$/g
+H
+:any
+${
+ g
+ s/^\n//
+ s/\n/ /g
+ p
+}
+'
+DEFS=`sed -n "$ac_script" confdefs.h`
+
+
+ac_libobjs=
+ac_ltlibobjs=
+U=
+for ac_i in : $LIB@&t at OBJS; do test "x$ac_i" = x: && continue
+ # 1. Remove the extension, and $U if already installed.
+ ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
+ ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
+ # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
+ # will be set to the directory where LIBOBJS objects are built.
+ as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+ as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
+done
+LIB@&t at OBJS=$ac_libobjs
+
+LTLIBOBJS=$ac_ltlibobjs
+
+
+ if test -n "$EXEEXT"; then
+ am__EXEEXT_TRUE=
+ am__EXEEXT_FALSE='#'
+else
+ am__EXEEXT_TRUE='#'
+ am__EXEEXT_FALSE=
+fi
+
+if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
+ as_fn_error $? "conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+
+: "${CONFIG_STATUS=./config.status}"
+ac_write_fail=0
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files $CONFIG_STATUS"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
+$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
+as_write_fail=0
+cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+
+SHELL=\${CONFIG_SHELL-$SHELL}
+export SHELL
+_ASEOF
+cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in @%:@(
+ *posix*) :
+ set -o posix ;; @%:@(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in @%:@(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+as_myself=
+case $0 in @%:@((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+
+@%:@ as_fn_error STATUS ERROR [LINENO LOG_FD]
+@%:@ ----------------------------------------
+@%:@ Output "`basename @S|@0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+@%:@ provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+@%:@ script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} @%:@ as_fn_error
+
+
+@%:@ as_fn_set_status STATUS
+@%:@ -----------------------
+@%:@ Set @S|@? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} @%:@ as_fn_set_status
+
+@%:@ as_fn_exit STATUS
+@%:@ -----------------
+@%:@ Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} @%:@ as_fn_exit
+
+@%:@ as_fn_unset VAR
+@%:@ ---------------
+@%:@ Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+@%:@ as_fn_append VAR VALUE
+@%:@ ----------------------
+@%:@ Append the text in VALUE to the end of the definition contained in VAR. Take
+@%:@ advantage of any shell optimizations that allow amortized linear growth over
+@%:@ repeated appends, instead of the typical quadratic growth present in naive
+@%:@ implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+@%:@ as_fn_arith ARG...
+@%:@ ------------------
+@%:@ Perform arithmetic evaluation on the ARGs, and store the result in the
+@%:@ global @S|@as_val. Take advantage of shells that can avoid forks. The arguments
+@%:@ must be portable across @S|@(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in @%:@(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+
+@%:@ as_fn_mkdir_p
+@%:@ -------------
+@%:@ Create "@S|@as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} @%:@ as_fn_mkdir_p
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in @%:@(
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in @%:@((
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+exec 6>&1
+## ----------------------------------- ##
+## Main body of $CONFIG_STATUS script. ##
+## ----------------------------------- ##
+_ASEOF
+test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# Save the log message, to keep $0 and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling.
+ac_log="
+This file was extended by OpenBUGS $as_me 0.1, which was
+generated by GNU Autoconf 2.68. Invocation command line was
+
+ CONFIG_FILES = $CONFIG_FILES
+ CONFIG_HEADERS = $CONFIG_HEADERS
+ CONFIG_LINKS = $CONFIG_LINKS
+ CONFIG_COMMANDS = $CONFIG_COMMANDS
+ $ $0 $@
+
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
+"
+
+_ACEOF
+
+case $ac_config_files in *"
+"*) set x $ac_config_files; shift; ac_config_files=$*;;
+esac
+
+
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+# Files that config.status was made for.
+config_files="$ac_config_files"
+config_commands="$ac_config_commands"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ac_cs_usage="\
+\`$as_me' instantiates files and other configuration actions
+from templates according to the current configuration. Unless the files
+and actions are specified as TAGs, all are instantiated by default.
+
+Usage: $0 [OPTION]... [TAG]...
+
+ -h, --help print this help, then exit
+ -V, --version print version number and configuration settings, then exit
+ --config print configuration, then exit
+ -q, --quiet, --silent
+ do not print progress messages
+ -d, --debug don't remove temporary files
+ --recheck update $as_me by reconfiguring in the same conditions
+ --file=FILE[:TEMPLATE]
+ instantiate the configuration file FILE
+
+Configuration files:
+$config_files
+
+Configuration commands:
+$config_commands
+
+Report bugs to the package provider."
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
+ac_cs_version="\\
+OpenBUGS config.status 0.1
+configured by $0, generated by GNU Autoconf 2.68,
+ with options \\"\$ac_cs_config\\"
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+
+ac_pwd='$ac_pwd'
+srcdir='$srcdir'
+INSTALL='$INSTALL'
+MKDIR_P='$MKDIR_P'
+AWK='$AWK'
+test -n "\$AWK" || AWK=awk
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# The default lists apply if the user does not specify any file.
+ac_need_defaults=:
+while test $# != 0
+do
+ case $1 in
+ --*=?*)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
+ ac_shift=:
+ ;;
+ --*=)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=
+ ac_shift=:
+ ;;
+ *)
+ ac_option=$1
+ ac_optarg=$2
+ ac_shift=shift
+ ;;
+ esac
+
+ case $ac_option in
+ # Handling of the options.
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ ac_cs_recheck=: ;;
+ --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
+ $as_echo "$ac_cs_version"; exit ;;
+ --config | --confi | --conf | --con | --co | --c )
+ $as_echo "$ac_cs_config"; exit ;;
+ --debug | --debu | --deb | --de | --d | -d )
+ debug=: ;;
+ --file | --fil | --fi | --f )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ '') as_fn_error $? "missing file argument" ;;
+ esac
+ as_fn_append CONFIG_FILES " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --he | --h | --help | --hel | -h )
+ $as_echo "$ac_cs_usage"; exit ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil | --si | --s)
+ ac_cs_silent=: ;;
+
+ # This is an error.
+ -*) as_fn_error $? "unrecognized option: \`$1'
+Try \`$0 --help' for more information." ;;
+
+ *) as_fn_append ac_config_targets " $1"
+ ac_need_defaults=false ;;
+
+ esac
+ shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+ exec 6>/dev/null
+ ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+if \$ac_cs_recheck; then
+ set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+ shift
+ \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
+ CONFIG_SHELL='$SHELL'
+ export CONFIG_SHELL
+ exec "\$@"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+exec 5>>config.log
+{
+ echo
+ sed 'h;s/./-/g;s/^.../@%:@@%:@ /;s/...$/ @%:@@%:@/;p;x;p;x' <<_ASBOX
+@%:@@%:@ Running $as_me. @%:@@%:@
+_ASBOX
+ $as_echo "$ac_log"
+} >&5
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+#
+# INIT-COMMANDS
+#
+AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+
+# Handling of arguments.
+for ac_config_target in $ac_config_targets
+do
+ case $ac_config_target in
+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+ "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+
+ *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
+ esac
+done
+
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used. Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+ test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+ test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
+fi
+
+# Have a temporary directory for convenience. Make it in the build tree
+# simply because there is no reason against having it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Hook for its removal unless debugging.
+# Note that there is a small window in which the directory will not be cleaned:
+# after its creation but before its name has been assigned to `$tmp'.
+$debug ||
+{
+ tmp= ac_tmp=
+ trap 'exit_status=$?
+ : "${ac_tmp:=$tmp}"
+ { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status
+' 0
+ trap 'as_fn_exit 1' 1 2 13 15
+}
+# Create a (secure) tmp directory for tmp files.
+
+{
+ tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
+ test -d "$tmp"
+} ||
+{
+ tmp=./conf$$-$RANDOM
+ (umask 077 && mkdir "$tmp")
+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
+ac_tmp=$tmp
+
+# Set up the scripts for CONFIG_FILES section.
+# No need to generate them if there are no CONFIG_FILES.
+# This happens for instance with `./config.status config.h'.
+if test -n "$CONFIG_FILES"; then
+
+
+ac_cr=`echo X | tr X '\015'`
+# On cygwin, bash can eat \r inside `` if the user requested igncr.
+# But we know of no other shell where ac_cr would be empty at this
+# point, so we can use a bashism as a fallback.
+if test "x$ac_cr" = x; then
+ eval ac_cr=\$\'\\r\'
+fi
+ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
+if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
+ ac_cs_awk_cr='\\r'
+else
+ ac_cs_awk_cr=$ac_cr
+fi
+
+echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
+_ACEOF
+
+
+{
+ echo "cat >conf$$subs.awk <<_ACEOF" &&
+ echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
+ echo "_ACEOF"
+} >conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
+ac_delim='%!_!# '
+for ac_last_try in false false false false false :; do
+ . ./conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+
+ ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
+ if test $ac_delim_n = $ac_delim_num; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+rm -f conf$$subs.sh
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK &&
+_ACEOF
+sed -n '
+h
+s/^/S["/; s/!.*/"]=/
+p
+g
+s/^[^!]*!//
+:repl
+t repl
+s/'"$ac_delim"'$//
+t delim
+:nl
+h
+s/\(.\{148\}\)..*/\1/
+t more1
+s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
+p
+n
+b repl
+:more1
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t nl
+:delim
+h
+s/\(.\{148\}\)..*/\1/
+t more2
+s/["\\]/\\&/g; s/^/"/; s/$/"/
+p
+b
+:more2
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t delim
+' <conf$$subs.awk | sed '
+/^[^""]/{
+ N
+ s/\n//
+}
+' >>$CONFIG_STATUS || ac_write_fail=1
+rm -f conf$$subs.awk
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+_ACAWK
+cat >>"\$ac_tmp/subs1.awk" <<_ACAWK &&
+ for (key in S) S_is_set[key] = 1
+ FS = ""
+
+}
+{
+ line = $ 0
+ nfields = split(line, field, "@")
+ substed = 0
+ len = length(field[1])
+ for (i = 2; i < nfields; i++) {
+ key = field[i]
+ keylen = length(key)
+ if (S_is_set[key]) {
+ value = S[key]
+ line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
+ len += length(value) + length(field[++i])
+ substed = 1
+ } else
+ len += 1 + keylen
+ }
+
+ print line
+}
+
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
+ sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
+else
+ cat
+fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \
+ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
+_ACEOF
+
+# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
+# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
+# trailing colons and then remove the whole line if VPATH becomes empty
+# (actually we leave an empty line to preserve line numbers).
+if test "x$srcdir" = x.; then
+ ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{
+h
+s///
+s/^/:/
+s/[ ]*$/:/
+s/:\$(srcdir):/:/g
+s/:\${srcdir}:/:/g
+s/:@srcdir@:/:/g
+s/^:*//
+s/:*$//
+x
+s/\(=[ ]*\).*/\1/
+G
+s/\n//
+s/^[^=]*=[ ]*$//
+}'
+fi
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+fi # test -n "$CONFIG_FILES"
+
+
+eval set X " :F $CONFIG_FILES :C $CONFIG_COMMANDS"
+shift
+for ac_tag
+do
+ case $ac_tag in
+ :[FHLC]) ac_mode=$ac_tag; continue;;
+ esac
+ case $ac_mode$ac_tag in
+ :[FHL]*:*);;
+ :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;;
+ :[FH]-) ac_tag=-:-;;
+ :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
+ esac
+ ac_save_IFS=$IFS
+ IFS=:
+ set x $ac_tag
+ IFS=$ac_save_IFS
+ shift
+ ac_file=$1
+ shift
+
+ case $ac_mode in
+ :L) ac_source=$1;;
+ :[FH])
+ ac_file_inputs=
+ for ac_f
+ do
+ case $ac_f in
+ -) ac_f="$ac_tmp/stdin";;
+ *) # Look for the file first in the build tree, then in the source tree
+ # (if the path is not absolute). The absolute path cannot be DOS-style,
+ # because $ac_f cannot contain `:'.
+ test -f "$ac_f" ||
+ case $ac_f in
+ [\\/$]*) false;;
+ *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
+ esac ||
+ as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;;
+ esac
+ case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
+ as_fn_append ac_file_inputs " '$ac_f'"
+ done
+
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ configure_input='Generated from '`
+ $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
+ `' by configure.'
+ if test x"$ac_file" != x-; then
+ configure_input="$ac_file. $configure_input"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
+$as_echo "$as_me: creating $ac_file" >&6;}
+ fi
+ # Neutralize special characters interpreted by sed in replacement strings.
+ case $configure_input in #(
+ *\&* | *\|* | *\\* )
+ ac_sed_conf_input=`$as_echo "$configure_input" |
+ sed 's/[\\\\&|]/\\\\&/g'`;; #(
+ *) ac_sed_conf_input=$configure_input;;
+ esac
+
+ case $ac_tag in
+ *:-:* | *:-) cat >"$ac_tmp/stdin" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
+ esac
+ ;;
+ esac
+
+ ac_dir=`$as_dirname -- "$ac_file" ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir="$ac_dir"; as_fn_mkdir_p
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+
+ case $ac_mode in
+ :F)
+ #
+ # CONFIG_FILE
+ #
+
+ case $INSTALL in
+ [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
+ *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
+ esac
+ ac_MKDIR_P=$MKDIR_P
+ case $MKDIR_P in
+ [\\/$]* | ?:[\\/]* ) ;;
+ */*) ac_MKDIR_P=$ac_top_build_prefix$MKDIR_P ;;
+ esac
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# If the template does not know about datarootdir, expand it.
+# FIXME: This hack should be removed a few years after 2.60.
+ac_datarootdir_hack=; ac_datarootdir_seen=
+ac_sed_dataroot='
+/datarootdir/ {
+ p
+ q
+}
+/@datadir@/p
+/@docdir@/p
+/@infodir@/p
+/@localedir@/p
+/@mandir@/p'
+case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
+*datarootdir*) ac_datarootdir_seen=yes;;
+*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ ac_datarootdir_hack='
+ s&@datadir@&$datadir&g
+ s&@docdir@&$docdir&g
+ s&@infodir@&$infodir&g
+ s&@localedir@&$localedir&g
+ s&@mandir@&$mandir&g
+ s&\\\${datarootdir}&$datarootdir&g' ;;
+esac
+_ACEOF
+
+# Neutralize VPATH when `$srcdir' = `.'.
+# Shell code in configure.ac might set extrasub.
+# FIXME: do we really want to maintain this feature?
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_sed_extra="$ac_vpsub
+$extrasub
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+:t
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+s|@configure_input@|$ac_sed_conf_input|;t t
+s&@top_builddir@&$ac_top_builddir_sub&;t t
+s&@top_build_prefix@&$ac_top_build_prefix&;t t
+s&@srcdir@&$ac_srcdir&;t t
+s&@abs_srcdir@&$ac_abs_srcdir&;t t
+s&@top_srcdir@&$ac_top_srcdir&;t t
+s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
+s&@builddir@&$ac_builddir&;t t
+s&@abs_builddir@&$ac_abs_builddir&;t t
+s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
+s&@INSTALL@&$ac_INSTALL&;t t
+s&@MKDIR_P@&$ac_MKDIR_P&;t t
+$ac_datarootdir_hack
+"
+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \
+ >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+
+test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
+ { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } &&
+ { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \
+ "$ac_tmp/out"`; test -z "$ac_out"; } &&
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&5
+$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&2;}
+
+ rm -f "$ac_tmp/stdin"
+ case $ac_file in
+ -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";;
+ *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";;
+ esac \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ ;;
+
+
+ :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
+$as_echo "$as_me: executing $ac_file commands" >&6;}
+ ;;
+ esac
+
+
+ case $ac_file$ac_mode in
+ "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # are listed without --file. Let's play safe and only enable the eval
+ # if we detect the quoting.
+ case $CONFIG_FILES in
+ *\'*) eval set x "$CONFIG_FILES" ;;
+ *) set x $CONFIG_FILES ;;
+ esac
+ shift
+ for mf
+ do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
+ # limit of 2048, but all sed's we know have understand at least 4000.
+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
+ dirpart=`$as_dirname -- "$mf" ||
+$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$mf" : 'X\(//\)[^/]' \| \
+ X"$mf" : 'X\(//\)$' \| \
+ X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$mf" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`$as_dirname -- "$file" ||
+$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$file" : 'X\(//\)[^/]' \| \
+ X"$file" : 'X\(//\)$' \| \
+ X"$file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir=$dirpart/$fdir; as_fn_mkdir_p
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+ done
+}
+ ;;
+
+ esac
+done # for ac_tag
+
+
+as_fn_exit 0
+_ACEOF
+ac_clean_files=$ac_clean_files_save
+
+test $ac_write_fail = 0 ||
+ as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
+
+
+# configure is writing to config.log, and then calls config.status.
+# config.status does its own redirection, appending to config.log.
+# Unfortunately, on DOS this fails, as config.log is still kept open
+# by configure, so config.status won't be able to write to it; its
+# output is simply discarded. So we exec the FD to /dev/null,
+# effectively closing config.log, so it can be properly (re)opened and
+# appended to by config.status. When coming back to configure, we
+# need to make the FD available again.
+if test "$no_create" != yes; then
+ ac_cs_success=:
+ ac_config_status_args=
+ test "$silent" = yes &&
+ ac_config_status_args="$ac_config_status_args --quiet"
+ exec 5>/dev/null
+ $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
+ exec 5>>config.log
+ # Use ||, not &&, to avoid exiting from the if with $? = 1, which
+ # would make configure fail if this is the last instruction.
+ $ac_cs_success || as_fn_exit 1
+fi
+if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
+$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
+fi
+
diff --git a/autom4te.cache/output.1 b/autom4te.cache/output.1
new file mode 100644
index 0000000..d8319a1
--- /dev/null
+++ b/autom4te.cache/output.1
@@ -0,0 +1,4564 @@
+@%:@! /bin/sh
+@%:@ Guess values for system-dependent variables and create Makefiles.
+@%:@ Generated by GNU Autoconf 2.68 for OpenBUGS 0.1.
+@%:@
+@%:@
+@%:@ Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+@%:@ 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
+@%:@ Foundation, Inc.
+@%:@
+@%:@
+@%:@ This configure script is free software; the Free Software Foundation
+@%:@ gives unlimited permission to copy, distribute and modify it.
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in @%:@(
+ *posix*) :
+ set -o posix ;; @%:@(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in @%:@(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+as_myself=
+case $0 in @%:@((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test "x$CONFIG_SHELL" = x; then
+ as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
+else
+ case \`(set -o) 2>/dev/null\` in @%:@(
+ *posix*) :
+ set -o posix ;; @%:@(
+ *) :
+ ;;
+esac
+fi
+"
+ as_required="as_fn_return () { (exit \$1); }
+as_fn_success () { as_fn_return 0; }
+as_fn_failure () { as_fn_return 1; }
+as_fn_ret_success () { return 0; }
+as_fn_ret_failure () { return 1; }
+
+exitcode=0
+as_fn_success || { exitcode=1; echo as_fn_success failed.; }
+as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
+as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
+as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
+if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
+
+else
+ exitcode=1; echo positional parameters were not saved.
+fi
+test x\$exitcode = x0 || exit 1"
+ as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
+ as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
+ eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
+ test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1"
+ if (eval "$as_required") 2>/dev/null; then :
+ as_have_required=yes
+else
+ as_have_required=no
+fi
+ if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
+
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+as_found=false
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ as_found=:
+ case $as_dir in @%:@(
+ /*)
+ for as_base in sh bash ksh sh5; do
+ # Try only shells that exist, to save several forks.
+ as_shell=$as_dir/$as_base
+ if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ CONFIG_SHELL=$as_shell as_have_required=yes
+ if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ break 2
+fi
+fi
+ done;;
+ esac
+ as_found=false
+done
+$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
+ CONFIG_SHELL=$SHELL as_have_required=yes
+fi; }
+IFS=$as_save_IFS
+
+
+ if test "x$CONFIG_SHELL" != x; then :
+ # We cannot yet assume a decent shell, so we have to provide a
+ # neutralization value for shells without unset; and this also
+ # works around shells that cannot unset nonexistent variables.
+ # Preserve -v and -x to the replacement shell.
+ BASH_ENV=/dev/null
+ ENV=/dev/null
+ (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+ export CONFIG_SHELL
+ case $- in @%:@ ((((
+ *v*x* | *x*v* ) as_opts=-vx ;;
+ *v* ) as_opts=-v ;;
+ *x* ) as_opts=-x ;;
+ * ) as_opts= ;;
+ esac
+ exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"}
+fi
+
+ if test x$as_have_required = xno; then :
+ $as_echo "$0: This script requires a shell more modern than all"
+ $as_echo "$0: the shells that I found on your system."
+ if test x${ZSH_VERSION+set} = xset ; then
+ $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
+ $as_echo "$0: be upgraded to zsh 4.3.4 or later."
+ else
+ $as_echo "$0: Please tell bug-autoconf at gnu.org about your system,
+$0: including any error possibly output before this
+$0: message. Then install a modern shell, or manually run
+$0: the script under such a shell if you do have one."
+ fi
+ exit 1
+fi
+fi
+fi
+SHELL=${CONFIG_SHELL-/bin/sh}
+export SHELL
+# Unset more variables known to interfere with behavior of common tools.
+CLICOLOR_FORCE= GREP_OPTIONS=
+unset CLICOLOR_FORCE GREP_OPTIONS
+
+## --------------------- ##
+## M4sh Shell Functions. ##
+## --------------------- ##
+@%:@ as_fn_unset VAR
+@%:@ ---------------
+@%:@ Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+
+@%:@ as_fn_set_status STATUS
+@%:@ -----------------------
+@%:@ Set @S|@? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} @%:@ as_fn_set_status
+
+@%:@ as_fn_exit STATUS
+@%:@ -----------------
+@%:@ Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} @%:@ as_fn_exit
+
+@%:@ as_fn_mkdir_p
+@%:@ -------------
+@%:@ Create "@S|@as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} @%:@ as_fn_mkdir_p
+@%:@ as_fn_append VAR VALUE
+@%:@ ----------------------
+@%:@ Append the text in VALUE to the end of the definition contained in VAR. Take
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+@%:@ repeated appends, instead of the typical quadratic growth present in naive
+@%:@ implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+@%:@ as_fn_arith ARG...
+@%:@ ------------------
+@%:@ Perform arithmetic evaluation on the ARGs, and store the result in the
+@%:@ global @S|@as_val. Take advantage of shells that can avoid forks. The arguments
+@%:@ must be portable across @S|@(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+@%:@ as_fn_error STATUS ERROR [LINENO LOG_FD]
+@%:@ ----------------------------------------
+@%:@ Output "`basename @S|@0`: error: ERROR" to stderr. If LINENO and LOG_FD are
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+@%:@ script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
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+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} @%:@ as_fn_error
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
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+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
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+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+
+ as_lineno_1=$LINENO as_lineno_1a=$LINENO
+ as_lineno_2=$LINENO as_lineno_2a=$LINENO
+ eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
+ test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
+ # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-)
+ sed -n '
+ p
+ /[$]LINENO/=
+ ' <$as_myself |
+ sed '
+ s/[$]LINENO.*/&-/
+ t lineno
+ b
+ :lineno
+ N
+ :loop
+ s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+ t loop
+ s/-\n.*//
+ ' >$as_me.lineno &&
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+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
+
+ # Don't try to exec as it changes $[0], causing all sort of problems
+ # (the dirname of $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensitive to this).
+ . "./$as_me.lineno"
+ # Exit status is that of the last command.
+ exit
+}
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in @%:@(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
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+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
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+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
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+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
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+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
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+as_executable_p=$as_test_x
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+
+# Sed expression to map a string onto a valid variable name.
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+
+
+test -n "$DJDIR" || exec 7<&0 </dev/null
+exec 6>&1
+
+# Name of the host.
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+ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
+
+#
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+#
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+ac_clean_files=
+ac_config_libobj_dir=.
+LIB@&t at OBJS=
+cross_compiling=no
+subdirs=
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+PACKAGE_TARNAME='openbugs'
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+CC
+am__untar
+am__tar
+AMTAR
+am__leading_dot
+SET_MAKE
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+mkdir_p
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+INSTALL_STRIP_PROGRAM
+STRIP
+install_sh
+MAKEINFO
+AUTOHEADER
+AUTOMAKE
+AUTOCONF
+ACLOCAL
+VERSION
+PACKAGE
+CYGPATH_W
+am__isrc
+INSTALL_DATA
+INSTALL_SCRIPT
+INSTALL_PROGRAM
+target_alias
+host_alias
+build_alias
+LIBS
+ECHO_T
+ECHO_N
+ECHO_C
+DEFS
+mandir
+localedir
+libdir
+psdir
+pdfdir
+dvidir
+htmldir
+infodir
+docdir
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+includedir
+localstatedir
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+sysconfdir
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+ac_user_opts='
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+ ac_precious_vars='build_alias
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+
+# Initialize some variables set by options.
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+ac_init_version=false
+ac_unrecognized_opts=
+ac_unrecognized_sep=
+# The variables have the same names as the options, with
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+no_recursion=
+prefix=NONE
+program_prefix=NONE
+program_suffix=NONE
+program_transform_name=s,x,x,
+silent=
+site=
+srcdir=
+verbose=
+x_includes=NONE
+x_libraries=NONE
+
+# Installation directory options.
+# These are left unexpanded so users can "make install exec_prefix=/foo"
+# and all the variables that are supposed to be based on exec_prefix
+# by default will actually change.
+# Use braces instead of parens because sh, perl, etc. also accept them.
+# (The list follows the same order as the GNU Coding Standards.)
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+sbindir='${exec_prefix}/sbin'
+libexecdir='${exec_prefix}/libexec'
+datarootdir='${prefix}/share'
+datadir='${datarootdir}'
+sysconfdir='${prefix}/etc'
+sharedstatedir='${prefix}/com'
+localstatedir='${prefix}/var'
+includedir='${prefix}/include'
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+infodir='${datarootdir}/info'
+htmldir='${docdir}'
+dvidir='${docdir}'
+pdfdir='${docdir}'
+psdir='${docdir}'
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+localedir='${datarootdir}/locale'
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+
+ac_prev=
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+do
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+ case $ac_option in
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+ *) ac_optarg=yes ;;
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+ # Accept the important Cygnus configure options, so we can diagnose typos.
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+ case $ac_dashdash$ac_option in
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+ ac_dashdash=yes ;;
+
+ -bindir | --bindir | --bindi | --bind | --bin | --bi)
+ ac_prev=bindir ;;
+ -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
+ bindir=$ac_optarg ;;
+
+ -build | --build | --buil | --bui | --bu)
+ ac_prev=build_alias ;;
+ -build=* | --build=* | --buil=* | --bui=* | --bu=*)
+ build_alias=$ac_optarg ;;
+
+ -cache-file | --cache-file | --cache-fil | --cache-fi \
+ | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
+ ac_prev=cache_file ;;
+ -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
+ | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)
+ cache_file=$ac_optarg ;;
+
+ --config-cache | -C)
+ cache_file=config.cache ;;
+
+ -datadir | --datadir | --datadi | --datad)
+ ac_prev=datadir ;;
+ -datadir=* | --datadir=* | --datadi=* | --datad=*)
+ datadir=$ac_optarg ;;
+
+ -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \
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+ ac_prev=datarootdir ;;
+ -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \
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+ datarootdir=$ac_optarg ;;
+
+ -disable-* | --disable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
+ # Reject names that are not valid shell variable names.
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+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
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+ -docdir | --docdir | --docdi | --doc | --do)
+ ac_prev=docdir ;;
+ -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*)
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+
+ -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv)
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+
+ -enable-* | --enable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid feature name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=\$ac_optarg ;;
+
+ -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
+ | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
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+ ac_prev=exec_prefix ;;
+ -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \
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+\`configure' configures OpenBUGS 0.1 to adapt to many kinds of systems.
+
+Usage: $0 [OPTION]... [VAR=VALUE]...
+
+To assign environment variables (e.g., CC, CFLAGS...), specify them as
+VAR=VALUE. See below for descriptions of some of the useful variables.
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+Defaults for the options are specified in brackets.
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+Configuration:
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+ --help=short display options specific to this package
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+Fine tuning of the installation directories:
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+ --sbindir=DIR system admin executables [EPREFIX/sbin]
+ --libexecdir=DIR program executables [EPREFIX/libexec]
+ --sysconfdir=DIR read-only single-machine data [PREFIX/etc]
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+ --infodir=DIR info documentation [DATAROOTDIR/info]
+ --localedir=DIR locale-dependent data [DATAROOTDIR/locale]
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+ --htmldir=DIR html documentation [DOCDIR]
+ --dvidir=DIR dvi documentation [DOCDIR]
+ --pdfdir=DIR pdf documentation [DOCDIR]
+ --psdir=DIR ps documentation [DOCDIR]
+_ACEOF
+
+ cat <<\_ACEOF
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+Program names:
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+ cat <<\_ACEOF
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+Optional Features:
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+ --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
+ --enable-FEATURE[=ARG] include FEATURE [ARG=yes]
+ --disable-dependency-tracking speeds up one-time build
+ --enable-dependency-tracking do not reject slow dependency extractors
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+Some influential environment variables:
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+ LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
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+ LIBS libraries to pass to the linker, e.g. -l<library>
+ CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
+ you have headers in a nonstandard directory <include dir>
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+Use these variables to override the choices made by `configure' or to help
+it to find libraries and programs with nonstandard names/locations.
+
+Report bugs to the package provider.
+_ACEOF
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+
+if test "$ac_init_help" = "recursive"; then
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+case "$ac_dir" in
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+fi
+
+test -n "$ac_init_help" && exit $ac_status
+if $ac_init_version; then
+ cat <<\_ACEOF
+OpenBUGS configure 0.1
+generated by GNU Autoconf 2.68
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This configure script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it.
+_ACEOF
+ exit
+fi
+
+## ------------------------ ##
+## Autoconf initialization. ##
+## ------------------------ ##
+
+@%:@ ac_fn_c_try_compile LINENO
+@%:@ --------------------------
+@%:@ Try to compile conftest. at S|@ac_ext, and return whether this succeeded.
+ac_fn_c_try_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext
+ if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+ as_fn_set_status $ac_retval
+
+} @%:@ ac_fn_c_try_compile
+cat >config.log <<_ACEOF
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by OpenBUGS $as_me 0.1, which was
+generated by GNU Autoconf 2.68. Invocation command line was
+
+ $ $0 $@
+
+_ACEOF
+exec 5>>config.log
+{
+cat <<_ASUNAME
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown`
+
+/bin/arch = `(/bin/arch) 2>/dev/null || echo unknown`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
+/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown`
+/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown`
+/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown`
+
+_ASUNAME
+
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ $as_echo "PATH: $as_dir"
+ done
+IFS=$as_save_IFS
+
+} >&5
+
+cat >&5 <<_ACEOF
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+_ACEOF
+
+
+# Keep a trace of the command line.
+# Strip out --no-create and --no-recursion so they do not pile up.
+# Strip out --silent because we don't want to record it for future runs.
+# Also quote any args containing shell meta-characters.
+# Make two passes to allow for proper duplicate-argument suppression.
+ac_configure_args=
+ac_configure_args0=
+ac_configure_args1=
+ac_must_keep_next=false
+for ac_pass in 1 2
+do
+ for ac_arg
+ do
+ case $ac_arg in
+ -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ continue ;;
+ *\'*)
+ ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ case $ac_pass in
+ 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;;
+ 2)
+ as_fn_append ac_configure_args1 " '$ac_arg'"
+ if test $ac_must_keep_next = true; then
+ ac_must_keep_next=false # Got value, back to normal.
+ else
+ case $ac_arg in
+ *=* | --config-cache | -C | -disable-* | --disable-* \
+ | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \
+ | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \
+ | -with-* | --with-* | -without-* | --without-* | --x)
+ case "$ac_configure_args0 " in
+ "$ac_configure_args1"*" '$ac_arg' "* ) continue ;;
+ esac
+ ;;
+ -* ) ac_must_keep_next=true ;;
+ esac
+ fi
+ as_fn_append ac_configure_args " '$ac_arg'"
+ ;;
+ esac
+ done
+done
+{ ac_configure_args0=; unset ac_configure_args0;}
+{ ac_configure_args1=; unset ac_configure_args1;}
+
+# When interrupted or exit'd, cleanup temporary files, and complete
+# config.log. We remove comments because anyway the quotes in there
+# would cause problems or look ugly.
+# WARNING: Use '\'' to represent an apostrophe within the trap.
+# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug.
+trap 'exit_status=$?
+ # Save into config.log some information that might help in debugging.
+ {
+ echo
+
+ $as_echo "## ---------------- ##
+## Cache variables. ##
+## ---------------- ##"
+ echo
+ # The following way of writing the cache mishandles newlines in values,
+(
+ for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+ (set) 2>&1 |
+ case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ sed -n \
+ "s/'\''/'\''\\\\'\'''\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p"
+ ;; #(
+ *)
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+)
+ echo
+
+ $as_echo "## ----------------- ##
+## Output variables. ##
+## ----------------- ##"
+ echo
+ for ac_var in $ac_subst_vars
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+
+ if test -n "$ac_subst_files"; then
+ $as_echo "## ------------------- ##
+## File substitutions. ##
+## ------------------- ##"
+ echo
+ for ac_var in $ac_subst_files
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+ fi
+
+ if test -s confdefs.h; then
+ $as_echo "## ----------- ##
+## confdefs.h. ##
+## ----------- ##"
+ echo
+ cat confdefs.h
+ echo
+ fi
+ test "$ac_signal" != 0 &&
+ $as_echo "$as_me: caught signal $ac_signal"
+ $as_echo "$as_me: exit $exit_status"
+ } >&5
+ rm -f core *.core core.conftest.* &&
+ rm -f -r conftest* confdefs* conf$$* $ac_clean_files &&
+ exit $exit_status
+' 0
+for ac_signal in 1 2 13 15; do
+ trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal
+done
+ac_signal=0
+
+# confdefs.h avoids OS command line length limits that DEFS can exceed.
+rm -f -r conftest* confdefs.h
+
+$as_echo "/* confdefs.h */" > confdefs.h
+
+# Predefined preprocessor variables.
+
+cat >>confdefs.h <<_ACEOF
+@%:@define PACKAGE_NAME "$PACKAGE_NAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+@%:@define PACKAGE_TARNAME "$PACKAGE_TARNAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+@%:@define PACKAGE_VERSION "$PACKAGE_VERSION"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+@%:@define PACKAGE_STRING "$PACKAGE_STRING"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+@%:@define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+@%:@define PACKAGE_URL "$PACKAGE_URL"
+_ACEOF
+
+
+# Let the site file select an alternate cache file if it wants to.
+# Prefer an explicitly selected file to automatically selected ones.
+ac_site_file1=NONE
+ac_site_file2=NONE
+if test -n "$CONFIG_SITE"; then
+ # We do not want a PATH search for config.site.
+ case $CONFIG_SITE in @%:@((
+ -*) ac_site_file1=./$CONFIG_SITE;;
+ */*) ac_site_file1=$CONFIG_SITE;;
+ *) ac_site_file1=./$CONFIG_SITE;;
+ esac
+elif test "x$prefix" != xNONE; then
+ ac_site_file1=$prefix/share/config.site
+ ac_site_file2=$prefix/etc/config.site
+else
+ ac_site_file1=$ac_default_prefix/share/config.site
+ ac_site_file2=$ac_default_prefix/etc/config.site
+fi
+for ac_site_file in "$ac_site_file1" "$ac_site_file2"
+do
+ test "x$ac_site_file" = xNONE && continue
+ if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
+$as_echo "$as_me: loading site script $ac_site_file" >&6;}
+ sed 's/^/| /' "$ac_site_file" >&5
+ . "$ac_site_file" \
+ || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "failed to load site script $ac_site_file
+See \`config.log' for more details" "$LINENO" 5; }
+ fi
+done
+
+if test -r "$cache_file"; then
+ # Some versions of bash will fail to source /dev/null (special files
+ # actually), so we avoid doing that. DJGPP emulates it as a regular file.
+ if test /dev/null != "$cache_file" && test -f "$cache_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
+$as_echo "$as_me: loading cache $cache_file" >&6;}
+ case $cache_file in
+ [\\/]* | ?:[\\/]* ) . "$cache_file";;
+ *) . "./$cache_file";;
+ esac
+ fi
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
+$as_echo "$as_me: creating cache $cache_file" >&6;}
+ >$cache_file
+fi
+
+# Check that the precious variables saved in the cache have kept the same
+# value.
+ac_cache_corrupted=false
+for ac_var in $ac_precious_vars; do
+ eval ac_old_set=\$ac_cv_env_${ac_var}_set
+ eval ac_new_set=\$ac_env_${ac_var}_set
+ eval ac_old_val=\$ac_cv_env_${ac_var}_value
+ eval ac_new_val=\$ac_env_${ac_var}_value
+ case $ac_old_set,$ac_new_set in
+ set,)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,set)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,);;
+ *)
+ if test "x$ac_old_val" != "x$ac_new_val"; then
+ # differences in whitespace do not lead to failure.
+ ac_old_val_w=`echo x $ac_old_val`
+ ac_new_val_w=`echo x $ac_new_val`
+ if test "$ac_old_val_w" != "$ac_new_val_w"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5
+$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
+ ac_cache_corrupted=:
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
+$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;}
+ eval $ac_var=\$ac_old_val
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5
+$as_echo "$as_me: former value: \`$ac_old_val'" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5
+$as_echo "$as_me: current value: \`$ac_new_val'" >&2;}
+ fi;;
+ esac
+ # Pass precious variables to config.status.
+ if test "$ac_new_set" = set; then
+ case $ac_new_val in
+ *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
+ *) ac_arg=$ac_var=$ac_new_val ;;
+ esac
+ case " $ac_configure_args " in
+ *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
+ *) as_fn_append ac_configure_args " '$ac_arg'" ;;
+ esac
+ fi
+done
+if $ac_cache_corrupted; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
+$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
+ as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+fi
+## -------------------- ##
+## Main body of script. ##
+## -------------------- ##
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+
+
+am__api_version='1.11'
+
+ac_aux_dir=
+for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
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+ ac_install_sh="$ac_aux_dir/install-sh -c"
+ break
+ elif test -f "$ac_dir/install.sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install.sh -c"
+ break
+ elif test -f "$ac_dir/shtool"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/shtool install -c"
+ break
+ fi
+done
+if test -z "$ac_aux_dir"; then
+ as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5
+fi
+
+# These three variables are undocumented and unsupported,
+# and are intended to be withdrawn in a future Autoconf release.
+# They can cause serious problems if a builder's source tree is in a directory
+# whose full name contains unusual characters.
+ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var.
+ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
+ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
+
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
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+# Reject install programs that cannot install multiple files.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
+$as_echo_n "checking for a BSD-compatible install... " >&6; }
+if test -z "$INSTALL"; then
+if ${ac_cv_path_install+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
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+ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+ ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \
+ /usr/ucb/* ) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+ if test $ac_prog = install &&
+ grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ elif test $ac_prog = install &&
+ grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # program-specific install script used by HP pwplus--don't use.
+ :
+ else
+ rm -rf conftest.one conftest.two conftest.dir
+ echo one > conftest.one
+ echo two > conftest.two
+ mkdir conftest.dir
+ if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
+ test -s conftest.one && test -s conftest.two &&
+ test -s conftest.dir/conftest.one &&
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+ then
+ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+ break 3
+ fi
+ fi
+ fi
+ done
+ done
+ ;;
+esac
+
+ done
+IFS=$as_save_IFS
+
+rm -rf conftest.one conftest.two conftest.dir
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL=$ac_cv_path_install
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ INSTALL=$ac_install_sh
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5
+$as_echo "$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
+$as_echo_n "checking whether build environment is sane... " >&6; }
+# Just in case
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+echo timestamp > conftest.file
+# Reject unsafe characters in $srcdir or the absolute working directory
+# name. Accept space and tab only in the latter.
+am_lf='
+'
+case `pwd` in
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+ as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5;;
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+case $srcdir in
+ *[\\\"\#\$\&\'\`$am_lf\ \ ]*)
+ as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;;
+esac
+
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments. Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+ if test "$*" = "X"; then
+ # -L didn't work.
+ set X `ls -t "$srcdir/configure" conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$*" != "X $srcdir/configure conftest.file" \
+ && test "$*" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
+alias in your environment" "$LINENO" 5
+ fi
+
+ test "$2" = conftest.file
+ )
+then
+ # Ok.
+ :
+else
+ as_fn_error $? "newly created file is older than distributed files!
+Check your system clock" "$LINENO" 5
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+test "$program_prefix" != NONE &&
+ program_transform_name="s&^&$program_prefix&;$program_transform_name"
+# Use a double $ so make ignores it.
+test "$program_suffix" != NONE &&
+ program_transform_name="s&\$&$program_suffix&;$program_transform_name"
+# Double any \ or $.
+# By default was `s,x,x', remove it if useless.
+ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
+program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
+
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+
+if test x"${MISSING+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+ *)
+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
+ esac
+fi
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+ am_missing_run="$MISSING --run "
+else
+ am_missing_run=
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5
+$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
+fi
+
+if test x"${install_sh}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+if test "$cross_compiling" != no; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_STRIP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_STRIP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5
+$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
+if test -z "$MKDIR_P"; then
+ if ${ac_cv_path_mkdir+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in mkdir gmkdir; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
+ case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
+ 'mkdir (GNU coreutils) '* | \
+ 'mkdir (coreutils) '* | \
+ 'mkdir (fileutils) '4.1*)
+ ac_cv_path_mkdir=$as_dir/$ac_prog$ac_exec_ext
+ break 3;;
+ esac
+ done
+ done
+ done
+IFS=$as_save_IFS
+
+fi
+
+ test -d ./--version && rmdir ./--version
+ if test "${ac_cv_path_mkdir+set}" = set; then
+ MKDIR_P="$ac_cv_path_mkdir -p"
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for MKDIR_P within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ MKDIR_P="$ac_install_sh -d"
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
+$as_echo "$MKDIR_P" >&6; }
+
+mkdir_p="$MKDIR_P"
+case $mkdir_p in
+ [\\/$]* | ?:[\\/]*) ;;
+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
+esac
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_AWK+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AWK="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+$as_echo "$AWK" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$AWK" && break
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
+set x ${MAKE-make}
+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if eval \${ac_cv_prog_make_${ac_make}_set+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+ @echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+ *@@@%%%=?*=@@@%%%*)
+ eval ac_cv_prog_make_${ac_make}_set=yes;;
+ *)
+ eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ SET_MAKE=
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+ am__leading_dot=.
+else
+ am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+
+if test "`cd $srcdir && pwd`" != "`pwd`"; then
+ # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
+ # is not polluted with repeated "-I."
+ am__isrc=' -I$(srcdir)'
+ # test to see if srcdir already configured
+ if test -f $srcdir/config.status; then
+ as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
+ fi
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+ if (cygpath --version) >/dev/null 2>/dev/null; then
+ CYGPATH_W='cygpath -w'
+ else
+ CYGPATH_W=echo
+ fi
+fi
+
+
+# Define the identity of the package.
+ PACKAGE='openbugs'
+ VERSION='0.1'
+
+
+cat >>confdefs.h <<_ACEOF
+@%:@define PACKAGE "$PACKAGE"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+@%:@define VERSION "$VERSION"
+_ACEOF
+
+# Some tools Automake needs.
+
+ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
+
+
+AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}
+
+
+AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
+
+
+AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
+
+
+MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
+
+# We need awk for the "check" target. The system "awk" is bad on
+# some platforms.
+# Always define AMTAR for backward compatibility. Yes, it's still used
+# in the wild :-( We should find a proper way to deprecate it ...
+AMTAR='$${TAR-tar}'
+
+am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
+
+
+
+
+
+
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_CC"; then
+ ac_ct_CC=$CC
+ # Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+else
+ CC="$ac_cv_prog_CC"
+fi
+
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ fi
+fi
+if test -z "$CC"; then
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+ ac_prog_rejected=yes
+ continue
+ fi
+ ac_cv_prog_CC="cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+if test $ac_prog_rejected = yes; then
+ # We found a bogon in the path, so make sure we never use it.
+ set dummy $ac_cv_prog_CC
+ shift
+ if test $@%:@ != 0; then
+ # We chose a different compiler from the bogus one.
+ # However, it has the same basename, so the bogon will be chosen
+ # first if we set CC to just the basename; use the full file name.
+ shift
+ ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+ fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in cl.exe
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CC" && break
+ done
+fi
+if test -z "$CC"; then
+ ac_ct_CC=$CC
+ for ac_prog in cl.exe
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CC" && break
+done
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+fi
+
+fi
+
+
+test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "no acceptable C compiler found in \$PATH
+See \`config.log' for more details" "$LINENO" 5; }
+
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
+# Try to create an executable without -o first, disregard a.out.
+# It will help us diagnose broken compilers, and finding out an intuition
+# of exeext.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5
+$as_echo_n "checking whether the C compiler works... " >&6; }
+ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
+
+# The possible output files:
+ac_files="a.out conftest.exe conftest a.exe a_out.exe b.out conftest.*"
+
+ac_rmfiles=
+for ac_file in $ac_files
+do
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ * ) ac_rmfiles="$ac_rmfiles $ac_file";;
+ esac
+done
+rm -f $ac_rmfiles
+
+if { { ac_try="$ac_link_default"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link_default") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
+# So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
+# in a Makefile. We should not override ac_cv_exeext if it was cached,
+# so that the user can short-circuit this test for compilers unknown to
+# Autoconf.
+for ac_file in $ac_files ''
+do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj )
+ ;;
+ [ab].out )
+ # We found the default executable, but exeext='' is most
+ # certainly right.
+ break;;
+ *.* )
+ if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
+ then :; else
+ ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ fi
+ # We set ac_cv_exeext here because the later test for it is not
+ # safe: cross compilers may not add the suffix if given an `-o'
+ # argument, so we may need to know it at that point already.
+ # Even if this section looks crufty: it has the advantage of
+ # actually working.
+ break;;
+ * )
+ break;;
+ esac
+done
+test "$ac_cv_exeext" = no && ac_cv_exeext=
+
+else
+ ac_file=''
+fi
+if test -z "$ac_file"; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error 77 "C compiler cannot create executables
+See \`config.log' for more details" "$LINENO" 5; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5
+$as_echo_n "checking for C compiler default output file name... " >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
+$as_echo "$ac_file" >&6; }
+ac_exeext=$ac_cv_exeext
+
+rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
+$as_echo_n "checking for suffix of executables... " >&6; }
+if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # If both `conftest.exe' and `conftest' are `present' (well, observable)
+# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will
+# work properly (i.e., refer to `conftest.exe'), while it won't with
+# `rm'.
+for ac_file in conftest.exe conftest conftest.*; do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ break;;
+ * ) break;;
+ esac
+done
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details" "$LINENO" 5; }
+fi
+rm -f conftest conftest$ac_cv_exeext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
+$as_echo "$ac_cv_exeext" >&6; }
+
+rm -f conftest.$ac_ext
+EXEEXT=$ac_cv_exeext
+ac_exeext=$EXEEXT
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+@%:@include <stdio.h>
+int
+main ()
+{
+FILE *f = fopen ("conftest.out", "w");
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files="$ac_clean_files conftest.out"
+# Check that the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+if test "$cross_compiling" != yes; then
+ { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ if { ac_try='./conftest$ac_cv_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then
+ cross_compiling=no
+ else
+ if test "$cross_compiling" = maybe; then
+ cross_compiling=yes
+ else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details" "$LINENO" 5; }
+ fi
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
+$as_echo "$cross_compiling" >&6; }
+
+rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
+$as_echo_n "checking for suffix of object files... " >&6; }
+if ${ac_cv_objext+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.o conftest.obj
+if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ for ac_file in conftest.o conftest.obj conftest.*; do
+ test -f "$ac_file" || continue;
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
+ *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
+ break;;
+ esac
+done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of object files: cannot compile
+See \`config.log' for more details" "$LINENO" 5; }
+fi
+rm -f conftest.$ac_cv_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5
+$as_echo "$ac_cv_objext" >&6; }
+OBJEXT=$ac_cv_objext
+ac_objext=$OBJEXT
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
+$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
+if ${ac_cv_c_compiler_gnu+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
+$as_echo "$ac_cv_c_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GCC=yes
+else
+ GCC=
+fi
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
+$as_echo_n "checking whether $CC accepts -g... " >&6; }
+if ${ac_cv_prog_cc_g+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_c_werror_flag=$ac_c_werror_flag
+ ac_c_werror_flag=yes
+ ac_cv_prog_cc_g=no
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+else
+ CFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+else
+ ac_c_werror_flag=$ac_save_c_werror_flag
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_c_werror_flag=$ac_save_c_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
+$as_echo "$ac_cv_prog_cc_g" >&6; }
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
+$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
+if ${ac_cv_prog_cc_c89+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_prog_cc_c89=no
+ac_save_CC=$CC
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdarg.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+ char **p;
+ int i;
+{
+ return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+ char *s;
+ va_list v;
+ va_start (v,p);
+ s = g (p, va_arg (v,int));
+ va_end (v);
+ return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
+ function prototypes and stuff, but not '\xHH' hex character constants.
+ These don't provoke an error unfortunately, instead are silently treated
+ as 'x'. The following induces an error, until -std is added to get
+ proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
+ array size at least. It's necessary to write '\x00'==0 to get something
+ that's true only with -std. */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
+ inside strings and character constants. */
+#define FOO(x) 'x'
+int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+ ;
+ return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+ CC="$ac_save_CC $ac_arg"
+ if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_c89=$ac_arg
+fi
+rm -f core conftest.err conftest.$ac_objext
+ test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+ x)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
+$as_echo "none needed" >&6; } ;;
+ xno)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
+$as_echo "unsupported" >&6; } ;;
+ *)
+ CC="$CC $ac_cv_prog_cc_c89"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+if test "x$ac_cv_prog_cc_c89" != xno; then :
+
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+DEPDIR="${am__leading_dot}deps"
+
+ac_config_commands="$ac_config_commands depfiles"
+
+
+am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+ @echo this is the am__doit target
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5
+$as_echo_n "checking for style of include used by $am_make... " >&6; }
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# Ignore all kinds of additional output from `make'.
+case `$am_make -s -f confmf 2> /dev/null` in #(
+*the\ am__doit\ target*)
+ am__include=include
+ am__quote=
+ _am_result=GNU
+ ;;
+esac
+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+ echo '.include "confinc"' > confmf
+ case `$am_make -s -f confmf 2> /dev/null` in #(
+ *the\ am__doit\ target*)
+ am__include=.include
+ am__quote="\""
+ _am_result=BSD
+ ;;
+ esac
+fi
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5
+$as_echo "$_am_result" >&6; }
+rm -f confinc confmf
+
+@%:@ Check whether --enable-dependency-tracking was given.
+if test "${enable_dependency_tracking+set}" = set; then :
+ enableval=$enable_dependency_tracking;
+fi
+
+if test "x$enable_dependency_tracking" != xno; then
+ am_depcomp="$ac_aux_dir/depcomp"
+ AMDEPBACKSLASH='\'
+ am__nodep='_no'
+fi
+ if test "x$enable_dependency_tracking" != xno; then
+ AMDEP_TRUE=
+ AMDEP_FALSE='#'
+else
+ AMDEP_TRUE='#'
+ AMDEP_FALSE=
+fi
+
+
+
+depcc="$CC" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if ${am_cv_CC_dependencies_compiler_type+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CC_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvc7 | msvc7msys | msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CC_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+ am__fastdepCC_TRUE=
+ am__fastdepCC_FALSE='#'
+else
+ am__fastdepCC_TRUE='#'
+ am__fastdepCC_FALSE=
+fi
+
+
+
+ac_config_files="$ac_config_files Makefile src/Makefile"
+
+
+cat >confcache <<\_ACEOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs, see configure's option --config-cache.
+# It is not useful on other systems. If it contains results you don't
+# want to keep, you may remove or edit it.
+#
+# config.status only pays attention to the cache file if you give it
+# the --recheck option to rerun configure.
+#
+# `ac_cv_env_foo' variables (set or unset) will be overridden when
+# loading this file, other *unset* `ac_cv_foo' will be assigned the
+# following values.
+
+_ACEOF
+
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, we kill variables containing newlines.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+(
+ for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+
+ (set) 2>&1 |
+ case $as_nl`(ac_space=' '; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ # `set' does not quote correctly, so add quotes: double-quote
+ # substitution turns \\\\ into \\, and sed turns \\ into \.
+ sed -n \
+ "s/'/'\\\\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
+ ;; #(
+ *)
+ # `set' quotes correctly as required by POSIX, so do not add quotes.
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+) |
+ sed '
+ /^ac_cv_env_/b end
+ t clear
+ :clear
+ s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
+ t end
+ s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
+ :end' >>confcache
+if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
+ if test -w "$cache_file"; then
+ if test "x$cache_file" != "x/dev/null"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
+$as_echo "$as_me: updating cache $cache_file" >&6;}
+ if test ! -f "$cache_file" || test -h "$cache_file"; then
+ cat confcache >"$cache_file"
+ else
+ case $cache_file in #(
+ */* | ?:*)
+ mv -f confcache "$cache_file"$$ &&
+ mv -f "$cache_file"$$ "$cache_file" ;; #(
+ *)
+ mv -f confcache "$cache_file" ;;
+ esac
+ fi
+ fi
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
+$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
+ fi
+fi
+rm -f confcache
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+# Transform confdefs.h into DEFS.
+# Protect against shell expansion while executing Makefile rules.
+# Protect against Makefile macro expansion.
+#
+# If the first sed substitution is executed (which looks for macros that
+# take arguments), then branch to the quote section. Otherwise,
+# look for a macro that doesn't take arguments.
+ac_script='
+:mline
+/\\$/{
+ N
+ s,\\\n,,
+ b mline
+}
+t clear
+:clear
+s/^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*([^)]*)\)[ ]*\(.*\)/-D\1=\2/g
+t quote
+s/^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)/-D\1=\2/g
+t quote
+b any
+:quote
+s/[ `~#$^&*(){}\\|;'\''"<>?]/\\&/g
+s/\[/\\&/g
+s/\]/\\&/g
+s/\$/$$/g
+H
+:any
+${
+ g
+ s/^\n//
+ s/\n/ /g
+ p
+}
+'
+DEFS=`sed -n "$ac_script" confdefs.h`
+
+
+ac_libobjs=
+ac_ltlibobjs=
+U=
+for ac_i in : $LIB@&t at OBJS; do test "x$ac_i" = x: && continue
+ # 1. Remove the extension, and $U if already installed.
+ ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
+ ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
+ # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
+ # will be set to the directory where LIBOBJS objects are built.
+ as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+ as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
+done
+LIB@&t at OBJS=$ac_libobjs
+
+LTLIBOBJS=$ac_ltlibobjs
+
+
+ if test -n "$EXEEXT"; then
+ am__EXEEXT_TRUE=
+ am__EXEEXT_FALSE='#'
+else
+ am__EXEEXT_TRUE='#'
+ am__EXEEXT_FALSE=
+fi
+
+if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
+ as_fn_error $? "conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+
+: "${CONFIG_STATUS=./config.status}"
+ac_write_fail=0
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files $CONFIG_STATUS"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
+$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
+as_write_fail=0
+cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+
+SHELL=\${CONFIG_SHELL-$SHELL}
+export SHELL
+_ASEOF
+cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in @%:@(
+ *posix*) :
+ set -o posix ;; @%:@(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in @%:@(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+as_myself=
+case $0 in @%:@((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+
+@%:@ as_fn_error STATUS ERROR [LINENO LOG_FD]
+@%:@ ----------------------------------------
+@%:@ Output "`basename @S|@0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+@%:@ provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+@%:@ script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} @%:@ as_fn_error
+
+
+@%:@ as_fn_set_status STATUS
+@%:@ -----------------------
+@%:@ Set @S|@? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} @%:@ as_fn_set_status
+
+@%:@ as_fn_exit STATUS
+@%:@ -----------------
+@%:@ Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} @%:@ as_fn_exit
+
+@%:@ as_fn_unset VAR
+@%:@ ---------------
+@%:@ Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+@%:@ as_fn_append VAR VALUE
+@%:@ ----------------------
+@%:@ Append the text in VALUE to the end of the definition contained in VAR. Take
+@%:@ advantage of any shell optimizations that allow amortized linear growth over
+@%:@ repeated appends, instead of the typical quadratic growth present in naive
+@%:@ implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+@%:@ as_fn_arith ARG...
+@%:@ ------------------
+@%:@ Perform arithmetic evaluation on the ARGs, and store the result in the
+@%:@ global @S|@as_val. Take advantage of shells that can avoid forks. The arguments
+@%:@ must be portable across @S|@(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in @%:@(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+
+@%:@ as_fn_mkdir_p
+@%:@ -------------
+@%:@ Create "@S|@as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} @%:@ as_fn_mkdir_p
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in @%:@(
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in @%:@((
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+exec 6>&1
+## ----------------------------------- ##
+## Main body of $CONFIG_STATUS script. ##
+## ----------------------------------- ##
+_ASEOF
+test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# Save the log message, to keep $0 and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling.
+ac_log="
+This file was extended by OpenBUGS $as_me 0.1, which was
+generated by GNU Autoconf 2.68. Invocation command line was
+
+ CONFIG_FILES = $CONFIG_FILES
+ CONFIG_HEADERS = $CONFIG_HEADERS
+ CONFIG_LINKS = $CONFIG_LINKS
+ CONFIG_COMMANDS = $CONFIG_COMMANDS
+ $ $0 $@
+
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
+"
+
+_ACEOF
+
+case $ac_config_files in *"
+"*) set x $ac_config_files; shift; ac_config_files=$*;;
+esac
+
+
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+# Files that config.status was made for.
+config_files="$ac_config_files"
+config_commands="$ac_config_commands"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ac_cs_usage="\
+\`$as_me' instantiates files and other configuration actions
+from templates according to the current configuration. Unless the files
+and actions are specified as TAGs, all are instantiated by default.
+
+Usage: $0 [OPTION]... [TAG]...
+
+ -h, --help print this help, then exit
+ -V, --version print version number and configuration settings, then exit
+ --config print configuration, then exit
+ -q, --quiet, --silent
+ do not print progress messages
+ -d, --debug don't remove temporary files
+ --recheck update $as_me by reconfiguring in the same conditions
+ --file=FILE[:TEMPLATE]
+ instantiate the configuration file FILE
+
+Configuration files:
+$config_files
+
+Configuration commands:
+$config_commands
+
+Report bugs to the package provider."
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
+ac_cs_version="\\
+OpenBUGS config.status 0.1
+configured by $0, generated by GNU Autoconf 2.68,
+ with options \\"\$ac_cs_config\\"
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+
+ac_pwd='$ac_pwd'
+srcdir='$srcdir'
+INSTALL='$INSTALL'
+MKDIR_P='$MKDIR_P'
+AWK='$AWK'
+test -n "\$AWK" || AWK=awk
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# The default lists apply if the user does not specify any file.
+ac_need_defaults=:
+while test $# != 0
+do
+ case $1 in
+ --*=?*)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
+ ac_shift=:
+ ;;
+ --*=)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=
+ ac_shift=:
+ ;;
+ *)
+ ac_option=$1
+ ac_optarg=$2
+ ac_shift=shift
+ ;;
+ esac
+
+ case $ac_option in
+ # Handling of the options.
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ ac_cs_recheck=: ;;
+ --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
+ $as_echo "$ac_cs_version"; exit ;;
+ --config | --confi | --conf | --con | --co | --c )
+ $as_echo "$ac_cs_config"; exit ;;
+ --debug | --debu | --deb | --de | --d | -d )
+ debug=: ;;
+ --file | --fil | --fi | --f )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ '') as_fn_error $? "missing file argument" ;;
+ esac
+ as_fn_append CONFIG_FILES " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --he | --h | --help | --hel | -h )
+ $as_echo "$ac_cs_usage"; exit ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil | --si | --s)
+ ac_cs_silent=: ;;
+
+ # This is an error.
+ -*) as_fn_error $? "unrecognized option: \`$1'
+Try \`$0 --help' for more information." ;;
+
+ *) as_fn_append ac_config_targets " $1"
+ ac_need_defaults=false ;;
+
+ esac
+ shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+ exec 6>/dev/null
+ ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+if \$ac_cs_recheck; then
+ set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+ shift
+ \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
+ CONFIG_SHELL='$SHELL'
+ export CONFIG_SHELL
+ exec "\$@"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+exec 5>>config.log
+{
+ echo
+ sed 'h;s/./-/g;s/^.../@%:@@%:@ /;s/...$/ @%:@@%:@/;p;x;p;x' <<_ASBOX
+@%:@@%:@ Running $as_me. @%:@@%:@
+_ASBOX
+ $as_echo "$ac_log"
+} >&5
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+#
+# INIT-COMMANDS
+#
+AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+
+# Handling of arguments.
+for ac_config_target in $ac_config_targets
+do
+ case $ac_config_target in
+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+ "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+
+ *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
+ esac
+done
+
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used. Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+ test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+ test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
+fi
+
+# Have a temporary directory for convenience. Make it in the build tree
+# simply because there is no reason against having it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Hook for its removal unless debugging.
+# Note that there is a small window in which the directory will not be cleaned:
+# after its creation but before its name has been assigned to `$tmp'.
+$debug ||
+{
+ tmp= ac_tmp=
+ trap 'exit_status=$?
+ : "${ac_tmp:=$tmp}"
+ { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status
+' 0
+ trap 'as_fn_exit 1' 1 2 13 15
+}
+# Create a (secure) tmp directory for tmp files.
+
+{
+ tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
+ test -d "$tmp"
+} ||
+{
+ tmp=./conf$$-$RANDOM
+ (umask 077 && mkdir "$tmp")
+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
+ac_tmp=$tmp
+
+# Set up the scripts for CONFIG_FILES section.
+# No need to generate them if there are no CONFIG_FILES.
+# This happens for instance with `./config.status config.h'.
+if test -n "$CONFIG_FILES"; then
+
+
+ac_cr=`echo X | tr X '\015'`
+# On cygwin, bash can eat \r inside `` if the user requested igncr.
+# But we know of no other shell where ac_cr would be empty at this
+# point, so we can use a bashism as a fallback.
+if test "x$ac_cr" = x; then
+ eval ac_cr=\$\'\\r\'
+fi
+ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
+if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
+ ac_cs_awk_cr='\\r'
+else
+ ac_cs_awk_cr=$ac_cr
+fi
+
+echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
+_ACEOF
+
+
+{
+ echo "cat >conf$$subs.awk <<_ACEOF" &&
+ echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
+ echo "_ACEOF"
+} >conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
+ac_delim='%!_!# '
+for ac_last_try in false false false false false :; do
+ . ./conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+
+ ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
+ if test $ac_delim_n = $ac_delim_num; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+rm -f conf$$subs.sh
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK &&
+_ACEOF
+sed -n '
+h
+s/^/S["/; s/!.*/"]=/
+p
+g
+s/^[^!]*!//
+:repl
+t repl
+s/'"$ac_delim"'$//
+t delim
+:nl
+h
+s/\(.\{148\}\)..*/\1/
+t more1
+s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
+p
+n
+b repl
+:more1
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t nl
+:delim
+h
+s/\(.\{148\}\)..*/\1/
+t more2
+s/["\\]/\\&/g; s/^/"/; s/$/"/
+p
+b
+:more2
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t delim
+' <conf$$subs.awk | sed '
+/^[^""]/{
+ N
+ s/\n//
+}
+' >>$CONFIG_STATUS || ac_write_fail=1
+rm -f conf$$subs.awk
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+_ACAWK
+cat >>"\$ac_tmp/subs1.awk" <<_ACAWK &&
+ for (key in S) S_is_set[key] = 1
+ FS = ""
+
+}
+{
+ line = $ 0
+ nfields = split(line, field, "@")
+ substed = 0
+ len = length(field[1])
+ for (i = 2; i < nfields; i++) {
+ key = field[i]
+ keylen = length(key)
+ if (S_is_set[key]) {
+ value = S[key]
+ line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
+ len += length(value) + length(field[++i])
+ substed = 1
+ } else
+ len += 1 + keylen
+ }
+
+ print line
+}
+
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
+ sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
+else
+ cat
+fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \
+ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
+_ACEOF
+
+# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
+# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
+# trailing colons and then remove the whole line if VPATH becomes empty
+# (actually we leave an empty line to preserve line numbers).
+if test "x$srcdir" = x.; then
+ ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{
+h
+s///
+s/^/:/
+s/[ ]*$/:/
+s/:\$(srcdir):/:/g
+s/:\${srcdir}:/:/g
+s/:@srcdir@:/:/g
+s/^:*//
+s/:*$//
+x
+s/\(=[ ]*\).*/\1/
+G
+s/\n//
+s/^[^=]*=[ ]*$//
+}'
+fi
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+fi # test -n "$CONFIG_FILES"
+
+
+eval set X " :F $CONFIG_FILES :C $CONFIG_COMMANDS"
+shift
+for ac_tag
+do
+ case $ac_tag in
+ :[FHLC]) ac_mode=$ac_tag; continue;;
+ esac
+ case $ac_mode$ac_tag in
+ :[FHL]*:*);;
+ :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;;
+ :[FH]-) ac_tag=-:-;;
+ :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
+ esac
+ ac_save_IFS=$IFS
+ IFS=:
+ set x $ac_tag
+ IFS=$ac_save_IFS
+ shift
+ ac_file=$1
+ shift
+
+ case $ac_mode in
+ :L) ac_source=$1;;
+ :[FH])
+ ac_file_inputs=
+ for ac_f
+ do
+ case $ac_f in
+ -) ac_f="$ac_tmp/stdin";;
+ *) # Look for the file first in the build tree, then in the source tree
+ # (if the path is not absolute). The absolute path cannot be DOS-style,
+ # because $ac_f cannot contain `:'.
+ test -f "$ac_f" ||
+ case $ac_f in
+ [\\/$]*) false;;
+ *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
+ esac ||
+ as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;;
+ esac
+ case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
+ as_fn_append ac_file_inputs " '$ac_f'"
+ done
+
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ configure_input='Generated from '`
+ $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
+ `' by configure.'
+ if test x"$ac_file" != x-; then
+ configure_input="$ac_file. $configure_input"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
+$as_echo "$as_me: creating $ac_file" >&6;}
+ fi
+ # Neutralize special characters interpreted by sed in replacement strings.
+ case $configure_input in #(
+ *\&* | *\|* | *\\* )
+ ac_sed_conf_input=`$as_echo "$configure_input" |
+ sed 's/[\\\\&|]/\\\\&/g'`;; #(
+ *) ac_sed_conf_input=$configure_input;;
+ esac
+
+ case $ac_tag in
+ *:-:* | *:-) cat >"$ac_tmp/stdin" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
+ esac
+ ;;
+ esac
+
+ ac_dir=`$as_dirname -- "$ac_file" ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir="$ac_dir"; as_fn_mkdir_p
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+
+ case $ac_mode in
+ :F)
+ #
+ # CONFIG_FILE
+ #
+
+ case $INSTALL in
+ [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
+ *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
+ esac
+ ac_MKDIR_P=$MKDIR_P
+ case $MKDIR_P in
+ [\\/$]* | ?:[\\/]* ) ;;
+ */*) ac_MKDIR_P=$ac_top_build_prefix$MKDIR_P ;;
+ esac
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# If the template does not know about datarootdir, expand it.
+# FIXME: This hack should be removed a few years after 2.60.
+ac_datarootdir_hack=; ac_datarootdir_seen=
+ac_sed_dataroot='
+/datarootdir/ {
+ p
+ q
+}
+/@datadir@/p
+/@docdir@/p
+/@infodir@/p
+/@localedir@/p
+/@mandir@/p'
+case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
+*datarootdir*) ac_datarootdir_seen=yes;;
+*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ ac_datarootdir_hack='
+ s&@datadir@&$datadir&g
+ s&@docdir@&$docdir&g
+ s&@infodir@&$infodir&g
+ s&@localedir@&$localedir&g
+ s&@mandir@&$mandir&g
+ s&\\\${datarootdir}&$datarootdir&g' ;;
+esac
+_ACEOF
+
+# Neutralize VPATH when `$srcdir' = `.'.
+# Shell code in configure.ac might set extrasub.
+# FIXME: do we really want to maintain this feature?
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_sed_extra="$ac_vpsub
+$extrasub
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+:t
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+s|@configure_input@|$ac_sed_conf_input|;t t
+s&@top_builddir@&$ac_top_builddir_sub&;t t
+s&@top_build_prefix@&$ac_top_build_prefix&;t t
+s&@srcdir@&$ac_srcdir&;t t
+s&@abs_srcdir@&$ac_abs_srcdir&;t t
+s&@top_srcdir@&$ac_top_srcdir&;t t
+s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
+s&@builddir@&$ac_builddir&;t t
+s&@abs_builddir@&$ac_abs_builddir&;t t
+s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
+s&@INSTALL@&$ac_INSTALL&;t t
+s&@MKDIR_P@&$ac_MKDIR_P&;t t
+$ac_datarootdir_hack
+"
+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \
+ >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+
+test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
+ { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } &&
+ { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \
+ "$ac_tmp/out"`; test -z "$ac_out"; } &&
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
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+$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&2;}
+
+ rm -f "$ac_tmp/stdin"
+ case $ac_file in
+ -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";;
+ *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";;
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+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ ;;
+
+
+ :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
+$as_echo "$as_me: executing $ac_file commands" >&6;}
+ ;;
+ esac
+
+
+ case $ac_file$ac_mode in
+ "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # are listed without --file. Let's play safe and only enable the eval
+ # if we detect the quoting.
+ case $CONFIG_FILES in
+ *\'*) eval set x "$CONFIG_FILES" ;;
+ *) set x $CONFIG_FILES ;;
+ esac
+ shift
+ for mf
+ do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
+ # limit of 2048, but all sed's we know have understand at least 4000.
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+$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$mf" : 'X\(//\)[^/]' \| \
+ X"$mf" : 'X\(//\)$' \| \
+ X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$mf" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`$as_dirname -- "$file" ||
+$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$file" : 'X\(//\)[^/]' \| \
+ X"$file" : 'X\(//\)$' \| \
+ X"$file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir=$dirpart/$fdir; as_fn_mkdir_p
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+ done
+}
+ ;;
+
+ esac
+done # for ac_tag
+
+
+as_fn_exit 0
+_ACEOF
+ac_clean_files=$ac_clean_files_save
+
+test $ac_write_fail = 0 ||
+ as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
+
+
+# configure is writing to config.log, and then calls config.status.
+# config.status does its own redirection, appending to config.log.
+# Unfortunately, on DOS this fails, as config.log is still kept open
+# by configure, so config.status won't be able to write to it; its
+# output is simply discarded. So we exec the FD to /dev/null,
+# effectively closing config.log, so it can be properly (re)opened and
+# appended to by config.status. When coming back to configure, we
+# need to make the FD available again.
+if test "$no_create" != yes; then
+ ac_cs_success=:
+ ac_config_status_args=
+ test "$silent" = yes &&
+ ac_config_status_args="$ac_config_status_args --quiet"
+ exec 5>/dev/null
+ $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
+ exec 5>>config.log
+ # Use ||, not &&, to avoid exiting from the if with $? = 1, which
+ # would make configure fail if this is the last instruction.
+ $ac_cs_success || as_fn_exit 1
+fi
+if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
+$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
+fi
+
diff --git a/autom4te.cache/requests b/autom4te.cache/requests
new file mode 100644
index 0000000..8bd348a
--- /dev/null
+++ b/autom4te.cache/requests
@@ -0,0 +1,144 @@
+# This file was generated by Autom4te Sun Nov 6 20:57:04 UTC 2011.
+# It contains the lists of macros which have been traced.
+# It can be safely removed.
+
+ at request = (
+ bless( [
+ '0',
+ 1,
+ [
+ '/usr/share/autoconf'
+ ],
+ [
+ '/usr/share/autoconf/autoconf/autoconf.m4f',
+ '/usr/share/aclocal-1.11/amversion.m4',
+ '/usr/share/aclocal-1.11/auxdir.m4',
+ '/usr/share/aclocal-1.11/cond.m4',
+ '/usr/share/aclocal-1.11/depend.m4',
+ '/usr/share/aclocal-1.11/depout.m4',
+ '/usr/share/aclocal-1.11/init.m4',
+ '/usr/share/aclocal-1.11/install-sh.m4',
+ '/usr/share/aclocal-1.11/lead-dot.m4',
+ '/usr/share/aclocal-1.11/make.m4',
+ '/usr/share/aclocal-1.11/missing.m4',
+ '/usr/share/aclocal-1.11/mkdirp.m4',
+ '/usr/share/aclocal-1.11/options.m4',
+ '/usr/share/aclocal-1.11/runlog.m4',
+ '/usr/share/aclocal-1.11/sanity.m4',
+ '/usr/share/aclocal-1.11/silent.m4',
+ '/usr/share/aclocal-1.11/strip.m4',
+ '/usr/share/aclocal-1.11/substnot.m4',
+ '/usr/share/aclocal-1.11/tar.m4',
+ 'configure.ac'
+ ],
+ {
+ 'm4_pattern_forbid' => 1,
+ 'AM_SET_CURRENT_AUTOMAKE_VERSION' => 1,
+ '_AM_SET_OPTION' => 1,
+ 'AC_DEFUN' => 1,
+ 'AM_PROG_MKDIR_P' => 1,
+ 'AM_INIT_AUTOMAKE' => 1,
+ 'AM_AUTOMAKE_VERSION' => 1,
+ 'AM_MISSING_HAS_RUN' => 1,
+ 'AM_SUBST_NOTMAKE' => 1,
+ 'AM_MISSING_PROG' => 1,
+ 'AM_OUTPUT_DEPENDENCY_COMMANDS' => 1,
+ 'AC_DEFUN_ONCE' => 1,
+ 'AM_PROG_INSTALL_STRIP' => 1,
+ '_m4_warn' => 1,
+ 'AM_SANITY_CHECK' => 1,
+ 'AM_SILENT_RULES' => 1,
+ 'include' => 1,
+ '_AM_PROG_TAR' => 1,
+ 'AM_AUX_DIR_EXPAND' => 1,
+ 'AM_DEP_TRACK' => 1,
+ '_AM_SET_OPTIONS' => 1,
+ '_AM_OUTPUT_DEPENDENCY_COMMANDS' => 1,
+ 'AM_RUN_LOG' => 1,
+ '_AM_IF_OPTION' => 1,
+ '_AM_SUBST_NOTMAKE' => 1,
+ 'm4_pattern_allow' => 1,
+ '_AM_AUTOCONF_VERSION' => 1,
+ '_AM_MANGLE_OPTION' => 1,
+ 'AM_CONDITIONAL' => 1,
+ 'AM_SET_LEADING_DOT' => 1,
+ 'AM_SET_DEPDIR' => 1,
+ '_AM_DEPENDENCIES' => 1,
+ 'AM_PROG_INSTALL_SH' => 1,
+ 'm4_include' => 1,
+ '_AC_AM_CONFIG_HEADER_HOOK' => 1,
+ 'AU_DEFUN' => 1,
+ 'AM_MAKE_INCLUDE' => 1
+ }
+ ], 'Autom4te::Request' ),
+ bless( [
+ '1',
+ 1,
+ [
+ '/usr/share/autoconf'
+ ],
+ [
+ '/usr/share/autoconf/autoconf/autoconf.m4f',
+ 'aclocal.m4',
+ 'configure.ac'
+ ],
+ {
+ '_LT_AC_TAGCONFIG' => 1,
+ 'AM_PROG_F77_C_O' => 1,
+ 'm4_pattern_forbid' => 1,
+ 'AC_INIT' => 1,
+ '_AM_COND_IF' => 1,
+ 'AC_CANONICAL_TARGET' => 1,
+ 'AC_SUBST' => 1,
+ 'AC_CONFIG_LIBOBJ_DIR' => 1,
+ 'AC_FC_SRCEXT' => 1,
+ 'AC_CANONICAL_HOST' => 1,
+ 'AC_PROG_LIBTOOL' => 1,
+ 'AM_INIT_AUTOMAKE' => 1,
+ 'AM_PATH_GUILE' => 1,
+ 'AC_CONFIG_SUBDIRS' => 1,
+ 'AM_AUTOMAKE_VERSION' => 1,
+ 'LT_CONFIG_LTDL_DIR' => 1,
+ 'AC_REQUIRE_AUX_FILE' => 1,
+ 'AC_CONFIG_LINKS' => 1,
+ 'm4_sinclude' => 1,
+ 'LT_SUPPORTED_TAG' => 1,
+ 'AM_MAINTAINER_MODE' => 1,
+ 'AM_NLS' => 1,
+ 'AM_GNU_GETTEXT_INTL_SUBDIR' => 1,
+ 'AM_MAKEFILE_INCLUDE' => 1,
+ '_m4_warn' => 1,
+ 'AM_PROG_CXX_C_O' => 1,
+ '_AM_COND_ENDIF' => 1,
+ '_AM_MAKEFILE_INCLUDE' => 1,
+ 'AM_ENABLE_MULTILIB' => 1,
+ 'AM_SILENT_RULES' => 1,
+ 'AM_PROG_MOC' => 1,
+ 'AC_CONFIG_FILES' => 1,
+ 'LT_INIT' => 1,
+ 'include' => 1,
+ 'AM_PROG_AR' => 1,
+ 'AM_GNU_GETTEXT' => 1,
+ 'AC_LIBSOURCE' => 1,
+ 'AM_PROG_FC_C_O' => 1,
+ 'AC_CANONICAL_BUILD' => 1,
+ 'AC_FC_FREEFORM' => 1,
+ 'AH_OUTPUT' => 1,
+ '_AM_SUBST_NOTMAKE' => 1,
+ 'AC_CONFIG_AUX_DIR' => 1,
+ 'sinclude' => 1,
+ 'AM_PROG_CC_C_O' => 1,
+ 'm4_pattern_allow' => 1,
+ 'AM_XGETTEXT_OPTION' => 1,
+ 'AC_CANONICAL_SYSTEM' => 1,
+ 'AM_CONDITIONAL' => 1,
+ 'AC_CONFIG_HEADERS' => 1,
+ 'AC_DEFINE_TRACE_LITERAL' => 1,
+ 'AM_POT_TOOLS' => 1,
+ 'm4_include' => 1,
+ '_AM_COND_ELSE' => 1,
+ 'AC_SUBST_TRACE' => 1
+ }
+ ], 'Autom4te::Request' )
+ );
+
diff --git a/autom4te.cache/traces.0 b/autom4te.cache/traces.0
new file mode 100644
index 0000000..cefd1f5
--- /dev/null
+++ b/autom4te.cache/traces.0
@@ -0,0 +1,776 @@
+m4trace:/usr/share/aclocal-1.11/amversion.m4:17: -1- AC_DEFUN([AM_AUTOMAKE_VERSION], [am__api_version='1.11'
+dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
+dnl require some minimum version. Point them to the right macro.
+m4_if([$1], [1.11.3], [],
+ [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
+])
+m4trace:/usr/share/aclocal-1.11/amversion.m4:36: -1- AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION], [AM_AUTOMAKE_VERSION([1.11.3])dnl
+m4_ifndef([AC_AUTOCONF_VERSION],
+ [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
+_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
+m4trace:/usr/share/aclocal-1.11/auxdir.m4:49: -1- AC_DEFUN([AM_AUX_DIR_EXPAND], [dnl Rely on autoconf to set up CDPATH properly.
+AC_PREREQ([2.50])dnl
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+])
+m4trace:/usr/share/aclocal-1.11/cond.m4:15: -1- AC_DEFUN([AM_CONDITIONAL], [AC_PREREQ(2.52)dnl
+ ifelse([$1], [TRUE], [AC_FATAL([$0: invalid condition: $1])],
+ [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
+AC_SUBST([$1_TRUE])dnl
+AC_SUBST([$1_FALSE])dnl
+_AM_SUBST_NOTMAKE([$1_TRUE])dnl
+_AM_SUBST_NOTMAKE([$1_FALSE])dnl
+m4_define([_AM_COND_VALUE_$1], [$2])dnl
+if $2; then
+ $1_TRUE=
+ $1_FALSE='#'
+else
+ $1_TRUE='#'
+ $1_FALSE=
+fi
+AC_CONFIG_COMMANDS_PRE(
+[if test -z "${$1_TRUE}" && test -z "${$1_FALSE}"; then
+ AC_MSG_ERROR([[conditional "$1" was never defined.
+Usually this means the macro was only invoked conditionally.]])
+fi])])
+m4trace:/usr/share/aclocal-1.11/depend.m4:28: -1- AC_DEFUN([_AM_DEPENDENCIES], [AC_REQUIRE([AM_SET_DEPDIR])dnl
+AC_REQUIRE([AM_OUTPUT_DEPENDENCY_COMMANDS])dnl
+AC_REQUIRE([AM_MAKE_INCLUDE])dnl
+AC_REQUIRE([AM_DEP_TRACK])dnl
+
+ifelse([$1], CC, [depcc="$CC" am_compiler_list=],
+ [$1], CXX, [depcc="$CXX" am_compiler_list=],
+ [$1], OBJC, [depcc="$OBJC" am_compiler_list='gcc3 gcc'],
+ [$1], UPC, [depcc="$UPC" am_compiler_list=],
+ [$1], GCJ, [depcc="$GCJ" am_compiler_list='gcc3 gcc'],
+ [depcc="$$1" am_compiler_list=])
+
+AC_CACHE_CHECK([dependency style of $depcc],
+ [am_cv_$1_dependencies_compiler_type],
+[if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
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+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_$1_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n ['s/^#*\([a-zA-Z0-9]*\))$/\1/p'] < ./depcomp`
+ fi
+ am__universal=false
+ m4_case([$1], [CC],
+ [case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac],
+ [CXX],
+ [case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac])
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
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+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
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+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvc7 | msvc7msys | msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
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+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
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+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_$1_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
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+fi
+])
+AC_SUBST([$1DEPMODE], [depmode=$am_cv_$1_dependencies_compiler_type])
+AM_CONDITIONAL([am__fastdep$1], [
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+ && test "$am_cv_$1_dependencies_compiler_type" = gcc3])
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+AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])dnl
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+[ --disable-dependency-tracking speeds up one-time build
+ --enable-dependency-tracking do not reject slow dependency extractors])
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+ AMDEPBACKSLASH='\'
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+])
+m4trace:/usr/share/aclocal-1.11/depout.m4:14: -1- AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS], [{
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # are listed without --file. Let's play safe and only enable the eval
+ # if we detect the quoting.
+ case $CONFIG_FILES in
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+ *) set x $CONFIG_FILES ;;
+ esac
+ shift
+ for mf
+ do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
+ # limit of 2048, but all sed's we know have understand at least 4000.
+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
+ dirpart=`AS_DIRNAME("$mf")`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
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+ fdir=`AS_DIRNAME(["$file"])`
+ AS_MKDIR_P([$dirpart/$fdir])
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+ done
+}
+])
+m4trace:/usr/share/aclocal-1.11/depout.m4:75: -1- AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS], [AC_CONFIG_COMMANDS([depfiles],
+ [test x"$AMDEP_TRUE" != x"" || _AM_OUTPUT_DEPENDENCY_COMMANDS],
+ [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"])
+])
+m4trace:/usr/share/aclocal-1.11/init.m4:26: -1- AC_DEFUN([AM_INIT_AUTOMAKE], [AC_PREREQ([2.62])dnl
+dnl Autoconf wants to disallow AM_ names. We explicitly allow
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+m4_pattern_allow([^AM_[A-Z]+FLAGS$])dnl
+AC_REQUIRE([AM_SET_CURRENT_AUTOMAKE_VERSION])dnl
+AC_REQUIRE([AC_PROG_INSTALL])dnl
+if test "`cd $srcdir && pwd`" != "`pwd`"; then
+ # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
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+ AC_SUBST([am__isrc], [' -I$(srcdir)'])_AM_SUBST_NOTMAKE([am__isrc])dnl
+ # test to see if srcdir already configured
+ if test -f $srcdir/config.status; then
+ AC_MSG_ERROR([source directory already configured; run "make distclean" there first])
+ fi
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+ if (cygpath --version) >/dev/null 2>/dev/null; then
+ CYGPATH_W='cygpath -w'
+ else
+ CYGPATH_W=echo
+ fi
+fi
+AC_SUBST([CYGPATH_W])
+
+# Define the identity of the package.
+dnl Distinguish between old-style and new-style calls.
+m4_ifval([$2],
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+ AC_SUBST([PACKAGE], [$1])dnl
+ AC_SUBST([VERSION], [$2])],
+[_AM_SET_OPTIONS([$1])dnl
+dnl Diagnose old-style AC_INIT with new-style AM_AUTOMAKE_INIT.
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+ AC_SUBST([PACKAGE], ['AC_PACKAGE_TARNAME'])dnl
+ AC_SUBST([VERSION], ['AC_PACKAGE_VERSION'])])dnl
+
+_AM_IF_OPTION([no-define],,
+[AC_DEFINE_UNQUOTED(PACKAGE, "$PACKAGE", [Name of package])
+ AC_DEFINE_UNQUOTED(VERSION, "$VERSION", [Version number of package])])dnl
+
+# Some tools Automake needs.
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+AC_REQUIRE([AC_ARG_PROGRAM])dnl
+AM_MISSING_PROG(ACLOCAL, aclocal-${am__api_version})
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+AC_REQUIRE([AC_PROG_AWK])dnl
+AC_REQUIRE([AC_PROG_MAKE_SET])dnl
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+_AM_IF_OPTION([no-dependencies],,
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+AC_PROVIDE_IFELSE([AC_PROG_CXX],
+ [_AM_DEPENDENCIES(CXX)],
+ [define([AC_PROG_CXX],
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+AC_PROVIDE_IFELSE([AC_PROG_OBJC],
+ [_AM_DEPENDENCIES(OBJC)],
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+_AM_IF_OPTION([silent-rules], [AC_REQUIRE([AM_SILENT_RULES])])dnl
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+AC_CONFIG_COMMANDS_PRE(dnl
+[m4_provide_if([_AM_COMPILER_EXEEXT],
+ [AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
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+_am_arg=$1
+_am_stamp_count=1
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+ _am_stamp_count=`expr $_am_stamp_count + 1` ;;
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+echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
+m4trace:/usr/share/aclocal-1.11/install-sh.m4:14: -1- AC_DEFUN([AM_PROG_INSTALL_SH], [AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
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+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
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+AC_SUBST(install_sh)])
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+ am__leading_dot=_
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+AC_SUBST([am__leading_dot])])
+m4trace:/usr/share/aclocal-1.11/make.m4:14: -1- AC_DEFUN([AM_MAKE_INCLUDE], [am_make=${MAKE-make}
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+am__doit:
+ @echo this is the am__doit target
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+# If we don't find an include directive, just comment out the code.
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+# Ignore all kinds of additional output from `make'.
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+ am__quote=
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+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+ echo '.include "confinc"' > confmf
+ case `$am_make -s -f confmf 2> /dev/null` in #(
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+ am__quote="\""
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+fi
+AC_SUBST([am__include])
+AC_SUBST([am__quote])
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+rm -f confinc confmf
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+ esac
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+ am_missing_run="$MISSING --run "
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+ am_missing_run=
+ AC_MSG_WARN([`missing' script is too old or missing])
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+[ --enable-silent-rules less verbose build output (undo: `make V=1')
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+ am_cv_make_support_nested_variables=yes
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+ am_cv_make_support_nested_variables=no
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+if test $am_cv_make_support_nested_variables = yes; then
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+else
+ AM_V=$AM_DEFAULT_VERBOSITY
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diff --git a/autom4te.cache/traces.1 b/autom4te.cache/traces.1
new file mode 100644
index 0000000..f0ddb94
--- /dev/null
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+m4trace:configure.ac:4: -1- AC_SUBST([CYGPATH_W])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([CYGPATH_W])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^CYGPATH_W$])
+m4trace:configure.ac:4: -1- AC_SUBST([PACKAGE], ['AC_PACKAGE_TARNAME'])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([PACKAGE])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^PACKAGE$])
+m4trace:configure.ac:4: -1- AC_SUBST([VERSION], ['AC_PACKAGE_VERSION'])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([VERSION])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^VERSION$])
+m4trace:configure.ac:4: -1- AC_DEFINE_TRACE_LITERAL([PACKAGE])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^PACKAGE$])
+m4trace:configure.ac:4: -1- AH_OUTPUT([PACKAGE], [/* Name of package */
+@%:@undef PACKAGE])
+m4trace:configure.ac:4: -1- AC_DEFINE_TRACE_LITERAL([VERSION])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^VERSION$])
+m4trace:configure.ac:4: -1- AH_OUTPUT([VERSION], [/* Version number of package */
+@%:@undef VERSION])
+m4trace:configure.ac:4: -1- AC_REQUIRE_AUX_FILE([missing])
+m4trace:configure.ac:4: -1- AC_SUBST([ACLOCAL])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([ACLOCAL])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^ACLOCAL$])
+m4trace:configure.ac:4: -1- AC_SUBST([AUTOCONF])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([AUTOCONF])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^AUTOCONF$])
+m4trace:configure.ac:4: -1- AC_SUBST([AUTOMAKE])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([AUTOMAKE])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^AUTOMAKE$])
+m4trace:configure.ac:4: -1- AC_SUBST([AUTOHEADER])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([AUTOHEADER])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^AUTOHEADER$])
+m4trace:configure.ac:4: -1- AC_SUBST([MAKEINFO])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([MAKEINFO])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^MAKEINFO$])
+m4trace:configure.ac:4: -1- AC_SUBST([install_sh])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([install_sh])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^install_sh$])
+m4trace:configure.ac:4: -1- AC_SUBST([STRIP])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([STRIP])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^STRIP$])
+m4trace:configure.ac:4: -1- AC_SUBST([INSTALL_STRIP_PROGRAM])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([INSTALL_STRIP_PROGRAM])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^INSTALL_STRIP_PROGRAM$])
+m4trace:configure.ac:4: -1- AC_REQUIRE_AUX_FILE([install-sh])
+m4trace:configure.ac:4: -1- AC_SUBST([MKDIR_P])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([MKDIR_P])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^MKDIR_P$])
+m4trace:configure.ac:4: -1- AC_SUBST([mkdir_p], ["$MKDIR_P"])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([mkdir_p])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^mkdir_p$])
+m4trace:configure.ac:4: -1- AC_SUBST([AWK])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([AWK])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^AWK$])
+m4trace:configure.ac:4: -1- AC_SUBST([SET_MAKE])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([SET_MAKE])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^SET_MAKE$])
+m4trace:configure.ac:4: -1- AC_SUBST([am__leading_dot])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([am__leading_dot])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^am__leading_dot$])
+m4trace:configure.ac:4: -1- AC_SUBST([AMTAR], ['$${TAR-tar}'])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([AMTAR])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^AMTAR$])
+m4trace:configure.ac:4: -1- AC_SUBST([am__tar])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([am__tar])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^am__tar$])
+m4trace:configure.ac:4: -1- AC_SUBST([am__untar])
+m4trace:configure.ac:4: -1- AC_SUBST_TRACE([am__untar])
+m4trace:configure.ac:4: -1- m4_pattern_allow([^am__untar$])
+m4trace:configure.ac:8: -1- AC_SUBST([CC])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([CC])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^CC$])
+m4trace:configure.ac:8: -1- AC_SUBST([CFLAGS])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([CFLAGS])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^CFLAGS$])
+m4trace:configure.ac:8: -1- AC_SUBST([LDFLAGS])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([LDFLAGS])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^LDFLAGS$])
+m4trace:configure.ac:8: -1- AC_SUBST([LIBS])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([LIBS])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^LIBS$])
+m4trace:configure.ac:8: -1- AC_SUBST([CPPFLAGS])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([CPPFLAGS])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^CPPFLAGS$])
+m4trace:configure.ac:8: -1- AC_SUBST([CC])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([CC])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^CC$])
+m4trace:configure.ac:8: -1- AC_SUBST([CC])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([CC])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^CC$])
+m4trace:configure.ac:8: -1- AC_SUBST([CC])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([CC])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^CC$])
+m4trace:configure.ac:8: -1- AC_SUBST([CC])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([CC])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^CC$])
+m4trace:configure.ac:8: -1- AC_SUBST([ac_ct_CC])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([ac_ct_CC])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^ac_ct_CC$])
+m4trace:configure.ac:8: -1- AC_SUBST([EXEEXT], [$ac_cv_exeext])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([EXEEXT])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^EXEEXT$])
+m4trace:configure.ac:8: -1- AC_SUBST([OBJEXT], [$ac_cv_objext])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([OBJEXT])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^OBJEXT$])
+m4trace:configure.ac:8: -1- AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([DEPDIR])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^DEPDIR$])
+m4trace:configure.ac:8: -1- AC_SUBST([am__include])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([am__include])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^am__include$])
+m4trace:configure.ac:8: -1- AC_SUBST([am__quote])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([am__quote])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^am__quote$])
+m4trace:configure.ac:8: -1- AM_CONDITIONAL([AMDEP], [test "x$enable_dependency_tracking" != xno])
+m4trace:configure.ac:8: -1- AC_SUBST([AMDEP_TRUE])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([AMDEP_TRUE])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^AMDEP_TRUE$])
+m4trace:configure.ac:8: -1- AC_SUBST([AMDEP_FALSE])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([AMDEP_FALSE])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^AMDEP_FALSE$])
+m4trace:configure.ac:8: -1- _AM_SUBST_NOTMAKE([AMDEP_TRUE])
+m4trace:configure.ac:8: -1- _AM_SUBST_NOTMAKE([AMDEP_FALSE])
+m4trace:configure.ac:8: -1- AC_SUBST([AMDEPBACKSLASH])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([AMDEPBACKSLASH])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^AMDEPBACKSLASH$])
+m4trace:configure.ac:8: -1- _AM_SUBST_NOTMAKE([AMDEPBACKSLASH])
+m4trace:configure.ac:8: -1- AC_SUBST([am__nodep])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([am__nodep])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^am__nodep$])
+m4trace:configure.ac:8: -1- _AM_SUBST_NOTMAKE([am__nodep])
+m4trace:configure.ac:8: -1- AC_SUBST([CCDEPMODE], [depmode=$am_cv_CC_dependencies_compiler_type])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([CCDEPMODE])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^CCDEPMODE$])
+m4trace:configure.ac:8: -1- AM_CONDITIONAL([am__fastdepCC], [
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3])
+m4trace:configure.ac:8: -1- AC_SUBST([am__fastdepCC_TRUE])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([am__fastdepCC_TRUE])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^am__fastdepCC_TRUE$])
+m4trace:configure.ac:8: -1- AC_SUBST([am__fastdepCC_FALSE])
+m4trace:configure.ac:8: -1- AC_SUBST_TRACE([am__fastdepCC_FALSE])
+m4trace:configure.ac:8: -1- m4_pattern_allow([^am__fastdepCC_FALSE$])
+m4trace:configure.ac:8: -1- _AM_SUBST_NOTMAKE([am__fastdepCC_TRUE])
+m4trace:configure.ac:8: -1- _AM_SUBST_NOTMAKE([am__fastdepCC_FALSE])
+m4trace:configure.ac:10: -1- AC_CONFIG_FILES([Makefile src/Makefile])
+m4trace:configure.ac:12: -1- AC_SUBST([LIB@&t at OBJS], [$ac_libobjs])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([LIB@&t at OBJS])
+m4trace:configure.ac:12: -1- m4_pattern_allow([^LIB@&t at OBJS$])
+m4trace:configure.ac:12: -1- AC_SUBST([LTLIBOBJS], [$ac_ltlibobjs])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([LTLIBOBJS])
+m4trace:configure.ac:12: -1- m4_pattern_allow([^LTLIBOBJS$])
+m4trace:configure.ac:12: -1- AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])
+m4trace:configure.ac:12: -1- AC_SUBST([am__EXEEXT_TRUE])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([am__EXEEXT_TRUE])
+m4trace:configure.ac:12: -1- m4_pattern_allow([^am__EXEEXT_TRUE$])
+m4trace:configure.ac:12: -1- AC_SUBST([am__EXEEXT_FALSE])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([am__EXEEXT_FALSE])
+m4trace:configure.ac:12: -1- m4_pattern_allow([^am__EXEEXT_FALSE$])
+m4trace:configure.ac:12: -1- _AM_SUBST_NOTMAKE([am__EXEEXT_TRUE])
+m4trace:configure.ac:12: -1- _AM_SUBST_NOTMAKE([am__EXEEXT_FALSE])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([top_builddir])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([top_build_prefix])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([srcdir])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([abs_srcdir])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([top_srcdir])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([abs_top_srcdir])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([builddir])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([abs_builddir])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([abs_top_builddir])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([INSTALL])
+m4trace:configure.ac:12: -1- AC_SUBST_TRACE([MKDIR_P])
diff --git a/bin/OpenBUGS b/bin/OpenBUGS
new file mode 100755
index 0000000..b64ddb9
--- /dev/null
+++ b/bin/OpenBUGS
@@ -0,0 +1,172 @@
+#! /usr/bin/env bash
+
+usage () {
+ cat <<EOF
+SYNOPSIS
+
+ $0 [options] [args]
+
+EXAMPLES
+
+ OpenBUGS
+
+ OpenBUGS script.txt
+
+ OpenBUGS script.txt > res.lst
+
+ OpenBUGS < script.txt >res.lst
+
+ OpenBUGS -t script.txt
+
+ env BUGSIN="/dif/dir" BUGSOUT="/other/dir" OpenBUGS script.txt > /path/to/res.lst
+
+DESCRIPTION
+
+ Invoke OpenBUGS, usually specifying a script and performing template
+ expansion inside the script file to specifiy directory paths.
+
+
+ Names inside of curly brackets in a script file are interpreted
+ as environmental variables and the values of the environmental
+ variables are substituted. The environmental variables can be
+ set temporarily on the same command line as OpenBUGS execution
+ using the env function, or on a separate line or in a default
+ startup file.
+
+
+ Note: the OpenBUGS script command 'modelSetWD('path')' can now be
+ used as an easier way to set the path where OpenBUGS looks for
+ model, data and initial value files. The environment variable
+ mechanism is still available however, for backward compatibility.
+
+
+OPTIONS
+
+ -d
+ Dry run. Script will be printed on stdout.
+
+ -b
+ Specify the number of curly brackets used to delimit template
+ names.
+
+ -h
+
+ help
+
+ -t
+
+ do not perform template expansion
+
+
+ -- end of options
+
+EOF
+}
+
+
+#incomplete: maybe needed in the future for more complex file handling
+#file_norm () {
+# if test -e "$2"; then
+# res=$2
+# else
+# :
+# fi
+# eval $1=\$res
+#}
+
+#is this ever needed? 2008-08-28 nc
+#export LD_ASSUME_KERNEL-2.4.1
+
+### default configuration ###
+### end default configuration ###
+
+bin=$(dirname $0)
+
+if test -e "$mydir/../etc/OpenBUGS"; then
+ . "$mydir/../etc/OpenBUGS"
+fi
+
+if test -e "$HOME/etc/OpenBUGS"; then
+ . "$HOME/etc/OpenBUGS"
+fi
+
+opt_dry=0
+opt_template=1
+opt_brackets=1
+script=''
+scriptflag=''
+while :; do
+ case ${1+"$1"} in
+ --)
+ shift
+ break
+ ;;
+ -d)
+ opt_dry=1
+ ;;
+ -h|--help)
+ usage
+ exit 0
+ ;;
+ -b)
+ shift
+ opt_brackets="$1"
+ ;;
+ -t)
+ opt_template=0
+ ;;
+ *)
+ script="$1"
+ scriptdir=${script%/}
+ scriptdir=${scriptdir%/*}
+ if test -n "$scriptdir"; then
+ scriptdir=.
+ fi
+ break
+ ;;
+ esac
+ shift
+done
+
+if test -n "$script"; then
+ scriptflag="-s" # input supplied as e.g. OpenBUGS script.txt
+ exec <"$script"
+elif tty >/dev/null 2>&1; then
+ opt_template=0
+fi
+
+
+if test $opt_template -eq 1; then
+ for ((;opt_brackets;opt_brackets-=1)); do b_open=$b_open\{; done
+ #work around shell bug: don't use literal curly bracket in %% expression
+ b_close='}'
+ b_close="${b_open//?/$b_close}"
+ template=$(cat)
+ script=''
+ while :; do
+ before="${template%%$b_open*}"
+ script="$script$before"
+ if test "$before" = "$template"; then
+ break
+ else
+ template="${template#$before$b_open}"
+ var="${template%%$b_close*}"
+ script="$script${!var}"
+ template="${template#$var$b_close}"
+ fi
+ done
+ if test $opt_dry = 1; then
+ printf '%s' "$script"
+ exit 0
+ fi
+ exec <<<"$script"
+fi
+
+if ! [ -t 0 ]; then
+ scriptflag="-s" # input supplied from < file as e.g. OpenBUGS < script.txt , not interactively from terminal
+ if test -e "$script"; then
+ exec <"$script"
+ fi
+fi
+
+"$bin"/OpenBUGSCli $scriptflag
diff --git a/configure b/configure
new file mode 100755
index 0000000..cfa52c2
--- /dev/null
+++ b/configure
@@ -0,0 +1,4564 @@
+#! /bin/sh
+# Guess values for system-dependent variables and create Makefiles.
+# Generated by GNU Autoconf 2.68 for OpenBUGS 0.1.
+#
+#
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
+# Foundation, Inc.
+#
+#
+# This configure script is free software; the Free Software Foundation
+# gives unlimited permission to copy, distribute and modify it.
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in #(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+as_myself=
+case $0 in #((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test "x$CONFIG_SHELL" = x; then
+ as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
+else
+ case \`(set -o) 2>/dev/null\` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+"
+ as_required="as_fn_return () { (exit \$1); }
+as_fn_success () { as_fn_return 0; }
+as_fn_failure () { as_fn_return 1; }
+as_fn_ret_success () { return 0; }
+as_fn_ret_failure () { return 1; }
+
+exitcode=0
+as_fn_success || { exitcode=1; echo as_fn_success failed.; }
+as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
+as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
+as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
+if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
+
+else
+ exitcode=1; echo positional parameters were not saved.
+fi
+test x\$exitcode = x0 || exit 1"
+ as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
+ as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
+ eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
+ test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1"
+ if (eval "$as_required") 2>/dev/null; then :
+ as_have_required=yes
+else
+ as_have_required=no
+fi
+ if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
+
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+as_found=false
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ as_found=:
+ case $as_dir in #(
+ /*)
+ for as_base in sh bash ksh sh5; do
+ # Try only shells that exist, to save several forks.
+ as_shell=$as_dir/$as_base
+ if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ CONFIG_SHELL=$as_shell as_have_required=yes
+ if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ break 2
+fi
+fi
+ done;;
+ esac
+ as_found=false
+done
+$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
+ CONFIG_SHELL=$SHELL as_have_required=yes
+fi; }
+IFS=$as_save_IFS
+
+
+ if test "x$CONFIG_SHELL" != x; then :
+ # We cannot yet assume a decent shell, so we have to provide a
+ # neutralization value for shells without unset; and this also
+ # works around shells that cannot unset nonexistent variables.
+ # Preserve -v and -x to the replacement shell.
+ BASH_ENV=/dev/null
+ ENV=/dev/null
+ (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+ export CONFIG_SHELL
+ case $- in # ((((
+ *v*x* | *x*v* ) as_opts=-vx ;;
+ *v* ) as_opts=-v ;;
+ *x* ) as_opts=-x ;;
+ * ) as_opts= ;;
+ esac
+ exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"}
+fi
+
+ if test x$as_have_required = xno; then :
+ $as_echo "$0: This script requires a shell more modern than all"
+ $as_echo "$0: the shells that I found on your system."
+ if test x${ZSH_VERSION+set} = xset ; then
+ $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
+ $as_echo "$0: be upgraded to zsh 4.3.4 or later."
+ else
+ $as_echo "$0: Please tell bug-autoconf at gnu.org about your system,
+$0: including any error possibly output before this
+$0: message. Then install a modern shell, or manually run
+$0: the script under such a shell if you do have one."
+ fi
+ exit 1
+fi
+fi
+fi
+SHELL=${CONFIG_SHELL-/bin/sh}
+export SHELL
+# Unset more variables known to interfere with behavior of common tools.
+CLICOLOR_FORCE= GREP_OPTIONS=
+unset CLICOLOR_FORCE GREP_OPTIONS
+
+## --------------------- ##
+## M4sh Shell Functions. ##
+## --------------------- ##
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+
+ as_lineno_1=$LINENO as_lineno_1a=$LINENO
+ as_lineno_2=$LINENO as_lineno_2a=$LINENO
+ eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
+ test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
+ # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-)
+ sed -n '
+ p
+ /[$]LINENO/=
+ ' <$as_myself |
+ sed '
+ s/[$]LINENO.*/&-/
+ t lineno
+ b
+ :lineno
+ N
+ :loop
+ s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+ t loop
+ s/-\n.*//
+ ' >$as_me.lineno &&
+ chmod +x "$as_me.lineno" ||
+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
+
+ # Don't try to exec as it changes $[0], causing all sort of problems
+ # (the dirname of $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensitive to this).
+ . "./$as_me.lineno"
+ # Exit status is that of the last command.
+ exit
+}
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in #(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in #(
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+test -n "$DJDIR" || exec 7<&0 </dev/null
+exec 6>&1
+
+# Name of the host.
+# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
+# so uname gets run too.
+ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
+
+#
+# Initializations.
+#
+ac_default_prefix=/usr/local
+ac_clean_files=
+ac_config_libobj_dir=.
+LIBOBJS=
+cross_compiling=no
+subdirs=
+MFLAGS=
+MAKEFLAGS=
+
+# Identity of this package.
+PACKAGE_NAME='OpenBUGS'
+PACKAGE_TARNAME='openbugs'
+PACKAGE_VERSION='0.1'
+PACKAGE_STRING='OpenBUGS 0.1'
+PACKAGE_BUGREPORT=''
+PACKAGE_URL=''
+
+ac_unique_file="src/OpenBUGSCli.c"
+ac_default_prefix=/usr/local
+ac_subst_vars='am__EXEEXT_FALSE
+am__EXEEXT_TRUE
+LTLIBOBJS
+LIBOBJS
+am__fastdepCC_FALSE
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+am__nodep
+AMDEPBACKSLASH
+AMDEP_FALSE
+AMDEP_TRUE
+am__quote
+am__include
+DEPDIR
+OBJEXT
+EXEEXT
+ac_ct_CC
+CPPFLAGS
+LDFLAGS
+CFLAGS
+CC
+am__untar
+am__tar
+AMTAR
+am__leading_dot
+SET_MAKE
+AWK
+mkdir_p
+MKDIR_P
+INSTALL_STRIP_PROGRAM
+STRIP
+install_sh
+MAKEINFO
+AUTOHEADER
+AUTOMAKE
+AUTOCONF
+ACLOCAL
+VERSION
+PACKAGE
+CYGPATH_W
+am__isrc
+INSTALL_DATA
+INSTALL_SCRIPT
+INSTALL_PROGRAM
+target_alias
+host_alias
+build_alias
+LIBS
+ECHO_T
+ECHO_N
+ECHO_C
+DEFS
+mandir
+localedir
+libdir
+psdir
+pdfdir
+dvidir
+htmldir
+infodir
+docdir
+oldincludedir
+includedir
+localstatedir
+sharedstatedir
+sysconfdir
+datadir
+datarootdir
+libexecdir
+sbindir
+bindir
+program_transform_name
+prefix
+exec_prefix
+PACKAGE_URL
+PACKAGE_BUGREPORT
+PACKAGE_STRING
+PACKAGE_VERSION
+PACKAGE_TARNAME
+PACKAGE_NAME
+PATH_SEPARATOR
+SHELL'
+ac_subst_files=''
+ac_user_opts='
+enable_option_checking
+enable_dependency_tracking
+'
+ ac_precious_vars='build_alias
+host_alias
+target_alias
+CC
+CFLAGS
+LDFLAGS
+LIBS
+CPPFLAGS'
+
+
+# Initialize some variables set by options.
+ac_init_help=
+ac_init_version=false
+ac_unrecognized_opts=
+ac_unrecognized_sep=
+# The variables have the same names as the options, with
+# dashes changed to underlines.
+cache_file=/dev/null
+exec_prefix=NONE
+no_create=
+no_recursion=
+prefix=NONE
+program_prefix=NONE
+program_suffix=NONE
+program_transform_name=s,x,x,
+silent=
+site=
+srcdir=
+verbose=
+x_includes=NONE
+x_libraries=NONE
+
+# Installation directory options.
+# These are left unexpanded so users can "make install exec_prefix=/foo"
+# and all the variables that are supposed to be based on exec_prefix
+# by default will actually change.
+# Use braces instead of parens because sh, perl, etc. also accept them.
+# (The list follows the same order as the GNU Coding Standards.)
+bindir='${exec_prefix}/bin'
+sbindir='${exec_prefix}/sbin'
+libexecdir='${exec_prefix}/libexec'
+datarootdir='${prefix}/share'
+datadir='${datarootdir}'
+sysconfdir='${prefix}/etc'
+sharedstatedir='${prefix}/com'
+localstatedir='${prefix}/var'
+includedir='${prefix}/include'
+oldincludedir='/usr/include'
+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
+infodir='${datarootdir}/info'
+htmldir='${docdir}'
+dvidir='${docdir}'
+pdfdir='${docdir}'
+psdir='${docdir}'
+libdir='${exec_prefix}/lib'
+localedir='${datarootdir}/locale'
+mandir='${datarootdir}/man'
+
+ac_prev=
+ac_dashdash=
+for ac_option
+do
+ # If the previous option needs an argument, assign it.
+ if test -n "$ac_prev"; then
+ eval $ac_prev=\$ac_option
+ ac_prev=
+ continue
+ fi
+
+ case $ac_option in
+ *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+ *=) ac_optarg= ;;
+ *) ac_optarg=yes ;;
+ esac
+
+ # Accept the important Cygnus configure options, so we can diagnose typos.
+
+ case $ac_dashdash$ac_option in
+ --)
+ ac_dashdash=yes ;;
+
+ -bindir | --bindir | --bindi | --bind | --bin | --bi)
+ ac_prev=bindir ;;
+ -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
+ bindir=$ac_optarg ;;
+
+ -build | --build | --buil | --bui | --bu)
+ ac_prev=build_alias ;;
+ -build=* | --build=* | --buil=* | --bui=* | --bu=*)
+ build_alias=$ac_optarg ;;
+
+ -cache-file | --cache-file | --cache-fil | --cache-fi \
+ | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
+ ac_prev=cache_file ;;
+ -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
+ | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)
+ cache_file=$ac_optarg ;;
+
+ --config-cache | -C)
+ cache_file=config.cache ;;
+
+ -datadir | --datadir | --datadi | --datad)
+ ac_prev=datadir ;;
+ -datadir=* | --datadir=* | --datadi=* | --datad=*)
+ datadir=$ac_optarg ;;
+
+ -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \
+ | --dataroo | --dataro | --datar)
+ ac_prev=datarootdir ;;
+ -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \
+ | --dataroot=* | --dataroo=* | --dataro=* | --datar=*)
+ datarootdir=$ac_optarg ;;
+
+ -disable-* | --disable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid feature name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=no ;;
+
+ -docdir | --docdir | --docdi | --doc | --do)
+ ac_prev=docdir ;;
+ -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*)
+ docdir=$ac_optarg ;;
+
+ -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv)
+ ac_prev=dvidir ;;
+ -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*)
+ dvidir=$ac_optarg ;;
+
+ -enable-* | --enable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid feature name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=\$ac_optarg ;;
+
+ -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
+ | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
+ | --exec | --exe | --ex)
+ ac_prev=exec_prefix ;;
+ -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \
+ | --exec-pref=* | --exec-pre=* | --exec-pr=* | --exec-p=* | --exec-=* \
+ | --exec=* | --exe=* | --ex=*)
+ exec_prefix=$ac_optarg ;;
+
+ -gas | --gas | --ga | --g)
+ # Obsolete; use --with-gas.
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+To assign environment variables (e.g., CC, CFLAGS...), specify them as
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+_ACEOF
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+Optional Features:
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+if $ac_init_version; then
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+OpenBUGS configure 0.1
+generated by GNU Autoconf 2.68
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This configure script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it.
+_ACEOF
+ exit
+fi
+
+## ------------------------ ##
+## Autoconf initialization. ##
+## ------------------------ ##
+
+# ac_fn_c_try_compile LINENO
+# --------------------------
+# Try to compile conftest.$ac_ext, and return whether this succeeded.
+ac_fn_c_try_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext
+ if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_compile
+cat >config.log <<_ACEOF
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by OpenBUGS $as_me 0.1, which was
+generated by GNU Autoconf 2.68. Invocation command line was
+
+ $ $0 $@
+
+_ACEOF
+exec 5>>config.log
+{
+cat <<_ASUNAME
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown`
+
+/bin/arch = `(/bin/arch) 2>/dev/null || echo unknown`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
+/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown`
+/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown`
+/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown`
+
+_ASUNAME
+
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ $as_echo "PATH: $as_dir"
+ done
+IFS=$as_save_IFS
+
+} >&5
+
+cat >&5 <<_ACEOF
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+_ACEOF
+
+
+# Keep a trace of the command line.
+# Strip out --no-create and --no-recursion so they do not pile up.
+# Strip out --silent because we don't want to record it for future runs.
+# Also quote any args containing shell meta-characters.
+# Make two passes to allow for proper duplicate-argument suppression.
+ac_configure_args=
+ac_configure_args0=
+ac_configure_args1=
+ac_must_keep_next=false
+for ac_pass in 1 2
+do
+ for ac_arg
+ do
+ case $ac_arg in
+ -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ continue ;;
+ *\'*)
+ ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ case $ac_pass in
+ 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;;
+ 2)
+ as_fn_append ac_configure_args1 " '$ac_arg'"
+ if test $ac_must_keep_next = true; then
+ ac_must_keep_next=false # Got value, back to normal.
+ else
+ case $ac_arg in
+ *=* | --config-cache | -C | -disable-* | --disable-* \
+ | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \
+ | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \
+ | -with-* | --with-* | -without-* | --without-* | --x)
+ case "$ac_configure_args0 " in
+ "$ac_configure_args1"*" '$ac_arg' "* ) continue ;;
+ esac
+ ;;
+ -* ) ac_must_keep_next=true ;;
+ esac
+ fi
+ as_fn_append ac_configure_args " '$ac_arg'"
+ ;;
+ esac
+ done
+done
+{ ac_configure_args0=; unset ac_configure_args0;}
+{ ac_configure_args1=; unset ac_configure_args1;}
+
+# When interrupted or exit'd, cleanup temporary files, and complete
+# config.log. We remove comments because anyway the quotes in there
+# would cause problems or look ugly.
+# WARNING: Use '\'' to represent an apostrophe within the trap.
+# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug.
+trap 'exit_status=$?
+ # Save into config.log some information that might help in debugging.
+ {
+ echo
+
+ $as_echo "## ---------------- ##
+## Cache variables. ##
+## ---------------- ##"
+ echo
+ # The following way of writing the cache mishandles newlines in values,
+(
+ for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+ (set) 2>&1 |
+ case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ sed -n \
+ "s/'\''/'\''\\\\'\'''\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p"
+ ;; #(
+ *)
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+)
+ echo
+
+ $as_echo "## ----------------- ##
+## Output variables. ##
+## ----------------- ##"
+ echo
+ for ac_var in $ac_subst_vars
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+
+ if test -n "$ac_subst_files"; then
+ $as_echo "## ------------------- ##
+## File substitutions. ##
+## ------------------- ##"
+ echo
+ for ac_var in $ac_subst_files
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+ fi
+
+ if test -s confdefs.h; then
+ $as_echo "## ----------- ##
+## confdefs.h. ##
+## ----------- ##"
+ echo
+ cat confdefs.h
+ echo
+ fi
+ test "$ac_signal" != 0 &&
+ $as_echo "$as_me: caught signal $ac_signal"
+ $as_echo "$as_me: exit $exit_status"
+ } >&5
+ rm -f core *.core core.conftest.* &&
+ rm -f -r conftest* confdefs* conf$$* $ac_clean_files &&
+ exit $exit_status
+' 0
+for ac_signal in 1 2 13 15; do
+ trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal
+done
+ac_signal=0
+
+# confdefs.h avoids OS command line length limits that DEFS can exceed.
+rm -f -r conftest* confdefs.h
+
+$as_echo "/* confdefs.h */" > confdefs.h
+
+# Predefined preprocessor variables.
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_NAME "$PACKAGE_NAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_TARNAME "$PACKAGE_TARNAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_VERSION "$PACKAGE_VERSION"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_STRING "$PACKAGE_STRING"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_URL "$PACKAGE_URL"
+_ACEOF
+
+
+# Let the site file select an alternate cache file if it wants to.
+# Prefer an explicitly selected file to automatically selected ones.
+ac_site_file1=NONE
+ac_site_file2=NONE
+if test -n "$CONFIG_SITE"; then
+ # We do not want a PATH search for config.site.
+ case $CONFIG_SITE in #((
+ -*) ac_site_file1=./$CONFIG_SITE;;
+ */*) ac_site_file1=$CONFIG_SITE;;
+ *) ac_site_file1=./$CONFIG_SITE;;
+ esac
+elif test "x$prefix" != xNONE; then
+ ac_site_file1=$prefix/share/config.site
+ ac_site_file2=$prefix/etc/config.site
+else
+ ac_site_file1=$ac_default_prefix/share/config.site
+ ac_site_file2=$ac_default_prefix/etc/config.site
+fi
+for ac_site_file in "$ac_site_file1" "$ac_site_file2"
+do
+ test "x$ac_site_file" = xNONE && continue
+ if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
+$as_echo "$as_me: loading site script $ac_site_file" >&6;}
+ sed 's/^/| /' "$ac_site_file" >&5
+ . "$ac_site_file" \
+ || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "failed to load site script $ac_site_file
+See \`config.log' for more details" "$LINENO" 5; }
+ fi
+done
+
+if test -r "$cache_file"; then
+ # Some versions of bash will fail to source /dev/null (special files
+ # actually), so we avoid doing that. DJGPP emulates it as a regular file.
+ if test /dev/null != "$cache_file" && test -f "$cache_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
+$as_echo "$as_me: loading cache $cache_file" >&6;}
+ case $cache_file in
+ [\\/]* | ?:[\\/]* ) . "$cache_file";;
+ *) . "./$cache_file";;
+ esac
+ fi
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
+$as_echo "$as_me: creating cache $cache_file" >&6;}
+ >$cache_file
+fi
+
+# Check that the precious variables saved in the cache have kept the same
+# value.
+ac_cache_corrupted=false
+for ac_var in $ac_precious_vars; do
+ eval ac_old_set=\$ac_cv_env_${ac_var}_set
+ eval ac_new_set=\$ac_env_${ac_var}_set
+ eval ac_old_val=\$ac_cv_env_${ac_var}_value
+ eval ac_new_val=\$ac_env_${ac_var}_value
+ case $ac_old_set,$ac_new_set in
+ set,)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,set)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,);;
+ *)
+ if test "x$ac_old_val" != "x$ac_new_val"; then
+ # differences in whitespace do not lead to failure.
+ ac_old_val_w=`echo x $ac_old_val`
+ ac_new_val_w=`echo x $ac_new_val`
+ if test "$ac_old_val_w" != "$ac_new_val_w"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5
+$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
+ ac_cache_corrupted=:
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
+$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;}
+ eval $ac_var=\$ac_old_val
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5
+$as_echo "$as_me: former value: \`$ac_old_val'" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5
+$as_echo "$as_me: current value: \`$ac_new_val'" >&2;}
+ fi;;
+ esac
+ # Pass precious variables to config.status.
+ if test "$ac_new_set" = set; then
+ case $ac_new_val in
+ *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
+ *) ac_arg=$ac_var=$ac_new_val ;;
+ esac
+ case " $ac_configure_args " in
+ *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
+ *) as_fn_append ac_configure_args " '$ac_arg'" ;;
+ esac
+ fi
+done
+if $ac_cache_corrupted; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
+$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
+ as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+fi
+## -------------------- ##
+## Main body of script. ##
+## -------------------- ##
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+
+
+am__api_version='1.11'
+
+ac_aux_dir=
+for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
+ if test -f "$ac_dir/install-sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install-sh -c"
+ break
+ elif test -f "$ac_dir/install.sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install.sh -c"
+ break
+ elif test -f "$ac_dir/shtool"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/shtool install -c"
+ break
+ fi
+done
+if test -z "$ac_aux_dir"; then
+ as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5
+fi
+
+# These three variables are undocumented and unsupported,
+# and are intended to be withdrawn in a future Autoconf release.
+# They can cause serious problems if a builder's source tree is in a directory
+# whose full name contains unusual characters.
+ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var.
+ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
+ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
+
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+# Reject install programs that cannot install multiple files.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
+$as_echo_n "checking for a BSD-compatible install... " >&6; }
+if test -z "$INSTALL"; then
+if ${ac_cv_path_install+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in #((
+ ./ | .// | /[cC]/* | \
+ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+ ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \
+ /usr/ucb/* ) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+ if test $ac_prog = install &&
+ grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ elif test $ac_prog = install &&
+ grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # program-specific install script used by HP pwplus--don't use.
+ :
+ else
+ rm -rf conftest.one conftest.two conftest.dir
+ echo one > conftest.one
+ echo two > conftest.two
+ mkdir conftest.dir
+ if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
+ test -s conftest.one && test -s conftest.two &&
+ test -s conftest.dir/conftest.one &&
+ test -s conftest.dir/conftest.two
+ then
+ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+ break 3
+ fi
+ fi
+ fi
+ done
+ done
+ ;;
+esac
+
+ done
+IFS=$as_save_IFS
+
+rm -rf conftest.one conftest.two conftest.dir
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL=$ac_cv_path_install
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ INSTALL=$ac_install_sh
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5
+$as_echo "$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
+$as_echo_n "checking whether build environment is sane... " >&6; }
+# Just in case
+sleep 1
+echo timestamp > conftest.file
+# Reject unsafe characters in $srcdir or the absolute working directory
+# name. Accept space and tab only in the latter.
+am_lf='
+'
+case `pwd` in
+ *[\\\"\#\$\&\'\`$am_lf]*)
+ as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5;;
+esac
+case $srcdir in
+ *[\\\"\#\$\&\'\`$am_lf\ \ ]*)
+ as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;;
+esac
+
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments. Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+ if test "$*" = "X"; then
+ # -L didn't work.
+ set X `ls -t "$srcdir/configure" conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$*" != "X $srcdir/configure conftest.file" \
+ && test "$*" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
+alias in your environment" "$LINENO" 5
+ fi
+
+ test "$2" = conftest.file
+ )
+then
+ # Ok.
+ :
+else
+ as_fn_error $? "newly created file is older than distributed files!
+Check your system clock" "$LINENO" 5
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+test "$program_prefix" != NONE &&
+ program_transform_name="s&^&$program_prefix&;$program_transform_name"
+# Use a double $ so make ignores it.
+test "$program_suffix" != NONE &&
+ program_transform_name="s&\$&$program_suffix&;$program_transform_name"
+# Double any \ or $.
+# By default was `s,x,x', remove it if useless.
+ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
+program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
+
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+
+if test x"${MISSING+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+ *)
+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
+ esac
+fi
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+ am_missing_run="$MISSING --run "
+else
+ am_missing_run=
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5
+$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
+fi
+
+if test x"${install_sh}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+if test "$cross_compiling" != no; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_STRIP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_STRIP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5
+$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
+if test -z "$MKDIR_P"; then
+ if ${ac_cv_path_mkdir+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in mkdir gmkdir; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
+ case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
+ 'mkdir (GNU coreutils) '* | \
+ 'mkdir (coreutils) '* | \
+ 'mkdir (fileutils) '4.1*)
+ ac_cv_path_mkdir=$as_dir/$ac_prog$ac_exec_ext
+ break 3;;
+ esac
+ done
+ done
+ done
+IFS=$as_save_IFS
+
+fi
+
+ test -d ./--version && rmdir ./--version
+ if test "${ac_cv_path_mkdir+set}" = set; then
+ MKDIR_P="$ac_cv_path_mkdir -p"
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for MKDIR_P within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ MKDIR_P="$ac_install_sh -d"
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
+$as_echo "$MKDIR_P" >&6; }
+
+mkdir_p="$MKDIR_P"
+case $mkdir_p in
+ [\\/$]* | ?:[\\/]*) ;;
+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
+esac
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_AWK+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AWK="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+$as_echo "$AWK" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$AWK" && break
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
+set x ${MAKE-make}
+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if eval \${ac_cv_prog_make_${ac_make}_set+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+ @echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+ *@@@%%%=?*=@@@%%%*)
+ eval ac_cv_prog_make_${ac_make}_set=yes;;
+ *)
+ eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ SET_MAKE=
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+ am__leading_dot=.
+else
+ am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+
+if test "`cd $srcdir && pwd`" != "`pwd`"; then
+ # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
+ # is not polluted with repeated "-I."
+ am__isrc=' -I$(srcdir)'
+ # test to see if srcdir already configured
+ if test -f $srcdir/config.status; then
+ as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
+ fi
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+ if (cygpath --version) >/dev/null 2>/dev/null; then
+ CYGPATH_W='cygpath -w'
+ else
+ CYGPATH_W=echo
+ fi
+fi
+
+
+# Define the identity of the package.
+ PACKAGE='openbugs'
+ VERSION='0.1'
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE "$PACKAGE"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define VERSION "$VERSION"
+_ACEOF
+
+# Some tools Automake needs.
+
+ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
+
+
+AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}
+
+
+AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
+
+
+AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
+
+
+MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
+
+# We need awk for the "check" target. The system "awk" is bad on
+# some platforms.
+# Always define AMTAR for backward compatibility. Yes, it's still used
+# in the wild :-( We should find a proper way to deprecate it ...
+AMTAR='$${TAR-tar}'
+
+am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
+
+
+
+
+
+
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_CC"; then
+ ac_ct_CC=$CC
+ # Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+else
+ CC="$ac_cv_prog_CC"
+fi
+
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ fi
+fi
+if test -z "$CC"; then
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+ ac_prog_rejected=yes
+ continue
+ fi
+ ac_cv_prog_CC="cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+if test $ac_prog_rejected = yes; then
+ # We found a bogon in the path, so make sure we never use it.
+ set dummy $ac_cv_prog_CC
+ shift
+ if test $# != 0; then
+ # We chose a different compiler from the bogus one.
+ # However, it has the same basename, so the bogon will be chosen
+ # first if we set CC to just the basename; use the full file name.
+ shift
+ ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+ fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in cl.exe
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CC" && break
+ done
+fi
+if test -z "$CC"; then
+ ac_ct_CC=$CC
+ for ac_prog in cl.exe
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CC" && break
+done
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+fi
+
+fi
+
+
+test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "no acceptable C compiler found in \$PATH
+See \`config.log' for more details" "$LINENO" 5; }
+
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
+# Try to create an executable without -o first, disregard a.out.
+# It will help us diagnose broken compilers, and finding out an intuition
+# of exeext.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5
+$as_echo_n "checking whether the C compiler works... " >&6; }
+ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
+
+# The possible output files:
+ac_files="a.out conftest.exe conftest a.exe a_out.exe b.out conftest.*"
+
+ac_rmfiles=
+for ac_file in $ac_files
+do
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ * ) ac_rmfiles="$ac_rmfiles $ac_file";;
+ esac
+done
+rm -f $ac_rmfiles
+
+if { { ac_try="$ac_link_default"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link_default") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
+# So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
+# in a Makefile. We should not override ac_cv_exeext if it was cached,
+# so that the user can short-circuit this test for compilers unknown to
+# Autoconf.
+for ac_file in $ac_files ''
+do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj )
+ ;;
+ [ab].out )
+ # We found the default executable, but exeext='' is most
+ # certainly right.
+ break;;
+ *.* )
+ if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
+ then :; else
+ ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ fi
+ # We set ac_cv_exeext here because the later test for it is not
+ # safe: cross compilers may not add the suffix if given an `-o'
+ # argument, so we may need to know it at that point already.
+ # Even if this section looks crufty: it has the advantage of
+ # actually working.
+ break;;
+ * )
+ break;;
+ esac
+done
+test "$ac_cv_exeext" = no && ac_cv_exeext=
+
+else
+ ac_file=''
+fi
+if test -z "$ac_file"; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error 77 "C compiler cannot create executables
+See \`config.log' for more details" "$LINENO" 5; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5
+$as_echo_n "checking for C compiler default output file name... " >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
+$as_echo "$ac_file" >&6; }
+ac_exeext=$ac_cv_exeext
+
+rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
+$as_echo_n "checking for suffix of executables... " >&6; }
+if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # If both `conftest.exe' and `conftest' are `present' (well, observable)
+# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will
+# work properly (i.e., refer to `conftest.exe'), while it won't with
+# `rm'.
+for ac_file in conftest.exe conftest conftest.*; do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ break;;
+ * ) break;;
+ esac
+done
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details" "$LINENO" 5; }
+fi
+rm -f conftest conftest$ac_cv_exeext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
+$as_echo "$ac_cv_exeext" >&6; }
+
+rm -f conftest.$ac_ext
+EXEEXT=$ac_cv_exeext
+ac_exeext=$EXEEXT
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdio.h>
+int
+main ()
+{
+FILE *f = fopen ("conftest.out", "w");
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files="$ac_clean_files conftest.out"
+# Check that the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+if test "$cross_compiling" != yes; then
+ { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ if { ac_try='./conftest$ac_cv_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then
+ cross_compiling=no
+ else
+ if test "$cross_compiling" = maybe; then
+ cross_compiling=yes
+ else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details" "$LINENO" 5; }
+ fi
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
+$as_echo "$cross_compiling" >&6; }
+
+rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
+$as_echo_n "checking for suffix of object files... " >&6; }
+if ${ac_cv_objext+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.o conftest.obj
+if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ for ac_file in conftest.o conftest.obj conftest.*; do
+ test -f "$ac_file" || continue;
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
+ *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
+ break;;
+ esac
+done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of object files: cannot compile
+See \`config.log' for more details" "$LINENO" 5; }
+fi
+rm -f conftest.$ac_cv_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5
+$as_echo "$ac_cv_objext" >&6; }
+OBJEXT=$ac_cv_objext
+ac_objext=$OBJEXT
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
+$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
+if ${ac_cv_c_compiler_gnu+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
+$as_echo "$ac_cv_c_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GCC=yes
+else
+ GCC=
+fi
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
+$as_echo_n "checking whether $CC accepts -g... " >&6; }
+if ${ac_cv_prog_cc_g+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_c_werror_flag=$ac_c_werror_flag
+ ac_c_werror_flag=yes
+ ac_cv_prog_cc_g=no
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+else
+ CFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+else
+ ac_c_werror_flag=$ac_save_c_werror_flag
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_c_werror_flag=$ac_save_c_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
+$as_echo "$ac_cv_prog_cc_g" >&6; }
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
+$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
+if ${ac_cv_prog_cc_c89+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_prog_cc_c89=no
+ac_save_CC=$CC
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdarg.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+ char **p;
+ int i;
+{
+ return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+ char *s;
+ va_list v;
+ va_start (v,p);
+ s = g (p, va_arg (v,int));
+ va_end (v);
+ return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
+ function prototypes and stuff, but not '\xHH' hex character constants.
+ These don't provoke an error unfortunately, instead are silently treated
+ as 'x'. The following induces an error, until -std is added to get
+ proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
+ array size at least. It's necessary to write '\x00'==0 to get something
+ that's true only with -std. */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
+ inside strings and character constants. */
+#define FOO(x) 'x'
+int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+ ;
+ return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+ CC="$ac_save_CC $ac_arg"
+ if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_c89=$ac_arg
+fi
+rm -f core conftest.err conftest.$ac_objext
+ test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+ x)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
+$as_echo "none needed" >&6; } ;;
+ xno)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
+$as_echo "unsupported" >&6; } ;;
+ *)
+ CC="$CC $ac_cv_prog_cc_c89"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+if test "x$ac_cv_prog_cc_c89" != xno; then :
+
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+DEPDIR="${am__leading_dot}deps"
+
+ac_config_commands="$ac_config_commands depfiles"
+
+
+am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+ @echo this is the am__doit target
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5
+$as_echo_n "checking for style of include used by $am_make... " >&6; }
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# Ignore all kinds of additional output from `make'.
+case `$am_make -s -f confmf 2> /dev/null` in #(
+*the\ am__doit\ target*)
+ am__include=include
+ am__quote=
+ _am_result=GNU
+ ;;
+esac
+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+ echo '.include "confinc"' > confmf
+ case `$am_make -s -f confmf 2> /dev/null` in #(
+ *the\ am__doit\ target*)
+ am__include=.include
+ am__quote="\""
+ _am_result=BSD
+ ;;
+ esac
+fi
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5
+$as_echo "$_am_result" >&6; }
+rm -f confinc confmf
+
+# Check whether --enable-dependency-tracking was given.
+if test "${enable_dependency_tracking+set}" = set; then :
+ enableval=$enable_dependency_tracking;
+fi
+
+if test "x$enable_dependency_tracking" != xno; then
+ am_depcomp="$ac_aux_dir/depcomp"
+ AMDEPBACKSLASH='\'
+ am__nodep='_no'
+fi
+ if test "x$enable_dependency_tracking" != xno; then
+ AMDEP_TRUE=
+ AMDEP_FALSE='#'
+else
+ AMDEP_TRUE='#'
+ AMDEP_FALSE=
+fi
+
+
+
+depcc="$CC" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if ${am_cv_CC_dependencies_compiler_type+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CC_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvc7 | msvc7msys | msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CC_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+ am__fastdepCC_TRUE=
+ am__fastdepCC_FALSE='#'
+else
+ am__fastdepCC_TRUE='#'
+ am__fastdepCC_FALSE=
+fi
+
+
+
+ac_config_files="$ac_config_files Makefile src/Makefile"
+
+
+cat >confcache <<\_ACEOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs, see configure's option --config-cache.
+# It is not useful on other systems. If it contains results you don't
+# want to keep, you may remove or edit it.
+#
+# config.status only pays attention to the cache file if you give it
+# the --recheck option to rerun configure.
+#
+# `ac_cv_env_foo' variables (set or unset) will be overridden when
+# loading this file, other *unset* `ac_cv_foo' will be assigned the
+# following values.
+
+_ACEOF
+
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, we kill variables containing newlines.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+(
+ for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+
+ (set) 2>&1 |
+ case $as_nl`(ac_space=' '; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ # `set' does not quote correctly, so add quotes: double-quote
+ # substitution turns \\\\ into \\, and sed turns \\ into \.
+ sed -n \
+ "s/'/'\\\\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
+ ;; #(
+ *)
+ # `set' quotes correctly as required by POSIX, so do not add quotes.
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+) |
+ sed '
+ /^ac_cv_env_/b end
+ t clear
+ :clear
+ s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
+ t end
+ s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
+ :end' >>confcache
+if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
+ if test -w "$cache_file"; then
+ if test "x$cache_file" != "x/dev/null"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
+$as_echo "$as_me: updating cache $cache_file" >&6;}
+ if test ! -f "$cache_file" || test -h "$cache_file"; then
+ cat confcache >"$cache_file"
+ else
+ case $cache_file in #(
+ */* | ?:*)
+ mv -f confcache "$cache_file"$$ &&
+ mv -f "$cache_file"$$ "$cache_file" ;; #(
+ *)
+ mv -f confcache "$cache_file" ;;
+ esac
+ fi
+ fi
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
+$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
+ fi
+fi
+rm -f confcache
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+# Transform confdefs.h into DEFS.
+# Protect against shell expansion while executing Makefile rules.
+# Protect against Makefile macro expansion.
+#
+# If the first sed substitution is executed (which looks for macros that
+# take arguments), then branch to the quote section. Otherwise,
+# look for a macro that doesn't take arguments.
+ac_script='
+:mline
+/\\$/{
+ N
+ s,\\\n,,
+ b mline
+}
+t clear
+:clear
+s/^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*([^)]*)\)[ ]*\(.*\)/-D\1=\2/g
+t quote
+s/^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)/-D\1=\2/g
+t quote
+b any
+:quote
+s/[ `~#$^&*(){}\\|;'\''"<>?]/\\&/g
+s/\[/\\&/g
+s/\]/\\&/g
+s/\$/$$/g
+H
+:any
+${
+ g
+ s/^\n//
+ s/\n/ /g
+ p
+}
+'
+DEFS=`sed -n "$ac_script" confdefs.h`
+
+
+ac_libobjs=
+ac_ltlibobjs=
+U=
+for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
+ # 1. Remove the extension, and $U if already installed.
+ ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
+ ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
+ # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
+ # will be set to the directory where LIBOBJS objects are built.
+ as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+ as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
+done
+LIBOBJS=$ac_libobjs
+
+LTLIBOBJS=$ac_ltlibobjs
+
+
+ if test -n "$EXEEXT"; then
+ am__EXEEXT_TRUE=
+ am__EXEEXT_FALSE='#'
+else
+ am__EXEEXT_TRUE='#'
+ am__EXEEXT_FALSE=
+fi
+
+if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
+ as_fn_error $? "conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+
+: "${CONFIG_STATUS=./config.status}"
+ac_write_fail=0
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files $CONFIG_STATUS"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
+$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
+as_write_fail=0
+cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+
+SHELL=\${CONFIG_SHELL-$SHELL}
+export SHELL
+_ASEOF
+cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in #(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+as_myself=
+case $0 in #((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in #(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in #(
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+exec 6>&1
+## ----------------------------------- ##
+## Main body of $CONFIG_STATUS script. ##
+## ----------------------------------- ##
+_ASEOF
+test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# Save the log message, to keep $0 and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling.
+ac_log="
+This file was extended by OpenBUGS $as_me 0.1, which was
+generated by GNU Autoconf 2.68. Invocation command line was
+
+ CONFIG_FILES = $CONFIG_FILES
+ CONFIG_HEADERS = $CONFIG_HEADERS
+ CONFIG_LINKS = $CONFIG_LINKS
+ CONFIG_COMMANDS = $CONFIG_COMMANDS
+ $ $0 $@
+
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
+"
+
+_ACEOF
+
+case $ac_config_files in *"
+"*) set x $ac_config_files; shift; ac_config_files=$*;;
+esac
+
+
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+# Files that config.status was made for.
+config_files="$ac_config_files"
+config_commands="$ac_config_commands"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ac_cs_usage="\
+\`$as_me' instantiates files and other configuration actions
+from templates according to the current configuration. Unless the files
+and actions are specified as TAGs, all are instantiated by default.
+
+Usage: $0 [OPTION]... [TAG]...
+
+ -h, --help print this help, then exit
+ -V, --version print version number and configuration settings, then exit
+ --config print configuration, then exit
+ -q, --quiet, --silent
+ do not print progress messages
+ -d, --debug don't remove temporary files
+ --recheck update $as_me by reconfiguring in the same conditions
+ --file=FILE[:TEMPLATE]
+ instantiate the configuration file FILE
+
+Configuration files:
+$config_files
+
+Configuration commands:
+$config_commands
+
+Report bugs to the package provider."
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
+ac_cs_version="\\
+OpenBUGS config.status 0.1
+configured by $0, generated by GNU Autoconf 2.68,
+ with options \\"\$ac_cs_config\\"
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+
+ac_pwd='$ac_pwd'
+srcdir='$srcdir'
+INSTALL='$INSTALL'
+MKDIR_P='$MKDIR_P'
+AWK='$AWK'
+test -n "\$AWK" || AWK=awk
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# The default lists apply if the user does not specify any file.
+ac_need_defaults=:
+while test $# != 0
+do
+ case $1 in
+ --*=?*)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
+ ac_shift=:
+ ;;
+ --*=)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=
+ ac_shift=:
+ ;;
+ *)
+ ac_option=$1
+ ac_optarg=$2
+ ac_shift=shift
+ ;;
+ esac
+
+ case $ac_option in
+ # Handling of the options.
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ ac_cs_recheck=: ;;
+ --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
+ $as_echo "$ac_cs_version"; exit ;;
+ --config | --confi | --conf | --con | --co | --c )
+ $as_echo "$ac_cs_config"; exit ;;
+ --debug | --debu | --deb | --de | --d | -d )
+ debug=: ;;
+ --file | --fil | --fi | --f )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ '') as_fn_error $? "missing file argument" ;;
+ esac
+ as_fn_append CONFIG_FILES " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --he | --h | --help | --hel | -h )
+ $as_echo "$ac_cs_usage"; exit ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil | --si | --s)
+ ac_cs_silent=: ;;
+
+ # This is an error.
+ -*) as_fn_error $? "unrecognized option: \`$1'
+Try \`$0 --help' for more information." ;;
+
+ *) as_fn_append ac_config_targets " $1"
+ ac_need_defaults=false ;;
+
+ esac
+ shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+ exec 6>/dev/null
+ ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+if \$ac_cs_recheck; then
+ set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+ shift
+ \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
+ CONFIG_SHELL='$SHELL'
+ export CONFIG_SHELL
+ exec "\$@"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+exec 5>>config.log
+{
+ echo
+ sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
+## Running $as_me. ##
+_ASBOX
+ $as_echo "$ac_log"
+} >&5
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+#
+# INIT-COMMANDS
+#
+AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+
+# Handling of arguments.
+for ac_config_target in $ac_config_targets
+do
+ case $ac_config_target in
+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+ "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+
+ *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
+ esac
+done
+
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used. Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+ test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+ test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
+fi
+
+# Have a temporary directory for convenience. Make it in the build tree
+# simply because there is no reason against having it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Hook for its removal unless debugging.
+# Note that there is a small window in which the directory will not be cleaned:
+# after its creation but before its name has been assigned to `$tmp'.
+$debug ||
+{
+ tmp= ac_tmp=
+ trap 'exit_status=$?
+ : "${ac_tmp:=$tmp}"
+ { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status
+' 0
+ trap 'as_fn_exit 1' 1 2 13 15
+}
+# Create a (secure) tmp directory for tmp files.
+
+{
+ tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
+ test -d "$tmp"
+} ||
+{
+ tmp=./conf$$-$RANDOM
+ (umask 077 && mkdir "$tmp")
+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
+ac_tmp=$tmp
+
+# Set up the scripts for CONFIG_FILES section.
+# No need to generate them if there are no CONFIG_FILES.
+# This happens for instance with `./config.status config.h'.
+if test -n "$CONFIG_FILES"; then
+
+
+ac_cr=`echo X | tr X '\015'`
+# On cygwin, bash can eat \r inside `` if the user requested igncr.
+# But we know of no other shell where ac_cr would be empty at this
+# point, so we can use a bashism as a fallback.
+if test "x$ac_cr" = x; then
+ eval ac_cr=\$\'\\r\'
+fi
+ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
+if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
+ ac_cs_awk_cr='\\r'
+else
+ ac_cs_awk_cr=$ac_cr
+fi
+
+echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
+_ACEOF
+
+
+{
+ echo "cat >conf$$subs.awk <<_ACEOF" &&
+ echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
+ echo "_ACEOF"
+} >conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
+ac_delim='%!_!# '
+for ac_last_try in false false false false false :; do
+ . ./conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+
+ ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
+ if test $ac_delim_n = $ac_delim_num; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+rm -f conf$$subs.sh
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK &&
+_ACEOF
+sed -n '
+h
+s/^/S["/; s/!.*/"]=/
+p
+g
+s/^[^!]*!//
+:repl
+t repl
+s/'"$ac_delim"'$//
+t delim
+:nl
+h
+s/\(.\{148\}\)..*/\1/
+t more1
+s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
+p
+n
+b repl
+:more1
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t nl
+:delim
+h
+s/\(.\{148\}\)..*/\1/
+t more2
+s/["\\]/\\&/g; s/^/"/; s/$/"/
+p
+b
+:more2
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t delim
+' <conf$$subs.awk | sed '
+/^[^""]/{
+ N
+ s/\n//
+}
+' >>$CONFIG_STATUS || ac_write_fail=1
+rm -f conf$$subs.awk
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+_ACAWK
+cat >>"\$ac_tmp/subs1.awk" <<_ACAWK &&
+ for (key in S) S_is_set[key] = 1
+ FS = ""
+
+}
+{
+ line = $ 0
+ nfields = split(line, field, "@")
+ substed = 0
+ len = length(field[1])
+ for (i = 2; i < nfields; i++) {
+ key = field[i]
+ keylen = length(key)
+ if (S_is_set[key]) {
+ value = S[key]
+ line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
+ len += length(value) + length(field[++i])
+ substed = 1
+ } else
+ len += 1 + keylen
+ }
+
+ print line
+}
+
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
+ sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
+else
+ cat
+fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \
+ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
+_ACEOF
+
+# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
+# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
+# trailing colons and then remove the whole line if VPATH becomes empty
+# (actually we leave an empty line to preserve line numbers).
+if test "x$srcdir" = x.; then
+ ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{
+h
+s///
+s/^/:/
+s/[ ]*$/:/
+s/:\$(srcdir):/:/g
+s/:\${srcdir}:/:/g
+s/:@srcdir@:/:/g
+s/^:*//
+s/:*$//
+x
+s/\(=[ ]*\).*/\1/
+G
+s/\n//
+s/^[^=]*=[ ]*$//
+}'
+fi
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+fi # test -n "$CONFIG_FILES"
+
+
+eval set X " :F $CONFIG_FILES :C $CONFIG_COMMANDS"
+shift
+for ac_tag
+do
+ case $ac_tag in
+ :[FHLC]) ac_mode=$ac_tag; continue;;
+ esac
+ case $ac_mode$ac_tag in
+ :[FHL]*:*);;
+ :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;;
+ :[FH]-) ac_tag=-:-;;
+ :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
+ esac
+ ac_save_IFS=$IFS
+ IFS=:
+ set x $ac_tag
+ IFS=$ac_save_IFS
+ shift
+ ac_file=$1
+ shift
+
+ case $ac_mode in
+ :L) ac_source=$1;;
+ :[FH])
+ ac_file_inputs=
+ for ac_f
+ do
+ case $ac_f in
+ -) ac_f="$ac_tmp/stdin";;
+ *) # Look for the file first in the build tree, then in the source tree
+ # (if the path is not absolute). The absolute path cannot be DOS-style,
+ # because $ac_f cannot contain `:'.
+ test -f "$ac_f" ||
+ case $ac_f in
+ [\\/$]*) false;;
+ *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
+ esac ||
+ as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;;
+ esac
+ case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
+ as_fn_append ac_file_inputs " '$ac_f'"
+ done
+
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ configure_input='Generated from '`
+ $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
+ `' by configure.'
+ if test x"$ac_file" != x-; then
+ configure_input="$ac_file. $configure_input"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
+$as_echo "$as_me: creating $ac_file" >&6;}
+ fi
+ # Neutralize special characters interpreted by sed in replacement strings.
+ case $configure_input in #(
+ *\&* | *\|* | *\\* )
+ ac_sed_conf_input=`$as_echo "$configure_input" |
+ sed 's/[\\\\&|]/\\\\&/g'`;; #(
+ *) ac_sed_conf_input=$configure_input;;
+ esac
+
+ case $ac_tag in
+ *:-:* | *:-) cat >"$ac_tmp/stdin" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
+ esac
+ ;;
+ esac
+
+ ac_dir=`$as_dirname -- "$ac_file" ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir="$ac_dir"; as_fn_mkdir_p
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+
+ case $ac_mode in
+ :F)
+ #
+ # CONFIG_FILE
+ #
+
+ case $INSTALL in
+ [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
+ *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
+ esac
+ ac_MKDIR_P=$MKDIR_P
+ case $MKDIR_P in
+ [\\/$]* | ?:[\\/]* ) ;;
+ */*) ac_MKDIR_P=$ac_top_build_prefix$MKDIR_P ;;
+ esac
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# If the template does not know about datarootdir, expand it.
+# FIXME: This hack should be removed a few years after 2.60.
+ac_datarootdir_hack=; ac_datarootdir_seen=
+ac_sed_dataroot='
+/datarootdir/ {
+ p
+ q
+}
+/@datadir@/p
+/@docdir@/p
+/@infodir@/p
+/@localedir@/p
+/@mandir@/p'
+case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
+*datarootdir*) ac_datarootdir_seen=yes;;
+*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ ac_datarootdir_hack='
+ s&@datadir@&$datadir&g
+ s&@docdir@&$docdir&g
+ s&@infodir@&$infodir&g
+ s&@localedir@&$localedir&g
+ s&@mandir@&$mandir&g
+ s&\\\${datarootdir}&$datarootdir&g' ;;
+esac
+_ACEOF
+
+# Neutralize VPATH when `$srcdir' = `.'.
+# Shell code in configure.ac might set extrasub.
+# FIXME: do we really want to maintain this feature?
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_sed_extra="$ac_vpsub
+$extrasub
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+:t
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+s|@configure_input@|$ac_sed_conf_input|;t t
+s&@top_builddir@&$ac_top_builddir_sub&;t t
+s&@top_build_prefix@&$ac_top_build_prefix&;t t
+s&@srcdir@&$ac_srcdir&;t t
+s&@abs_srcdir@&$ac_abs_srcdir&;t t
+s&@top_srcdir@&$ac_top_srcdir&;t t
+s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
+s&@builddir@&$ac_builddir&;t t
+s&@abs_builddir@&$ac_abs_builddir&;t t
+s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
+s&@INSTALL@&$ac_INSTALL&;t t
+s&@MKDIR_P@&$ac_MKDIR_P&;t t
+$ac_datarootdir_hack
+"
+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \
+ >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+
+test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
+ { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } &&
+ { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \
+ "$ac_tmp/out"`; test -z "$ac_out"; } &&
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&5
+$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&2;}
+
+ rm -f "$ac_tmp/stdin"
+ case $ac_file in
+ -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";;
+ *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";;
+ esac \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ ;;
+
+
+ :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
+$as_echo "$as_me: executing $ac_file commands" >&6;}
+ ;;
+ esac
+
+
+ case $ac_file$ac_mode in
+ "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # are listed without --file. Let's play safe and only enable the eval
+ # if we detect the quoting.
+ case $CONFIG_FILES in
+ *\'*) eval set x "$CONFIG_FILES" ;;
+ *) set x $CONFIG_FILES ;;
+ esac
+ shift
+ for mf
+ do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
+ # limit of 2048, but all sed's we know have understand at least 4000.
+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
+ dirpart=`$as_dirname -- "$mf" ||
+$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$mf" : 'X\(//\)[^/]' \| \
+ X"$mf" : 'X\(//\)$' \| \
+ X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$mf" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`$as_dirname -- "$file" ||
+$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$file" : 'X\(//\)[^/]' \| \
+ X"$file" : 'X\(//\)$' \| \
+ X"$file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir=$dirpart/$fdir; as_fn_mkdir_p
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+ done
+}
+ ;;
+
+ esac
+done # for ac_tag
+
+
+as_fn_exit 0
+_ACEOF
+ac_clean_files=$ac_clean_files_save
+
+test $ac_write_fail = 0 ||
+ as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
+
+
+# configure is writing to config.log, and then calls config.status.
+# config.status does its own redirection, appending to config.log.
+# Unfortunately, on DOS this fails, as config.log is still kept open
+# by configure, so config.status won't be able to write to it; its
+# output is simply discarded. So we exec the FD to /dev/null,
+# effectively closing config.log, so it can be properly (re)opened and
+# appended to by config.status. When coming back to configure, we
+# need to make the FD available again.
+if test "$no_create" != yes; then
+ ac_cs_success=:
+ ac_config_status_args=
+ test "$silent" = yes &&
+ ac_config_status_args="$ac_config_status_args --quiet"
+ exec 5>/dev/null
+ $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
+ exec 5>>config.log
+ # Use ||, not &&, to avoid exiting from the if with $? = 1, which
+ # would make configure fail if this is the last instruction.
+ $ac_cs_success || as_fn_exit 1
+fi
+if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
+$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
+fi
+
diff --git a/configure.ac b/configure.ac
new file mode 100644
index 0000000..3da9535
--- /dev/null
+++ b/configure.ac
@@ -0,0 +1,12 @@
+AC_INIT(OpenBUGS, 3.2.3)
+AC_CONFIG_SRCDIR([src/OpenBUGSCli.c])
+
+AM_INIT_AUTOMAKE
+
+AC_PREFIX_DEFAULT(/usr/local)
+
+AC_PROG_CC
+
+AC_CONFIG_FILES([Makefile src/Makefile])
+
+AC_OUTPUT
diff --git a/doc/Developer/BRugsH.html b/doc/Developer/BRugsH.html
new file mode 100755
index 0000000..c8b916c
--- /dev/null
+++ b/doc/Developer/BRugsH.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BRugsH</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">/*
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1"><img src="brugsh0.bmp" alt="[brugsh0]">
</font><font face="Courier New" color="#000100" size="6">OpenBUGS header file <br>
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Arial" color="#008040" size="3">GNU General Public Licence<br><br> Thanks to Nathan Coulter for help with writing this file<br> <br> An ascii version of this file is in Developer/OpenBUGS.h<br> <br>
</font><font face="Arial" color="#000100" size="3">*/<br><br>extern void CLI ();<br>extern void BugsCmd(char **command, int *len);<br>extern void CharArray (char **procedure, int *len, char **x, int *lenX, int *res);<br>extern void CmdInterpreter (char **command, int *len, int *res);<br>extern void Guard (char **procedure, int *len, int *x, int *res);<br>extern void Integer (char **procedure, int *len, int *x, int *res);<br>extern void IntegerArray (char **procedure, int *len, int *x, int [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Developer/BlueDiamonds.html b/doc/Developer/BlueDiamonds.html
new file mode 100755
index 0000000..e1576c2
--- /dev/null
+++ b/doc/Developer/BlueDiamonds.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BlueDiamonds</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="4"><strong><img src="bluediamonds0.bmp" alt="[bluediamonds0]">
</strong></font><font face="Courier New" color="#000100" size="6">Blue Diamonds
</font><font face="Arial" color="#000100" size="3"><br><br>I like blue diamonds, maybe you also like blue diamonds? Your version of OpenBUGS (WinBUGS to be more precise) can now have new improved blue diamonds. A modified version of the module DevDebug has been written. The Node Info tool will now give you blue diamonds so that you can explore Graph and Updater objects. The blue diamonds allow complex graphical model build by OpenBUGS to be explored in detail. Where possible hexidecimal n [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">r[i] ~ dbin(p[i],n[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logit(p[i]) <- alpha.star + beta * (x[i] - mean(x[]))<br>
</font><font face="Arial" color="#000100" size="3"><br>Happy clicking!
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Developer/CBugs.html b/doc/Developer/CBugs.html
new file mode 100755
index 0000000..e8356fd
--- /dev/null
+++ b/doc/Developer/CBugs.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>CBugs</title>
</head>
<body>
<p>
<font face="Arial" color="#008040" size="3">/*<img src="cbugs0.bmp" alt="[cbugs0]"> GNU General Public Licence<br><br> This small C program loads the LibOpenBUGS.so ELF shared library and calls the <br> CLI function. Save it as a .c file and then compile it on Linux using <br> <br> gcc -o bugs OpenBUGS.c -ldl <br> <br>   [...]
</font><font face="Arial" color="#000100" size="3">#include <dlfcn.h><br>#include <stdio.h><br>#include <string.h><br><br>int
</font><font face="Arial" color="#804000" size="3"><strong>main
</strong></font><font face="Arial" color="#000100" size="3">(int argc, char **argv)<br>{<br> void * handle;<br>void (*cli)(void);<br><br>handle = dlopen("./LibOpenBUGS.so", RTLD_LAZY);<br>if (!handle)<br>return 1;<br><br>* (void **) (&cli) = dlsym(handle, "CLI");<br>(*cli)();<br>dlclose(handle);<br><br>return 0;<br> <br>}<br><br><br>
</font><font face="Arial" color="#008040" size="3">/*<br><br> As an alternative to using dlopen to load the OpenBUGS library Nathan Coulter has <br> developed the following short C program. Compile it on Linux using <br> <br>
</font><font face="Arial" color="#008000" size="3">gcc -o bin/OpenBUGS -L ./lib -Wl,-rpath,\$ORIGIN/../lib src/OpenBUGSCli.c -l OpenBUGS
</font><font face="Arial" color="#008040" size="3"><br> <br>
</font><font face="Arial" color="#000000" size="3">#include <OpenBUGS.h><br><br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">int
</font><font face="Arial" color="#804000" size="3"><strong>main
</strong></font><font face="Arial" color="#000000" size="3"> ()<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">{<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> CLI();<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">}
</font><font face="Arial" color="#008040" size="3"><br><br>*/<br><br><br>/*<br><br> This is equivalent to the component Pascal program<br> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">MODULE BugsClassic;<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> IMPORT BugsBRugs;<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">BEGIN<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> BugsBRugs.CLI<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">END BugsClassic.<br>
</font><font face="Arial" color="#008040" size="3"> <br> (*
</font><font face="Arial" color="#000000" size="3"><img src="cbugs1.bmp" alt="[cbugs1]">DevLinker.Link dos classicbugs.exe := BugsClassic$ 1 Bugslogo.ico <img src="cbugs2.bmp" alt="[cbugs2]">
</font><font face="Arial" color="#008040" size="3">*)<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#008040" size="3">'/
</font><font face="Arial" color="#000100" size="3"><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Developer/Compiling.html b/doc/Developer/Compiling.html
new file mode 100755
index 0000000..dd64494
--- /dev/null
+++ b/doc/Developer/Compiling.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Compiling</title>
</head>
<body>
<p>
<font face="Arial" color="#0000FF" size="3"><a id="Compiling"><img src="compiling0.bmp" alt="[compiling0]">
</font><font face="Arial" color="#000000" size="4"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Compiling the Source Code
</font><font face="Arial" color="#0000FF" size="3"></a><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>To compile the complete Component Pascal source code open the
</font><font face="Arial" color="#0000FF" size="3"><a href="../Developer/Make.html">
</font><font face="Arial" color="#0000FF" size="3"><u>make file
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> and use the mouse to click into the round blob containing an ! mark. If the compiler detects an error in a module the compilation will stop at that module which will be opened in a window with the error marked and described. If the directory into which the compiler wishes to place a code or symbol file does not exist the user will be prompted to create the directory. Note that if you change the interface to a module your new module may n [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">There are also a few other modules in the OpenBUGS source code. These files need to the compiled when the executable version are linked (see below for details)<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Developer/Distributing.html b/doc/Developer/Distributing.html
new file mode 100755
index 0000000..c4a88e7
--- /dev/null
+++ b/doc/Developer/Distributing.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Distributing</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"><img src="distributing0.bmp" alt="[distributing0]">
</font><font face="Arial" color="#000100" size="6"><strong><a id="Distributing">
</strong></font><font face="Courier New" color="#000100" size="6">Distributing OpenBUGS
</font><font face="Arial" color="#0000FF" size="3"></a><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>To distribute OpenBUGS pick the "Copy OpenBUGS..." option from the developer menu. Type the name of the directory were you want to put OpenBUGS into the dialog box and click the button. All the compiled code, libraries, resource files and documentation needed for a fuctioning version of OpenBUGS will be copied (but not the BlackBox developement tools). The source code for OpenBUGS will also be copied plus the source code of [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Developer/Documenting.html b/doc/Developer/Documenting.html
new file mode 100755
index 0000000..f476ff7
--- /dev/null
+++ b/doc/Developer/Documenting.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Documenting</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="documenting0.bmp" alt="[documenting0]">
</font><font face="Courier New" color="#000100" size="6">Documenting the OpenBUGS API<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>A tool has been developed to produce documentation of the interface of each module in the OpenBUGS software. This documentation contains the needed mark up so that the documentation tools of BlackBox component builder work. The tool uses a modified version of the browser from BlackBox (module DevBrowser). The tools works by extracting tagged comments from the source code and displaying them in a relavent position in the documentation. [...]
</font><font face="Arial" color="#0000FF" size="3"><u>
</u></font><font face="Arial" color="#0000FF" size="3"><a href="../Bugs/Mod/Names.html">BugsNames</a>
</font><font face="Arial" color="#000100" size="3">. In the Text menu pick the Show Marks option to make the tag pairs visible. Holding the control key down and clicking into one of the circle marks will show the tag pair in text form. The tag can then be closed again by highlighting the text between the openening < and the final > in the closing <> and then picking Create Target from the Tools menu.<br><br>A dialog box for the documentation tool is under DevInfo. Documen [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Developer/Guestbook.html b/doc/Developer/Guestbook.html
new file mode 100755
index 0000000..61a0b2a
--- /dev/null
+++ b/doc/Developer/Guestbook.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Guestbook</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="5"><strong>OpenBUGS Developer Guestbook<br>
</strong></font><font face="Arial" color="#000100" size="3">Please feel free to sign-in below...<br><br>Dave Lunn<br>Steve Miller<br><br><br><br><br><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Developer/Initializing.html b/doc/Developer/Initializing.html
new file mode 100755
index 0000000..521f24a
--- /dev/null
+++ b/doc/Developer/Initializing.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Initializing</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"><img src="initializing0.bmp" alt="[initializing0]">
</font><font face="Arial" color="#0000FF" size="3"><a id="Inits">
</font><font face="Courier New" color="#000100" size="6">Initializing OpenBUGS
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>Before the OpenBUGS software runs it needs to be initialized.
</font><font face="Arial" color="#000100" size="3">The code to initialize OpenBUGS is in module Startup in file Bugs/Startup.odc in the Setup procedure. Each subsystem, Xxx, that needs initializing contains a XxxResources module which contains an exported initialization procedure Load to load resources. Meta programming is used to search for modules of with name XxxResources and load them if not already loaded, their Load procedures are then called. <br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Developer/LibOpenBUGS.html b/doc/Developer/LibOpenBUGS.html
new file mode 100755
index 0000000..cdc9538
--- /dev/null
+++ b/doc/Developer/LibOpenBUGS.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LibOpenBUGS</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="libopenbugs0.bmp" alt="[libopenbugs0]">
</font><font face="Courier New" color="#000100" size="6">The OpenBUGS library
</font><font face="Arial" color="#000100" size="6"><strong><sup><br>
</sup></strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><strong><sup><br>
</sup></strong></font><font face="Arial" color="#000100" size="3"><sup>The BRugs library provides an interface to some features of the OpenBUGS software via a C friendly set of procedures. The signatures of these procedures were chosen to make interfacing to the R/S-Plus statistical packages easy.<br><br>The BRugs library has the same interface as the Component Pascal module BugsC:<br><br>
</sup></font><font face="Arial" color="#000100" size="2"> DEFINITION BugsC (* nonportable (i386) *);<br><br> PROCEDURE [ccall] BugsCmd (VAR command: POINTER TO ARRAY [untagged] OF SHORTCHAR; <br> VAR len: INTEGER);<br> <br> PROCEDURE [ccall] CLI;<br> <br>   [...]
</font><font face="Arial" color="#000100" size="3"><br><br>In the C language this reads<br><br>
</font><font face="Arial" color="#000100" size="2"> void BugsCmd(char **command, int *len)<br> <br> void CLI ()<br> <br> void CharArray (char **procedure, int *len, char **x, int *lenX, int *res)<br> <br> void CmdInterpreter (char **command, int *len, int *res)<br> <br> void Guard (char **procedure, int *len, int *x, int *res)<br> &n [...]
</font><font face="Arial" color="#000100" size="3"> <br>The first two procedures in the library provide an interface to the BUGS scripting language and the command line interpreter version of OpenBUGS. BugsCmd takes one string argument 'command' and executes this command if it is a valid command in the BUGS scripting language. The CLI procedure sets up the command line interface and will terminate when 'modelQuit()' is typed at the command prompt. The first time CLI is ca [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">"modelCheck" <-<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">function(fileName)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Check that OpenBUGS model is syntactically correct<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">path <- dirname(fileName)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">path <- if(path == ".") getwd() else path<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">fileName <- file.path(path, basename(fileName))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">if(!file.exists(fileName))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">stop("File ", fileName, " does not exist")<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">if(file.info(fileName)$isdir) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">stop(fileName, " is a directory, but a file is required")<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">command <- paste("BugsEmbed.SetFilePath(", sQuote(fileName), <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">");BugsEmbed.ParseGuard;BugsEmbed.Parse", sep = "")<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">if (!is.R()) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">command <- gsub ("\\\\", "/", command)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">command <- gsub ("//", "/", command)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">.C("CmdInterpreter", command, nchar(command), integer(1), PACKAGE = "BRugs")<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">if(getOption("BRugsVerbose")) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">buffer()<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br> <br>
</font><font face="Arial" color="#000100" size="3">and
</font><font face="Arial" color="#000100" size="2"> <br><br> "currentValues" <- <br> function(nodeLabel)<br> # Get current value of node<br> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> nodeLabel <- as.character(nodeLabel)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> command <- "BugsRobjects.SetVariable"<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> len <- nchar(command)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> .C("CharArray", command, as.integer(len), nodeLabel, nchar(nodeLabel), integer(1), PACKAGE="BRugs")<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> command <- "BugsRobjects.GetSize"<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> nodeSize <- .C("Integer", command, nchar(command), integer(1), integer(1), PACKAGE="BRugs")[[3]]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> if(nodeSize == -1) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> stop(nodeLabel, " is not a node in BUGS model")<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> command <- "BugsRobjects.GetValues"<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> .C("RealArray", command, nchar(command), as.real(rep(NA, nodeSize)), <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> as.integer(nodeSize), integer(1), NAOK = TRUE, PACKAGE="BRugs")[[3]]<br> }<br><br><br>
</font><font face="Arial" color="#000100" size="3">Note in the second R function, the allocation of the array variable which will contain the current values of the node is done in R.
</font>
</p>
</body>
</html>
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diff --git a/doc/Developer/Linking.html b/doc/Developer/Linking.html
new file mode 100755
index 0000000..d5a0b6d
--- /dev/null
+++ b/doc/Developer/Linking.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Linking</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"><img src="linking0.bmp" alt="[linking0]">
</font><font face="Arial" color="#0000FF" size="3"><a id="Linking">
</font><font face="Arial" color="#000000" size="4"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Executable versions and<br> linking
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">The OpenBUGS software family is unusual in consisting of a large number of unlinked modules in a binary format .These modules can not be directly accessed by the operating system. A linker tool is used to link a number of binary modules into either an executable or a library. The BlackBox developement tools contain a special module the StdLoader which is able to load and link new modules into a running OpenBUGS application. There are two [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">There are various ways of running the OpenBUGS software on computers with the Microsoft Windows operating system. OpenBUGS.exe is small Microsoft Windows program which loads code files (ocf) as needed. The classicbugs.exe program has a similar interface to the old "ClassicBUGS" software. A shortcut BackBUGS runs OpenBUGS with the file name specified on the command line, after the key word /PAR, used as a source of commands in a [...]
</font><font face="Arial" color="#000100" size="3">cedures exported by the brugs library are specified in the module BugsBRugs
</font><font face="Arial" color="#000000" size="3">. In particular the CLI procedure sets up a simple command line interpreter -- the ClassicBUGS interface. It is also possible to use the dynamic link library from within a general C program (see
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Developer/BRugsH.html">BRugs header file</a>
</font><font face="Arial" color="#000000" size="3"> for details). <br><br>In general the ocf files are not operating system dependent. In the make file those modules in black should be usable from both Windows and Linux, whereas the modules in red are only used under Windows. With just a few changes the modules that are linked to form the Windows dynamic link library can also be linked to produce a shared object file for Linux. <br><br>The R functions for interfacing to the dynamic link l [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>To make the executable versions of the OpenBUGS software a linker tool is used to pack several code (ocf) files into one exe or dynamic link library (shared object file on Linux). The linker is given a list of module names (in the form subsystem prefix followed by a file name). The linker searches for the ocf file in the code subdirectory of the subsystem with the appropiate file name. Note that this ocf might correspond to a module w [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="5"><strong>How to link OpenBUGS
</strong></font><font face="Arial" color="#000100" size="3"><br><br>To create the OpenBUGS.exe file click in the round .blob containing an ! mark with the mouse<br><br>
</font><font face="Arial" color="#000000" size="3"><img src="linking1.bmp" alt="[linking1]">DevLinker.Link
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3">OpenBUGS.exe := Kernel$ + Files HostFiles HostPackedFiles StdLoader<br>1 Bugslogo.ico 2 Doclogo.ico 3 SFLogo.ico 4 CFLogo.ico 5 DtyLogo.ico<br>6 folderimg.ico 7 openimg.ico 8 leafimg.ico<br>1 Move.cur 2 Copy.cur 3 Link.cur 4 Pick.cur 5 Stop.cur 6 Hand.cur 7 Table.cur <img src="linking2.bmp" alt="[linking2]"><br><br>Bind licence file, menu files and about box into executable.<br><img src="linking3.bmp" alt="[linking3]"> DevPacker.PackThis [...]
</font><font face="Arial" color="#FF0000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3">To make a fully linked version of the dynamic link library for Windows click in the round blob below. To make a library that does not use the taucs sparse matrix code remove the module MathTaucsImp from the list of linked modules.<br><br><img src="linking5.bmp" alt="[linking5]">DevLinker.LinkDll<br>libOpenBUGS.dll := Kernel$+ Files HostFiles
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="3">Meta Console Math Strings Dialog Stores<br>Services<br><br>WinConsole BugsInterpreter<br><br>BugsMappers BugsStrings BugsFiles BugsStdInterpreter<br>BugsMsg BugsRegistry<br><br>MathSort MathMatrix <br>MathSparsematrix <br>MathFunc MathRandnum MathODE MathFunctional MathRungeKutta45<br>MathAESolver MathIntegrate<br>
</font><font face="Arial" color="#000100" size="3">MathLincon
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="3">MathTT800 MathDiagmatrix MathBGR MathSmooth<br><br>GraphRules GraphNodes GraphLogical GraphStochastic GraphScalar GraphVector<br>GraphLimits GraphUnivariate GraphMultivariate GraphConjugateMV GraphChain GraphGMRF<br>GraphBlock GraphCensoringTruncation<br><br>MonitorsSamples MonitorsSummary MonitorsDeviance MonitorsPlugin<br><br>UpdaterUpdaters UpdaterMethods UpdaterUnivariate UpdaterMultivariate UpdaterContinuous UpdaterEmpty UpdaterActio [...]
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000000" size="3">GraphConstant GraphMixture GraphStack GraphFlat GraphGeneric GraphClock<br><br>LindevCPM LindevCPT LindevCPB LindevCPS LindevCPP LindevCPE LindevCPH LindevCPL486 LindevCPC486 LindevCPV486<br><br>BugsVersion BugsGrammar BugsNames BugsIndex BugsVariables BugsParser BugsEvaluate BugsNodes
</font><font face="Arial" color="#8000FF" size="3">
</font><font face="Arial" color="#000000" size="3">BugsOptimize BugsChaingraph
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000000" size="3">BugsCodegen BugsCPCompiler BugsData BugsDeviance BugsInterface BugsInfo <br>Services<br><br>BugsScripting BugsTraphandler1 BugsPrettyprinter<br><br>BugsEmbed BugsRobjects<br><br>DiffExternal DiffResources UDevExternal UDevResources<br><br>BugsRectData BugsSplusData
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">SamplesMonitors SamplesIndex SamplesInterface SamplesFormatted SamplesEmbed<br><br>SummaryMonitors SummaryIndex SummaryInterface SummaryFormatted SummaryEmbed
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">RanksMonitors RanksIndex RanksInterface RanksFormatted RanksEmbed
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">DevianceMonitors DeviancePlugin DevianceIndex DevianceInterface DevianceFormatted DevianceEmbed
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">CorrelInterface
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000000" size="3">CorrelFormatted CorrelEmbed<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">GraphCloglog GraphCut GraphDensity GraphEigenvals GraphGammap GraphInprod GraphInverse GraphKepler GraphLog GraphLogdet GraphLogit GraphProbit GraphProduct GraphRanks GraphSumation GraphTable GraphFunctional GraphODEmath GraphODElang<br>GraphPiecewise GraphODEBlockL GraphODEBlockM <br>GraphPValue GraphReplicate GraphItermap<br><br>GraphBern GraphBinomial GraphCat GraphFounder GraphGeometric GraphGeometric0 GraphHypergeometric GraphMendeli [...]
</font><font face="Arial" color="#000100" size="3">UDevExternal UDevResources UDevScalar UDevScalarTemplate UDevVector UDevVectorTemplate UDevDJLPKIVbol2 UDevDJLPKIVbol3 UDevElicitorPiecewise UDevEmax UDevDJL2CompDisp UDevDJL3CompDisp UDevSparseMatrixVectorProduct<br>
</font><font face="Arial" color="#000000" size="3"><br>UpdaterHybrid1D UpdaterAM UpdaterDE UpdaterHybrid<br><br>UpdaterForward <br><br>UpdaterBeta UpdaterCatagorical UpdaterDFreeARS UpdaterDescreteSlice <br>UpdaterGriddy UpdaterGamma UpdaterMetover UpdaterDFreeHybrid1D UpdaterMetbinomial UpdaterMetnormal UpdaterNormal UpdaterPareto UpdaterPoisson UpdaterRejection UpdaterSCAM UpdaterSCDE UpdaterSlice UpdaterNaivemet<br><br>UpdaterAMblock UpdaterAMNLLS UpdaterChain UpdaterDEBlock UpdaterDir [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">SpatialBound SpatialCARl1 SpatialCARNormal SpatialCARProper SpatialStrucMVN SpatialDiscKrig SpatialExpKrig SpatialMaternKrig SpatialPoissconv SpatialMVCAR<br>UpdaterKrigparam<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">BugsExternal BugsMessages BugsScripts CorrelMessages DevianceMessages<br>GraphMessages RanksMessages SamplesMessages SpatialExternal SummaryMessages <br>UpdaterMessages UpdaterExternal MapsMessages<br><br>BugsResources CorrelResources DevianceResources GraphResources RanksResources <br>SamplesResources SpatialResources SummaryResources UpdaterResources MapsResources<br><br>
</font><font face="Arial" color="#000000" size="2">ReliabilityBS ReliabilityBurrXII ReliabilityBurrX ReliabilityExpPower ReliabilityExpoWeibull ReliabilityExtExp ReliabilityExtendedWeibull ReliabilityFlexibleWeibull ReliabilityGenExp ReliabilityGPWeibull ReliabilityGompertz ReliabilityGumbel ReliabilityInvGauss ReliabilityInvWeibull ReliabilityLinearFailure ReliabilityLogisticExp ReliabilityLogLogistic ReliabilityLogWeibull ReliabilityModifiedWeibull ReliabilityExternal ReliabilityResources
</font><font face="Arial" color="#FF0000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>Startup BugsCLI <br><br>BugsC# <img src="linking6.bmp" alt="[linking6]">
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#FF0000" size="3"><strong>(* need to have Linux version of Kernel.ocf and HostFile.ocf in correct place *)
</strong></font><font face="Arial" color="#000000" size="3"><br><br>To create a fully linked OpenBUGS library for Linux click in the round blob<br><img src="linking7.bmp" alt="[linking7]">DevElfLinker.LinkDll<br>libOpenBUGS.so := Kernel$+ Files HostFiles Meta Console LinConsole BugsInterpreter<br><br>Math Strings Dialog Stores Services<br><br>BugsMappers BugsStrings BugsFiles BugsStdInterpreter<br>BugsMsg BugsRegistry<br><br>MathSort MathMatrix MathSparsematrix MathFunc MathRandnum MathOD [...]
</font><font face="Arial" color="#000100" size="3">MathLincon
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="3">MathTT800 MathDiagmatrix MathBGR MathSmooth
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000000" size="3"><br><br>GraphRules GraphNodes GraphLogical GraphStochastic GraphScalar GraphVector GraphLimits GraphUnivariate GraphMultivariate GraphConjugateMV GraphChain GraphGMRF<br>GraphBlock GraphCensoringTruncation<br><br>MonitorsSamples MonitorsSummary MonitorsDeviance MonitorsPlugin<br><br>UpdaterUpdaters UpdaterMethods UpdaterUnivariate UpdaterMultivariate UpdaterContinuous UpdaterEmpty UpdaterActions UpdaterMetmonitor <br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000000" size="3">GraphConstant GraphMixture GraphStack GraphFlat GraphGeneric GraphClock<br><br>LindevCPM LindevCPT LindevCPB LindevCPS LindevCPP LindevCPE LindevCPH LindevCPL486 LindevCPC486 LindevCPV486<br><br>BugsVersion BugsGrammar BugsNames BugsIndex BugsVariables BugsParser BugsEvaluate BugsNodes BugsOptimize BugsChaingraph BugsCodegen BugsCPCompiler BugsData BugsDeviance BugsInterface BugsInfo <br><br>BugsScripting BugsTraphandler1 BugsPrettyprinte [...]
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>SamplesMonitors SamplesIndex SamplesInterface SamplesFormatted SamplesEmbed<br><br>SummaryMonitors SummaryIndex SummaryInterface SummaryFormatted SummaryEmbed
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">RanksMonitors RanksIndex RanksInterface RanksFormatted RanksEmbed
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">DevianceMonitors DeviancePlugin DevianceIndex DevianceInterface DevianceFormatted DevianceEmbed
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">CorrelInterface
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000000" size="3">CorrelFormatted CorrelEmbed<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">GraphCloglog GraphCut GraphDensity GraphEigenvals GraphGammap GraphInprod GraphInverse GraphKepler GraphLog GraphLogdet GraphLogit GraphProbit GraphProduct GraphRanks GraphSumation GraphTable GraphFunctional GraphODEmath GraphODElang<br>GraphPiecewise GraphODEBlockL GraphODEBlockM <br>GraphPValue GraphReplicate GraphItermap<br><br>GraphBern GraphBinomial GraphCat GraphFounder GraphGeometric GraphGeometric0 GraphHypergeometric GraphMendeli [...]
</font><font face="Arial" color="#000100" size="3">UDevExternal UDevResources UDevScalar UDevScalarTemplate UDevVector UDevVectorTemplate UDevDJLPKIVbol2 UDevDJLPKIVbol3 UDevElicitorPiecewise UDevEmax UDevDJL2CompDisp UDevDJL3CompDisp UDevSparseMatrixVectorProduct<br>
</font><font face="Arial" color="#000000" size="3"><br>UpdaterHybrid1D UpdaterAM UpdaterDE UpdaterHybrid<br><br>UpdaterForward <br><br>UpdaterBeta UpdaterCatagorical UpdaterDFreeARS UpdaterDescreteSlice <br>UpdaterGriddy UpdaterGamma UpdaterMetover UpdaterDFreeHybrid1D UpdaterMetbinomial UpdaterMetnormal UpdaterNormal UpdaterPareto UpdaterPoisson UpdaterRejection UpdaterSCAM UpdaterSCDE UpdaterSlice UpdaterNaivemet<br><br>UpdaterAMblock UpdaterAMNLLS UpdaterChain UpdaterDEBlock UpdaterDir [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">SpatialBound SpatialCARl1 SpatialCARNormal SpatialCARProper SpatialStrucMVN SpatialDiscKrig SpatialExpKrig SpatialMaternKrig SpatialPoissconv SpatialMVCAR<br>UpdaterKrigparam<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">BugsExternal BugsMessages BugsScripts CorrelMessages DevianceMessages GraphMessages RanksMessages SamplesMessages SpatialExternal SummaryMessages<br>UpdaterMessages UpdaterExternal MapsMessages<br><br>BugsResources CorrelResources DevianceResources GraphResources RanksResources <br>SamplesResources SpatialResources SummaryResources UpdaterResources MapsResources<br><br>
</font><font face="Arial" color="#000000" size="2">ReliabilityBS ReliabilityBurrXII ReliabilityBurrX ReliabilityExpPower ReliabilityExpoWeibull ReliabilityExtExp ReliabilityExtendedWeibull ReliabilityFlexibleWeibull ReliabilityGenExp ReliabilityGPWeibull ReliabilityGompertz ReliabilityGumbel ReliabilityInvGauss ReliabilityInvWeibull ReliabilityLinearFailure ReliabilityLogisticExp ReliabilityLogLogistic ReliabilityLogWeibull ReliabilityModifiedWeibull ReliabilityExternal ReliabilityResources
</font><font face="Arial" color="#000000" size="3"><br><br>Startup BugsCLI <br><br>BugsC# <img src="linking8.bmp" alt="[linking8]">
</font><font face="Arial" color="#0000FF" size="3"><br><br><br>
</font><font face="Arial" color="#000000" size="3">Click the blobs to make SlaveBUGS for multiprocessor updating.<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><img src="linking9.bmp" alt="[linking9]">DevLinker.Link
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3">WorkerBUGS.exe := Kernel$ + Files HostFiles HostPackedFiles StdLoader<br>1 Bugslogo.ico 2 Doclogo.ico 3 SFLogo.ico 4 CFLogo.ico 5 DtyLogo.ico<br>6 folderimg.ico 7 openimg.ico 8 leafimg.ico<br>1 Move.cur 2 Copy.cur 3 Link.cur 4 Pick.cur 5 Stop.cur 6 Hand.cur 7 Table.cur <img src="linking10.bmp" alt="[linking10]"><br><br><img src="linking11.bmp" alt="[linking11]"> DevPacker.PackThis WorkerBUGS.exe :=<br>gpl-3.0.txt<br>Bugs/Rsrc/Menus.odc<br [...]
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><img src="linking13.bmp" alt="[linking13]">DevLinker.Link
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3">MultiBUGS.exe := Kernel$ + Files HostFiles HostPackedFiles StdLoader<br>1 Bugslogo.ico 2 Doclogo.ico 3 SFLogo.ico 4 CFLogo.ico 5 DtyLogo.ico<br>6 folderimg.ico 7 openimg.ico 8 leafimg.ico<br>1 Move.cur 2 Copy.cur 3 Link.cur 4 Pick.cur 5 Stop.cur 6 Hand.cur 7 Table.cur <img src="linking14.bmp" alt="[linking14]"><br><br><img src="linking15.bmp" alt="[linking15]"> DevPacker.PackThis MultiBUGS.exe :=<br>gpl-3.0.txt<br>Bugs/Rsrc/MenusMulti.odc [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Developer/Make.html b/doc/Developer/Make.html
new file mode 100755
index 0000000..e2a7fff
--- /dev/null
+++ b/doc/Developer/Make.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Make</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"><img src="make0.bmp" alt="[make0]"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000000" size="3">Click in the blob containing a ! to compile the source code.<br><br>Modules in black are generic to Windows and Linux. Modules in red are for Windows only. Modules in blue are for Linux only. Modules in purple are some useful software development tools (they are not a part of OpenBUGS)<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><img src="make1.bmp" alt="[make1]">DevCompiler.CompileThis<br><br>Console<br><br>BugsInterpreter BugsMappers BugsStrings BugsFiles BugsStdInterpreter<br><br>BugsMsg BugsRegistry<br><br>BugsScripting<br><br>MathSort MathFunc MathMatrix MathSparsematrix MathTaucsLib MathTaucsImp<br>MathRandnum MathODE MathFunctional MathRungeKutta45<br>MathAESolver MathIntegrate<br>
</font><font face="Arial" color="#000000" size="3">MathLincon
</font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3">MathTT800 MathDiagmatrix MathBGR MathSmooth<br><br>GraphRules GraphNodes GraphLogical GraphStochastic GraphLimits GraphScalar GraphVector GraphUnivariate GraphMultivariate GraphConjugateMV GraphChain GraphGMRF<br>GraphBlock GraphMessages GraphResources GraphCensoringTruncation<br><br>MonitorsSamples MonitorsSummary MonitorsDeviance MonitorsPlugin<br><br>UpdaterUpdaters UpdaterMethods UpdaterUnivariate UpdaterMultivariate UpdaterContinuous [...]
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000000" size="3">RanksInterface RanksFormatted RanksEmbed <br>RanksMessages RanksResources<br><br>DevianceMonitors DeviancePlugin DevianceIndex <br>DevianceInterface DevianceFormatted DevianceEmbed DevianceMessages DevianceResources <br><br>CorrelInterface CorrelFormatted CorrelEmbed CorrelMessages CorrelResources <br><br>GraphCloglog GraphCut GraphDensity GraphEigenvals GraphGammap GraphInprod GraphInverse GraphKepler GraphLog GraphLogdet GraphLogit Grap [...]
</font><font face="Arial" color="#000100" size="3">UDevExternal UDevResources UDevScalar UDevScalarTemplate UDevVector UDevVectorTemplate UDevDJLPKIVbol2 UDevDJLPKIVbol3 UDevElicitorPiecewise UDevEmax UDevDJL2CompDisp UDevDJL3CompDisp UDevSparseMatrixVectorProduct<br>
</font><font face="Arial" color="#000000" size="3"><br>UpdaterHybrid1D UpdaterAM UpdaterDE UpdaterHybrid<br><br>UpdaterForward <br><br>UpdaterBeta UpdaterCatagorical UpdaterDFreeARS UpdaterDescreteSlice <br>UpdaterGriddy UpdaterGamma UpdaterMetover UpdaterDFreeHybrid1D UpdaterMetbinomial UpdaterMetnormal UpdaterNormal UpdaterPareto UpdaterPoisson UpdaterRejection UpdaterSCAAR UpdaterSDScale UpdaterSCAM UpdaterSCDE UpdaterSlice UpdaterNaivemet UpdaterMultinomialorder<br><br>UpdaterAMblock [...]
</font><font face="Arial" color="#000000" size="2">ReliabilityBS ReliabilityBurrXII ReliabilityBurrX ReliabilityExpPower ReliabilityExpoWeibull ReliabilityExtExp ReliabilityExtendedWeibull ReliabilityFlexibleWeibull ReliabilityGenExp ReliabilityGPWeibull ReliabilityGompertz ReliabilityGumbel ReliabilityInvGauss ReliabilityInvWeibull ReliabilityLinearFailure ReliabilityLogisticExp ReliabilityLogLogistic ReliabilityLogWeibull ReliabilityModifiedWeibull ReliabilityExternal ReliabilityResources
</font><font face="Arial" color="#FF0000" size="2"><br>
</font><font face="Arial" color="#FF0000" size="2">
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#FF0000" size="3">BugsClassic
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#FF0000" size="3">HostCmds HostMenus<br><br>HtmlEntitySets HtmlExporter HtmlImporter<br><br>WinConsole
</font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#FF0000" size="3">BugsTexts BugsDialog<br><br>UpdaterSettings<br><br>DevDebug DevBrowser DevSearch<br><br>BugsTraphandler BugsCmds BugsBatch BugsConfig <br><br><br>DoodleNodes DoodlePlates DoodleModels DoodleMenus DoodleDialog DoodleViews DoodleParser DoodleCmds DoodleMessages DoodleResources<br><br>BugsDebug BugsDocu<br><br>PlotsAxis PlotsViews PlotsDialog PlotsNomaxis PlotsStdaxis PlotsEmptyaxis<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#FF0000" size="3">SamplesViews SamplesPlots SamplesCmds <br>SamplesCorrelat SamplesDensity SamplesDiagnostics SamplesHistory SamplesQuantiles SamplesTrace SamplesJumpdist SamplesAccept<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#FF0000" size="3">SummaryCmds <br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#FF0000" size="3">RanksDensity
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#FF0000" size="3">RanksCmds <br><br>DevianceCmds <br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#FF0000" size="3">CompareViews CompareBoxplot CompareCaterpillar CompareDenstrip CompareModelFit CompareScatter CompareCmds
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#FF0000" size="3">CorrelBivariate CorrelMatrix CorrelPlots CorrelCmds<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#FF0000" size="3">UpdaterMetplots
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#FF0000" size="3">MapsMap MapsImporter MapsIndex MapsAdjacency MapsViews MapsViews1 MapsCmds MapsArcinfo MapsEpimap MapsSplus <br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#FF0000" size="3">StdCmds1<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#FF0000" size="3">TestScript<br>
</font><font face="Arial" color="#8000FF" size="3"><br>
</font><font face="Arial" color="#FF0000" size="3">BugsDistribute BugsDocusource BugsCopysource
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#8000FF" size="3"><br>
</font><font face="Arial" color="#0000FF" size="3">LinLibc LinConsole<br><br>
</font><font face="Arial" color="#8000FF" size="3">CpcBeautifierOptions CpcBeautifier DevElfLinker16
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><img src="make2.bmp" alt="[make2]"><br><br>The module WinConsole contains the code for console I/O on Windows<br>The module LinConsole
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000000" size="3">contains code for console I/O on Linux. <br><br><br>Click in blob below to compile modules for MultiBUGS the multiprocessor version of OpenBUGS<br><br><img src="make3.bmp" alt="[make3]">DevCompiler.CompileThis<br><br>BugsMultiproc BugsScriptsmulti SamplesDiscmonitors SummaryDiscmonitors RanksDiscmonitors DevianceDiscmonitors DevianceDiscPlugin<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">BugsWorker
</font><font face="Arial" color="#FF0000" size="3"><br><br>BugsCmdsmulti <br>UpdaterSettingsmulti<br>SamplesCmdsmulti SummaryCmdsmulti RanksCmdsmulti DevianceCmdsmulti<br>CompareCmdsmulti CorrelCmdsmulti<br>
</font><font face="Arial" color="#000000" size="3"><img src="make4.bmp" alt="[make4]"><br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font>
</p>
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<title>Manual</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="manual0.bmp" alt="[manual0]">
</font><font face="Courier New" color="#000100" size="6">OpenBUGS Developer Manual
</font><font face="Arial" color="#000100" size="6"><strong><sup><br>
</sup></strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="4">Version 3.2.3, March 2014
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Andrew Thomas
</font><font face="Arial" color="#000100" size="1"><sup>1
</sup></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="1"><sup>1
</sup></font><font face="Arial" color="#000100" size="3">Dept of Mathematics & Statistics,<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">University of St Andrews<br> St Andrews<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Scotland
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">e-mail: helsinkiant at gmail.com<br>
</font><font face="Arial" color="#000100" size="2"><br><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="../Developer/Tools.html">Setting up the development tools</a><br><br> <a href="../Developer/Compiling.html">Compiling the Source Code</a><br><br> <a href="../Developer/Linking.html">Executable versions and linking</a><br><br> <a hre [...]
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diff --git a/doc/Developer/MultiBUGS.html b/doc/Developer/MultiBUGS.html
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<head>
<title>MultiBUGS</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"><img src="multibugs0.bmp" alt="[multibugs0]">
</font><font face="Arial" color="#0000FF" size="3"><a id="Linking">
</font><font face="Arial" color="#000000" size="4"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Multiprocessor BUGS
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">There is a version of OpenBUGS software family which runs on multiple processors. Each chain of the simulation can run on a seperate processor. There are some overheads in running OpenBUGS this way, however for computationally intense models good speed ups can be achieved. This multiprocessor version of OpenBUGS is called
</font><font face="Arial" color="#000000" size="3"><strong>MultiBUGS
</strong></font><font face="Arial" color="#000000" size="3">, and is started by clicking on the MultiBUGS icon. The user interface of MultiBUGS is very similar to that of OpenBUGS.<br><br>Parsing and loading data are identical in MultiBUGS and single processor OpenBUGS. At compilation, one chain of the graphical model is compiled and then the graph writen out to multiple restart files, the seed of the random number generator being set differently in each file. Initial values for a particu [...]
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diff --git a/doc/Developer/Randnum.html b/doc/Developer/Randnum.html
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<html>
<head>
<title>Randnum</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"><img src="randnum0.bmp" alt="[randnum0]">
</font><font face="Courier New" color="#000100" size="6">Random Number Generators
</font><font face="Arial" color="#000100" size="6"><strong><sup> <br>
</sup></strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="3">The module MathRandnum defines an abstract class Generator for generating pseudo random numbers with a uniform distribution on [0,1]. Two implementations of the Generator class are given in modules MathLincon (a linear congruance algorithm) and MathTT800 (a twisted GFSR algorithm). The module MathRandnum implements several non-uniform random number generators using an object of class Generator to generate random uniforms. The state of the [...]
</font><font face="Arial" color="#0000FF" size="3"><u><a href="../Randnumseeds.html">seeds
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> gives seeds for the MathT800 updater that belong to random deviates 5*10^11 iterations apart. By default OpenBUGS uses a single Generator object for all the chains it simulates. This can be altered in the Compile options dialog of the Model menu so that each chain uses a seperate Generator object. Using a different Generator object for each chain will be needed in any parallel implementation of OpenBUGS.<br><br>A small test model -- mode [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><strong>mean sd 2.5% 5% 10% 25% 50% 75% 90% 95% 97.5%<br>
</strong></font><font face="Arial" color="#000100" size="2">0.5001 0.2887 0.02501 0.05004 0.1 0.25 0.5001 0.7501 0.9 0.9499 0.975 <br>0.4999 0.2887 0.02491 0.04994 0.09993 0.2499 0.4998 0 [...]
</font><font face="Arial" color="#000100" size="3"><br>Both random number generators appear to work well, but we have little experience with the MathTT800 algorithm and have had some difficulty coding this algorithm.
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<html>
<head>
<title>SamplingAlgorithms</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"><img src="samplingalgorithms0.bmp" alt="[samplingalgorithms0]">
</font><font face="Courier New" color="#000100" size="6">Sampling Algorithms
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="3"><a id="Choice">
</font><font face="Courier New" color="#000100" size="5">Choice of Sampling Algorithm
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>When OpenBUGS starts up a file called
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Updater/Mod/External.html">External
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">in Updater/Mod is processed. The modules implementing the sampling methods listed in this file are then loaded dynamically. Factory objects to create updater objects which use these methods are stored in an array (in the same order as in the file). The first factory object in this array is used to create updaters for all the stochastic nodes in the model that need updating and for which the associated sampling method is valid and wishes t [...]
</font><font face="Arial" color="#0000FF" size="3"><a id="Description">
</font><font face="Courier New" color="#000100" size="5">Description of Sampling Algorithms
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>Here is an alphabetical list of install procedures for updaters that can be used followed by a brief note on how the algorithm works and what type of situation it is appropiate to. <br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterAMblock.InstallGLM
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Current point Metropolis type updater with delayed rejection and continously adapted multivariate normal proposal distribution. For a fixed effect block of nodes all of which have a logistic or log-linear conditional distribution. Non-Markov algorithm. Not currently used.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterAMblock.InstallHetro
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Current point Metropolis type updater with delayed rejection and continously adapted multivariate normal proposal distribution. For a fixed effect block of nodes the first element of which has a generic conditional distribution. Non-Markov algorithm. Not currently used.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterAMblock.InstallHomo
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Current point Metropolis type updater with delayed rejection and continously adapted multivariate normal proposal distribution. For a fixed effect block of nodes all of which have a generic conditional distribution. Non-Markov algorithm. Not currently used.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterAMblock.InstallRE
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Current point Metropolis type updater with delayed rejection and continously adapted multivariate normal proposal distribution. For a random effect block of nodes all of which have a logit or log-linear conditional distribution. Non-Markov algorithm. Not currently used.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterAMNLLS.InstallMarginal
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Continously adaptive block Metropolis algorithm for non-linear least squares problem with the measurement error precision integrated out.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterAMNLLS.InstallCond
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Continously adaptive block Metropolis algorithm for non-linear least squares problem.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterBeta.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Gibbs type of updater for beta conditional distribution.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterCatagorical.Install
</strong></font><font face="Arial" color="#000100" size="3"> <br><br> Gibbs type of updater for univariate node which takes discrete values with a upper bound. Works by enumeration. Slow if many categories.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterChain.Install
</strong></font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3"> Updater for a node with chain graph prior. Works as a sequence of univariate updaters but can inpose a constraint such as the sum to zero constariant for CAR priors.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterDescreteSlice.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Slice type sampler for discrete variable. Competes with UpdaterCatagorical if discrete variable has upper bound and with UpdaterMetbinomial if no upper bound.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterDFreeHybrid.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Metropolis type of updater for a block of nodes which has a generic conditional distribution with unbounded support. Proposal distribution is based on integration of Hamilton's equations of classical mechanics. Derivatives of log likelihood are calculated numerically. Not currently used. There are three broad classes of updater: those that do Gibbs sampling, those that do Metropolis Hastings sampling and [...]
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterDirichlet.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Gibbs type of updater for a conditional distribution that is dirichlet.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterDirichletprior.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Slice sampler type of updater for a conditional distribution that has a dirichlet prior but non conjugate likelihood.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterForward.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Gibbs type of updater for univariate node which does not have any likelihood.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterGamma.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Gibbs type of updater for gamma conditional distribution.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterGLM.InstallGLM
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Metropolis Hastings type updater for a block of nodes which have either a log-linear or logistic conditional distribution with unbounded support.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterGLM.InstallNormal
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Gibbs type of updater for multivariate conditional distribution where the prior is a set of univariate normal nodes. Not currently used.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterGMRF.InstallGeneral
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Current point block Metropolis algorithm for nodes with a Gaussian Markov Random Field prior. Can update large blocks. Also able to implement contsraints. Uses sparse matrix algebra (see Rue)<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterGriddy.Install
</strong></font><font face="Arial" color="#000100" size="3"> <br><br> Independent Metropolis Hastings type updater for generic univariate distribution. Distribution must have bounded support. Builds a trapezoidal approximation to the conditional to use as the proposal. Slow algorithm. Not currently used, slice sampling is preferred but see note below about multimodality.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterHybridglm.Install<br><br>
</strong></font><font face="Arial" color="#000100" size="3"> Updater for random effect block of nodes with normal prior and logit, log-linear or normal likelihood.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterHybridglm.InstallChain<br><br>
</strong></font><font face="Arial" color="#000100" size="3"> Updater for chain graph prior and logit, log-linear or normal likelihood.<br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterHybridglm.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Metropolis type of updater for a block of nodes which has a normal, log-linear or logistic conditional distribution with unbounded support. Proposal distribution is based on integration of Hamiltons equations of classical mechanics. Used for random effects. Not currently used.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterMetbinomial.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Current point Metropolis type updater for univariate node which takes discrete values with no upper bound.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterMetnormal.InstallDelayed
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Current point Metropolis type updater for generic univariate distribution with unbounded support. Uses a normal proposal distribution that is adapted during a tuning phase. Uses delayed rejection if first proposal is rejected.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterMetnormal.InstallStd
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Current point Metropolis type updater for generic univariate distribution with unbounded support. Uses a normal proposal distribution that is adapted during a tuning phase. <br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterMultinomial.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Independence Metropolis type of updater for a conditional distribution that has a multinomial prior.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterMVNLinear.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> As for UpdaterMVNormal.Install but the likelihood can have terms that are multivariate normal of a different dimension to the prior and the link function does not have to be the identity but can have a linear form.<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterMVNormal.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Gibbs type of updater for multivariate normal conditional distribution where each term in the likelihood is either normal, log normal or multivariate normal of same dimension as the prior with a unit link function.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterNormal.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Gibbs type of updater for univariate normal conditional distribution.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterPareto.Install
</strong></font><font face="Arial" color="#000100" size="3"> <br><br> Gibbs type of updater for pareto conditional distribution.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterPoisson.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Gibbs type of updater for poisson prior with single binomial likelihood term having order equal to the prior.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterRejection.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Gibbs type of updater for univariate node with log-linear or logistic distribution and unbounded support.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterSCAAR.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Single component adaptive Metropolis algorithm that tunes the acceptance rate (see Roberts and Rosenthal).<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterSCAM.InstallDelayed
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Current point Metropolis type updater for generic univariate distribution with unbounded support. Uses a continously adapted normal proposal distribution. Non-Markov algorithm. Not currently used. Uses delayed rejection if first proposal rejected. <br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterSCAM.InstallDelayedB
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Current point Metropolis type updater for generic univariate distribution with bounded support. Uses a continously adapted normal proposal distribution. Non-Markov algorithm. Not currently used. Uses delayed rejection if first proposal rejected. <br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterSCAM.InstallStd
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Current point Metropolis type updater for generic univariate distribution with unbounded support. Uses a continously adapted normal proposal distribution. Non-Markov algorithm. Not currently used.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterSDScale.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Single component adaptive Metropolis algorithm that tunes the acceptance rate in a way that depends on the scale of the variable (see Roberts and Rosenthal).<br>
</font><font face="Arial" color="#000100" size="3"><strong><br>UpdaterSlice.Install
</strong></font><font face="Arial" color="#000100" size="3"> <br><br> Slice type of updater for generic univariate distribution. Uses stepping out search procedure to find the slice. Step length of search procedure adapted during tuning phase. Can miss modes for multimodal conditional distribution if the support is not bounded.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>UpdaterWishart.Install
</strong></font><font face="Arial" color="#000100" size="3"><br><br> Gibbs type of updater for Wishart conditional distributions.<br>
</font>
</p>
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<html>
<head>
<title>Test</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"><img src="test0.bmp" alt="[test0]">
</font><font face="Courier New" color="#000100" size="6">Test Scripts for OpenBUGS
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Click the blob to run test of all models in OpenBUGS distribution. This will take some time: about 30 minutes on a 3GHz computer. A file containing the results of the test is in file<br>Test/TestAllModels.<br><br><img src="test1.bmp" alt="[test1]">TestScript.AllModels
</font>
</p>
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<html>
<head>
<title>Tools</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"><img src="tools0.bmp" alt="[tools0]">
</font><font face="Courier New" color="#000100" size="6">Setting up the development<br> tools<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br><br>
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Courier New" color="#0000FF" size="3"><a href="#BlackBox">
</font><font face="Arial" color="#0000FF" size="3">BlackBox</a><br>
</font><font face="Courier New" color="#0000FF" size="3"><a href="#TAUCS">
</font><font face="Arial" color="#0000FF" size="3">TAUCS library</a><br>
</font><font face="Courier New" color="#0000FF" size="3"><a href="#SVN">
</font><font face="Arial" color="#0000FF" size="3">Subversion repository</a><br><br>
</font><font face="Arial" color="#000100" size="3"><a id="BlackBox">BlackBox</a>
</font><font face="Arial" color="#0000FF" size="3">[
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">
</font><font face="Arial" color="#0000FF" size="3">top</a>]<br>
</font><font face="Arial" color="#000100" size="3"><br>Download and install BlackBox component builder v1.6 from OberonMicrosystems (http://www.oberon.ch). <br><br>OberonMicrosystems have kindly made some tools for developing ELF format shared object files available under the Sleepy Cat Open Source licence (http://www.opensource.org/licenses/sleepycat.php). <br><br>Install OpenBUGS in some directory different from where you have installed BlackBox. If you have installed BlackBox in a dire [...]
</font><font face="Arial" color="#0000FF" size="3">[
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">
</font><font face="Arial" color="#0000FF" size="3">top</a>]
</font><font face="Arial" color="#000100" size="3"><br><br>The OpenBUGS can make use of the TAUCS sparse matrix library (http://www.tau.ac.il/~stoledo/taucs). A Windows version of this library, libtaucs.dll, is distributed with OpenBUGS. This library is used in a sampling algorithm for Gaussian Markov Random Field (GMRF). Without TAUCS the sampling algorithm for GMRF will be much slower for high dimension problems. If you do not want OpenBUGS to use the TAUCS library just remove libtaucs. [...]
</font><font face="Arial" color="#0000FF" size="3">[
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">
</font><font face="Arial" color="#0000FF" size="3">top</a>]<br>
</font><font face="Arial" color="#000100" size="3"><br>Source code of OpenBUGS is stored in the Subversion (SVN) repository at SourceForge (https://openbugs.svn.sourceforge.net/svnroot/openbugs). A fancier view of the repository is provided via ViewVC (http://openbugs.svn.sourceforge.net/viewvc/openbugs). Cominication with the SVN repository can be perfomred with any Subversion client. We recommend using the TortoiseSVN client (http://tortoisesvn.tigris.org).<br><br>BlackBox .odc files ar [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">java script diff program by josef temple, click on arrow and then use Tools->Decode to decode and place in correct location
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">compiled form of config module by josef temp, click on arrow and then use Tools->Decode to decode and place in correct location<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">source code for config file writen by josef temple<br><br>2. An alternative is to use the WinMerge program (http://winmerge.org). Since these files are in the binary form, there are some "scribbles" in the diffs, but the code and the differences are laid out nicely in the text form.<br><br>3. Online view of Subversion repository via ViewVC can also be used to see the .odc files - use "as text" link to see the content o [...]
</font>
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<html>
<head>
<title>WritingBUGSExtensions</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"><img src="writingbugsextensions0.bmp" alt="[writingbugsextensions0]">
</font><font face="Courier New" color="#000100" size="6">Writing OpenBUGS Extensions
</font><font face="Arial" color="#000100" size="2"><br><br><br><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#Introduction">Introduction</a><br> <br> <a href="#Graph">The Graph hierarchy</a><br> <br> <a href="#Updater">The Updater hierarchy</a><br>
</font><font face="Arial" color="#0000FF" size="4"> <br> <br>
</font><font face="Arial" color="#0000FF" size="3"><a id="Introduction">
</font><font face="Courier New" color="#000100" size="5">Introduction
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">[top]</a>
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">The OpenBUGS software is a framework that handles the logic of interaction between several class hierarchies. One class hierarchy, the Graph hierarchy, is used to build descriptions of complex Bayesian statistical models. A second, the Updater hierarchy, implements sampling algorithms for variables in the statistical model. New types of logical functions and distributions can be added to the BUGS language by implementing new classes in th [...]
</font><font face="Courier New" color="#000100" size="5"><a id="Graph">The Graph hierarchy
</font><font face="Arial" color="#000000" size="4"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">[top]</a>
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">OpenBUGS describes statistical models in terms of a graph. Each node in the graph is represented by an object belonging to one of the classes in the Graph hierarchy. Each of these classes is descendant from the class GraphNodes.Node (that is the class Node in module GraphNodes). The class GraphNodes.Node is first specialized to GraphLogial.Node to represent logical function and GraphStochastic.Node to represent distributions in the BUGS l [...]
</font><font face="Courier New" color="#000100" size="5"><a id="Updater">The Updater hierarchy
</font><font face="Arial" color="#000000" size="4"><strong></a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">[top]</a>
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">There is also a hierarchy of updater classes to implement the updating or sampling algorithms. The sampling algorithm for each node or block of nodes in the graphical model is contained in an object of the appropiate class. These updater classes use the graphical model to efficiently calculate the required conditional probabilities. All the updater objects for the graphical model are stored in a linked list sorted according to the topolog [...]
</font>
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<html>
<head>
<title>Abbey</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="abbey0.bmp" alt="[abbey0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Abbey National: A stable<br> distribution
</font><font face="Arial" color="#000100" size="5"><br><br>
</font><font face="Arial" color="#000100" size="3">Buckle considers the price of Abbey National shares on 50 conscutive working days. He models the price return using a stable distribution with unknown parameters. We run two chains for 1100 iterations with the thin box in the update tool set to 10. Our results are in fair agreement with Buckle who estimated the following mean values alpha = 1.61, beta = -0.55, gamma = 0.00053 and delta = 0.0079.<br>
</font><font face="Arial" color="#000100" size="5"><br> model{<br> for(i in 2 : N){<br> z[i] ~ dstable(alpha, beta, gamma, delta) <br> z[i] <- price[i] / price[i - 1] - 1<br> }<br> <br> alpha ~ dunif(1.1, 2)<br [...]
</font><font face="Arial" color="#0000FF" size="6">Data
</font><font face="Arial" color="#000100" size="5"><br><br>list(N = 50, price = c(<br>296, 296, 300, 302, 300, 304, 303, 299, 293, 294, 294, 293, 295,<br>287, 288, 297, 305, 307, 307, 304, 303, 304, 304, 309, 309, 309,<br>307, 306, 304, 300, 296, 301, 298, 295, 295, 293, 292, 297, 294,<br>293, 306, 303, 301, 303, 308, 305, 302, 301, 297, 299)<br>)<br><br>
</font><font face="Arial" color="#0000FF" size="6">Inits
</font><font face="Arial" color="#000100" size="5"><br><br>list(alpha = 1.7, beta = 0.5, <br>gamma = 0.00029, delta = 0.0065)<br><br><br>list(alpha = 1.2, beta = -0.5, <br>gamma = 0.00029, delta = 0.0065)<br><br>
</font><font face="Arial" color="#0000FF" size="6">Results<br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> alpha 1.558 0.1995 0.008487 1.17 1.56 1.923 1001 20000<br> beta -0.5499 0.3628 0.01235 -0.9743 -0.65 0.3909 1001 20000<br>&nbs [...]
</font>
</p>
</body>
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diff --git a/doc/Examples/Air.html b/doc/Examples/Air.html
new file mode 100755
index 0000000..ff6f7e6
--- /dev/null
+++ b/doc/Examples/Air.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Air</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="air0.bmp" alt="[air0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">
</font><font face="Courier New" color="#000100" size="6">Air: Berkson measurement error
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">Whittemore and Keller (1988) use an approximate maximum likelihood approach to analyse the data shown below on reported respiratory illness versus exposure to nitrogen dioxide (NO
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">) in 103 children. Stephens and Dellaportas (1992) later use Bayesian methods to analyse the same data.
</font><font face="Arial" color="#000100" size="2"><br><center><img src="air1.bmp" alt="[air1]"><br></center><br>
</font><font face="Arial" color="#000100" size="3">A discrete covariate z
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> (j = 1,2,3) representing NO
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> concentration in the child's bedroom classified into 3 categories is used as a surrogate for true exposure. The nature of the measurement error relationship associated with this covariate is known precisely via a calibration study, and is given by
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br> x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> z
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">e
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> <br><br>where
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> = 4.48,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> = 0.76 and
</font><font face="Symbol" color="#000100" size="3">e
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> is a random element having normal distribution with zero mean and variance
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"><sup> (
</sup></font><font face="Arial" color="#000100" size="3">=
</font><font face="Arial" color="#000100" size="3"><sup>
</sup></font><font face="Arial" color="#000100" size="3">1/
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"><sup>)
</sup></font><font face="Arial" color="#000100" size="3"> = 81.14. Note that this is a Berkson (1950) model of measurement error, in which the true values of the covariate are expressed as a function of the observed values. Hence the measurement error is independent of the latter, but is correlated with the true underlying covariate values. In the present example, the observed covariate z
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> takes values 10, 30 or 50 for j = 1, 2, or 3 respectively (i.e. the mid-point of each category), whilst x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> is interpreted as the "true average value" of NO
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> in group j. The response variable is binary, reflecting presence/absence of respiratory illness, and a logistic regression model is assumed. That is <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(p
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">, n
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logit(p
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">where p
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> is the probability of respiratory illness for children in the jth exposure group. The regression coefficients
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> are given vague independent normal priors. The graphical model is shown below:<br>
</font><font face="Arial" color="#000100" size="2"><center>
</font><font face="Arial" color="#0000FF" size="5"><strong><br><img src="air2.bmp" alt="[air2]"><br>
</strong></font><font face="Arial" color="#000100" size="1"><br></center><br>
</font><font face="Arial" color="#000100" size="3"> model<br> {<br> for(j in 1 : J) {<br> y[j] ~ dbin(p[j], n[j])<br> logit(p[j]) <- theta[1] + theta[2] * X[j]<br> X[j] ~ dnorm(mu[j], tau)<br> mu[j] <- alph [...]
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/airdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/airinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Examples/airinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates <br><center>
</font><font face="Arial" color="#000100" size="2"><br><img src="air3.bmp" alt="[air3]">
</font>
</center>
</p>
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diff --git a/doc/Examples/Airdata.html b/doc/Examples/Airdata.html
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+++ b/doc/Examples/Airdata.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Airdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(J = 3, y = c(21, 20, 15), n = c(48, 34, 21), Z = c(10, 30, 50), tau = 0.01234, alpha = 4.48, beta = 0.76)
</font>
</p>
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diff --git a/doc/Examples/Airdata.txt b/doc/Examples/Airdata.txt
new file mode 100755
index 0000000..3a75ef2
--- /dev/null
+++ b/doc/Examples/Airdata.txt
@@ -0,0 +1 @@
+list(J = 3, y = c(21, 20, 15), n = c(48, 34, 21), Z = c(10, 30, 50), tau = 0.01234, alpha = 4.48, beta = 0.76)
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diff --git a/doc/Examples/Airinits.html b/doc/Examples/Airinits.html
new file mode 100755
index 0000000..8649bf8
--- /dev/null
+++ b/doc/Examples/Airinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Airinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"> list(theta = c(0.0, 0.0), X = c(0.0, 0.0, 0.0))
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Airinits.txt b/doc/Examples/Airinits.txt
new file mode 100755
index 0000000..92f178b
--- /dev/null
+++ b/doc/Examples/Airinits.txt
@@ -0,0 +1 @@
+ list(theta = c(0.0, 0.0), X = c(0.0, 0.0, 0.0))
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diff --git a/doc/Examples/Airinits1.html b/doc/Examples/Airinits1.html
new file mode 100755
index 0000000..df0a17a
--- /dev/null
+++ b/doc/Examples/Airinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Airinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(theta = c(1.0, 1.0), X = c(10.0, 30.0, 40.0))
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Airinits1.txt b/doc/Examples/Airinits1.txt
new file mode 100755
index 0000000..63e2c51
--- /dev/null
+++ b/doc/Examples/Airinits1.txt
@@ -0,0 +1 @@
+list(theta = c(1.0, 1.0), X = c(10.0, 30.0, 40.0))
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diff --git a/doc/Examples/Airmodel.html b/doc/Examples/Airmodel.html
new file mode 100755
index 0000000..6627b2e
--- /dev/null
+++ b/doc/Examples/Airmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Airmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for(j in 1 : J) {<br> y[j] ~ dbin(p[j], n[j])<br> logit(p[j]) <- theta[1] + theta[2] * X[j]<br> X[j] ~ dnorm(mu[j], tau)<br> mu[j] <- alpha + bet [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Airmodel.txt b/doc/Examples/Airmodel.txt
new file mode 100755
index 0000000..9efb59a
--- /dev/null
+++ b/doc/Examples/Airmodel.txt
@@ -0,0 +1,11 @@
+ model
+ {
+ for(j in 1 : J) {
+ y[j] ~ dbin(p[j], n[j])
+ logit(p[j]) <- theta[1] + theta[2] * X[j]
+ X[j] ~ dnorm(mu[j], tau)
+ mu[j] <- alpha + beta * Z[j]
+ }
+ theta[1] ~ dnorm(0.0, 0.001)
+ theta[2] ~ dnorm(0.0, 0.001)
+ }
diff --git a/doc/Examples/Aligators.html b/doc/Examples/Aligators.html
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index 0000000..093d4ae
--- /dev/null
+++ b/doc/Examples/Aligators.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Aligators</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="aligators0.bmp" alt="[aligators0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Alligators: multinomial - logistic<br> regression
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">Agresti (1990) analyses a set of data on the feeding choice of 221 alligators, where the response measure for each alligator is one of 5 categories: fish, invertebrate, reptile, bird, other. Possible explanatory factors are the length of alligator (two categories: <= 2.3 metres and > 2.3 metres), and the lake (4 catgeories: Hancock, Oklawaha, Trafford, George). The full data is shown below.<br><center>
</font><font face="Arial" color="#000100" size="2"><br><br><img src="aligators1.bmp" alt="[aligators1]">
</font><font face="Arial" color="#000100" size="3"><br></center>Each combination of explanatory factors is assumed to give rise to a multinomial response with a logistic link, so that for lake i, size j, the observed vector of counts X
</font><font face="Arial" color="#000100" size="2">ij.
</font><font face="Arial" color="#000100" size="3"> = X
</font><font face="Arial" color="#000100" size="2">ij1
</font><font face="Arial" color="#000100" size="3">,...,X
</font><font face="Arial" color="#000100" size="2">ij5
</font><font face="Arial" color="#000100" size="3"> has distribution<br><br> X
</font><font face="Arial" color="#000100" size="2"><sub>ij.
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Multinomial(p
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>.
</sub></font><font face="Arial" color="#000100" size="3">,n
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">) <br> p
</font><font face="Arial" color="#000100" size="2"><sub>ijk
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>ijk
</sub></font><font face="Arial" color="#000100" size="3"> /
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>ijk
</sub></font><font face="Arial" color="#000100" size="3"><sub><br>
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>ijk
</sub></font><font face="Arial" color="#000100" size="3"> = e
</font><font face="Symbol" color="#000100" size="3"><sup>a
</sup></font><font face="Arial" color="#000100" size="2">k
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3"><sub><br>
</sub></font><font face="Arial" color="#000100" size="3"><br>where n
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> X
</font><font face="Arial" color="#000100" size="2"><sub>ijk
</sub></font><font face="Arial" color="#000100" size="3">, and
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1k
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>j1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>1k
</sub></font><font face="Arial" color="#000100" size="3"> = 0 for identifiability. This model is discussed in detail in the Classic BUGS manual (version 0.5) in the section on
</font><font face="Arial" color="#000100" size="3"><em>Multionomial LogisticModels
</em></font><font face="Arial" color="#000100" size="3">. All unknown
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">'s,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">'s ,
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3">'s are initially given independent "noninformative" priors. <br><br>The Classic BUGS manual (version 0.5) discusses two ways of fitting this model: directly in the form given above or by using the multinomial-Poisson transformation which will be somewhat more efficient. Both techniques are illustrated in the code given below. <br>
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># PRIORS<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha[1] <- 0; # zero contrast for baseline food<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 2 : K) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha[k] ~ dnorm(0, 0.00001) # vague priors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Loop around lakes:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1 : K){ <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta[1, k] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } # corner-point contrast with first lake <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 2 : I) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta[i, 1] <- 0 ; # zero contrast for baseline food<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 2 : K){ <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta[i, k] ~ dnorm(0, 0.00001) # vague priors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Loop around sizes:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1 : K){ <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma[1, k] <- 0 # corner-point contrast with first size <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 2 : J) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma[j, 1] <- 0 ; # zero contrast for baseline food<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for ( k in 2 : K){ <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma[j, k] ~ dnorm(0, 0.00001) # vague priors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># LIKELIHOOD <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : I) { # loop around lakes<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : J) { # loop around sizes<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Multinomial response<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># X[i,j,1 : K] ~ dmulti( p[i, j, 1 : K] , n[i, j] )<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># n[i, j] <- sum(X[i, j, ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for (k in 1 : K) { # loop around foods<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># p[i, j, k] <- phi[i, j, k] / sum(phi[i, j, ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># log(phi[i ,j, k]) <- alpha[k] + beta[i, k] + gamma[j, k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Fit standard Poisson regressions relative to baseline<br> lambda[i, j] ~ dflat() # vague priors <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1 : K) { # loop around foods<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> X[i, j, k] ~ dpois(mu[i, j, k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> log(mu[i, j, k]) <- lambda[i, j] + alpha[k] + beta[i, k] + gamma[j, k]<br> cumulative.X[i, j, k] <- cumulative(X[i, j, k], X[i, j, k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># TRANSFORM OUTPUT TO ENABLE COMPARISON <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># WITH AGRESTI'S RESULTS<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1 : K) { # loop around foods<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : I) { # loop around lakes<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> b[i, k] <- beta[i, k] - mean(beta[, k]); # sum to zero constraint<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : J) { # loop around sizes<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> g[j, k] <- gamma[j, k] - mean(gamma[, k]); # sum to zero constraint<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Aligatorsdata.html">Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Aligatorsinits.html">Inits for chain 1</a> <a href="../Examples/Aligatorsinits1.html"> Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates <br><center>
</font><font face="Arial" color="#000000" size="2"><br><img src="aligators2.bmp" alt="[aligators2]"><br></center><br>
</font>
</p>
</body>
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diff --git a/doc/Examples/Aligatorsdata.html b/doc/Examples/Aligatorsdata.html
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+++ b/doc/Examples/Aligatorsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Aligatorsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list( I = 4, J = 2, K = 5,<br> X = structure(.Data = c(23, 4, 2, 2, 8, 7, 0, 1, 3, 5, 5, 11, 1, 0, 3, 13, 8, 6, 1, 0,<br> 5, 11, 2, 1, 5, 8, 7, 6, 3, 5, 16, 19, 1, 2, 3, 17, 1, 0, 1, 3), .Dim = c(4, 2, 5)))
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Aligatorsdata.txt b/doc/Examples/Aligatorsdata.txt
new file mode 100755
index 0000000..4760685
--- /dev/null
+++ b/doc/Examples/Aligatorsdata.txt
@@ -0,0 +1,3 @@
+list( I = 4, J = 2, K = 5,
+ X = structure(.Data = c(23, 4, 2, 2, 8, 7, 0, 1, 3, 5, 5, 11, 1, 0, 3, 13, 8, 6, 1, 0,
+ 5, 11, 2, 1, 5, 8, 7, 6, 3, 5, 16, 19, 1, 2, 3, 17, 1, 0, 1, 3), .Dim = c(4, 2, 5)))
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diff --git a/doc/Examples/Aligatorsinits.html b/doc/Examples/Aligatorsinits.html
new file mode 100755
index 0000000..1a98151
--- /dev/null
+++ b/doc/Examples/Aligatorsinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Aligatorsinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha = c(NA, 0, 0, 0, 0),<br> beta = structure(.Data = c(NA, NA, NA, NA, NA,<br> NA, 0, 0, 0, 0,<br> NA, 0, 0, 0, 0,<br> &n [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Aligatorsinits.txt b/doc/Examples/Aligatorsinits.txt
new file mode 100755
index 0000000..8adb993
--- /dev/null
+++ b/doc/Examples/Aligatorsinits.txt
@@ -0,0 +1,9 @@
+list(alpha = c(NA, 0, 0, 0, 0),
+ beta = structure(.Data = c(NA, NA, NA, NA, NA,
+ NA, 0, 0, 0, 0,
+ NA, 0, 0, 0, 0,
+ NA, 0, 0, 0, 0), .Dim = c(4, 5)),
+ gamma = structure(.Data = c(NA, NA, NA, NA, NA,
+ NA, 0, 0, 0, 0), .Dim = c(2, 5)),
+ lambda = structure(.Data = c(0, 0, 0, 0,
+ 0, 0, 0, 0), .Dim = c(4, 2)))
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diff --git a/doc/Examples/Aligatorsinits1.html b/doc/Examples/Aligatorsinits1.html
new file mode 100755
index 0000000..adacd62
--- /dev/null
+++ b/doc/Examples/Aligatorsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Aligatorsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha = c(NA, 1, 1, 1, 1),<br> beta = structure(.Data = c(NA, NA, NA, NA, NA,<br> NA, 2, 2, 2, 2,<br> NA, 2, 2, 2, 2,<br> &n [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Aligatorsinits1.txt b/doc/Examples/Aligatorsinits1.txt
new file mode 100755
index 0000000..898a79d
--- /dev/null
+++ b/doc/Examples/Aligatorsinits1.txt
@@ -0,0 +1,9 @@
+list(alpha = c(NA, 1, 1, 1, 1),
+ beta = structure(.Data = c(NA, NA, NA, NA, NA,
+ NA, 2, 2, 2, 2,
+ NA, 2, 2, 2, 2,
+ NA, 2, 2, 2, 2), .Dim = c(4, 5)),
+ gamma = structure(.Data = c(NA, NA, NA, NA, NA,
+ NA, 3, 3, 3, 3), .Dim = c(2, 5)),
+ lambda = structure(.Data = c(4, 4, 4, 4,
+ 4, 4, 4, 4), .Dim = c(4, 2)))
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diff --git a/doc/Examples/Aligatorsmodel.html b/doc/Examples/Aligatorsmodel.html
new file mode 100755
index 0000000..b31d34e
--- /dev/null
+++ b/doc/Examples/Aligatorsmodel.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Aligatorsmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># PRIORS<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha[1] <- 0; # zero contrast for baseline food<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 2 : K) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha[k] ~ dnorm(0, 0.00001) # vague priors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Loop around lakes:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1 : K){ <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta[1, k] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } # corner-point contrast with first lake <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 2 : I) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta[i, 1] <- 0 ; # zero contrast for baseline food<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 2 : K){ <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta[i, k] ~ dnorm(0, 0.00001) # vague priors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Loop around sizes:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1 : K){ <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma[1, k] <- 0 # corner-point contrast with first size <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 2 : J) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma[j, 1] <- 0 ; # zero contrast for baseline food<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for ( k in 2 : K){ <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma[j, k] ~ dnorm(0, 0.00001) # vague priors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># LIKELIHOOD <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : I) { # loop around lakes<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : J) { # loop around sizes<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Multinomial response<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># X[i,j,1 : K] ~ dmulti( p[i, j, 1 : K] , n[i, j] )<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># n[i, j] <- sum(X[i, j, ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for (k in 1 : K) { # loop around foods<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># p[i, j, k] <- phi[i, j, k] / sum(phi[i, j, ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># log(phi[i ,j, k]) <- alpha[k] + beta[i, k] + gamma[j, k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Fit standard Poisson regressions relative to baseline<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> lambda[i, j] ~ dnorm(0, 0.00001) # vague priors <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1 : K) { # loop around foods<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> X[i, j, k] ~ dpois(mu[i, j, k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> log(mu[i, j, k]) <- lambda[i, j] + alpha[k] + beta[i, k] + gamma[j, k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># TRANSFORM OUTPUT TO ENABLE COMPARISON <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># WITH AGRESTI'S RESULTS<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1 : K) { # loop around foods<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : I) { # loop around lakes<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> b[i, k] <- beta[i, k] - mean(beta[, k]); # sum to zero constraint<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : J) { # loop around sizes<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> g[j, k] <- gamma[j, k] - mean(gamma[, k]); # sum to zero constraint<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br>
</font>
</p>
</body>
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diff --git a/doc/Examples/Aligatorsmodel.txt b/doc/Examples/Aligatorsmodel.txt
new file mode 100755
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--- /dev/null
+++ b/doc/Examples/Aligatorsmodel.txt
@@ -0,0 +1,62 @@
+ model
+ {
+
+ # PRIORS
+ alpha[1] <- 0; # zero contrast for baseline food
+ for (k in 2 : K) {
+ alpha[k] ~ dnorm(0, 0.00001) # vague priors
+ }
+ # Loop around lakes:
+ for (k in 1 : K){
+ beta[1, k] <- 0
+ } # corner-point contrast with first lake
+ for (i in 2 : I) {
+ beta[i, 1] <- 0 ; # zero contrast for baseline food
+ for (k in 2 : K){
+ beta[i, k] ~ dnorm(0, 0.00001) # vague priors
+ }
+ }
+ # Loop around sizes:
+ for (k in 1 : K){
+ gamma[1, k] <- 0 # corner-point contrast with first size
+ }
+ for (j in 2 : J) {
+ gamma[j, 1] <- 0 ; # zero contrast for baseline food
+ for ( k in 2 : K){
+ gamma[j, k] ~ dnorm(0, 0.00001) # vague priors
+ }
+ }
+
+ # LIKELIHOOD
+ for (i in 1 : I) { # loop around lakes
+ for (j in 1 : J) { # loop around sizes
+
+ # Multinomial response
+ # X[i,j,1 : K] ~ dmulti( p[i, j, 1 : K] , n[i, j] )
+ # n[i, j] <- sum(X[i, j, ])
+ # for (k in 1 : K) { # loop around foods
+ # p[i, j, k] <- phi[i, j, k] / sum(phi[i, j, ])
+ # log(phi[i ,j, k]) <- alpha[k] + beta[i, k] + gamma[j, k]
+ # }
+
+ # Fit standard Poisson regressions relative to baseline
+ lambda[i, j] ~ dnorm(0, 0.00001) # vague priors
+ for (k in 1 : K) { # loop around foods
+ X[i, j, k] ~ dpois(mu[i, j, k])
+ log(mu[i, j, k]) <- lambda[i, j] + alpha[k] + beta[i, k] + gamma[j, k]
+ }
+ }
+ }
+
+ # TRANSFORM OUTPUT TO ENABLE COMPARISON
+ # WITH AGRESTI'S RESULTS
+
+ for (k in 1 : K) { # loop around foods
+ for (i in 1 : I) { # loop around lakes
+ b[i, k] <- beta[i, k] - mean(beta[, k]); # sum to zero constraint
+ }
+ for (j in 1 : J) { # loop around sizes
+ g[j, k] <- gamma[j, k] - mean(gamma[, k]); # sum to zero constraint
+ }
+ }
+ }
diff --git a/doc/Examples/Asia.html b/doc/Examples/Asia.html
new file mode 100755
index 0000000..edcf816
--- /dev/null
+++ b/doc/Examples/Asia.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Asia</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="asia0.bmp" alt="[asia0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Asia: expert system
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"><strong>Evidence propagation
</strong></font><font face="Arial" color="#000100" size="3"><br><br>Lauritzen and Spiegelhalter (1988) introduce a fictitious "expert system" representing the diagnosis of a patient presenting to a chest clinic, having just come back from a trip to Asia and showing dyspnoea (shortness-of-breath). The BUGS code is shown below and the conditional probabilities used are given in Lauritzen and Spiegelhalter (1988). Note the use of
</font><font face="Courier" color="#000100" size="3">max
</font><font face="Arial" color="#000100" size="3">to do the logical-or. The
</font><font face="Courier" color="#000100" size="3">dcat
</font><font face="Arial" color="#000100" size="3"> distribution is used to sample values with domain (1,2) with probability distribution given by the relevant entries in the conditional probability<br>tables.
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">smoking ~ dcat(p.smoking[1:2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tuberculosis ~ dcat(p.tuberculosis[asia,1:2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">lung.cancer ~ dcat(p.lung.cancer[smoking,1:2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">bronchitis ~ dcat(p.bronchitis[smoking,1:2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">either <- max(tuberculosis,lung.cancer)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">xray ~ dcat(p.xray[either,1:2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">dyspnoea ~ dcat(p.dyspnoea[either,bronchitis,1:2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Asiadata.html">Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Asiainits.html">Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Asiainits1.html">Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="5"> <br><br><center><img src="asia1.bmp" alt="[asia1]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Asiadata.html b/doc/Examples/Asiadata.html
new file mode 100755
index 0000000..35695fb
--- /dev/null
+++ b/doc/Examples/Asiadata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Asiadata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(asia = 2, dyspnoea = 2,<br> p.tuberculosis = structure(.Data = c(0.99,0.01,0.95,0.05), .Dim = c(2,2)),<br> p.bronchitis = structure(.Data = c(0.70,0.30,0.40,0.60), .Dim = c(2,2)),<br> p.smoking = c(0.50,0.50),<br> p.lung.cancer = structure(.Data = c(0.99,0.01,0.90,0.10), .Dim = c(2,2)),<br> & [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Asiadata.txt b/doc/Examples/Asiadata.txt
new file mode 100755
index 0000000..22f7d6b
--- /dev/null
+++ b/doc/Examples/Asiadata.txt
@@ -0,0 +1,10 @@
+list(asia = 2, dyspnoea = 2,
+ p.tuberculosis = structure(.Data = c(0.99,0.01,0.95,0.05), .Dim = c(2,2)),
+ p.bronchitis = structure(.Data = c(0.70,0.30,0.40,0.60), .Dim = c(2,2)),
+ p.smoking = c(0.50,0.50),
+ p.lung.cancer = structure(.Data = c(0.99,0.01,0.90,0.10), .Dim = c(2,2)),
+ p.xray = structure(.Data = c(0.95,0.05,0.02,0.98), .Dim = c(2,2)),
+ p.dyspnoea = structure(.Data = c(0.9,0.1,
+ 0.2,0.8,
+ 0.3,0.7,
+ 0.1,0.9), .Dim = c(2,2,2)))
\ No newline at end of file
diff --git a/doc/Examples/Asiainits.html b/doc/Examples/Asiainits.html
new file mode 100755
index 0000000..ac0d0a0
--- /dev/null
+++ b/doc/Examples/Asiainits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Asiainits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(smoking = 1, tuberculosis = 1, lung.cancer = 1, bronchitis = 1, xray = 1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Asiainits.txt b/doc/Examples/Asiainits.txt
new file mode 100755
index 0000000..3a8a3db
--- /dev/null
+++ b/doc/Examples/Asiainits.txt
@@ -0,0 +1 @@
+list(smoking = 1, tuberculosis = 1, lung.cancer = 1, bronchitis = 1, xray = 1)
\ No newline at end of file
diff --git a/doc/Examples/Asiainits1.html b/doc/Examples/Asiainits1.html
new file mode 100755
index 0000000..31d9ab5
--- /dev/null
+++ b/doc/Examples/Asiainits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Asiainits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(smoking = 2, tuberculosis = 2, lung.cancer = 2, bronchitis = 2, xray = 2)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Asiainits1.txt b/doc/Examples/Asiainits1.txt
new file mode 100755
index 0000000..cc7a3a5
--- /dev/null
+++ b/doc/Examples/Asiainits1.txt
@@ -0,0 +1 @@
+list(smoking = 2, tuberculosis = 2, lung.cancer = 2, bronchitis = 2, xray = 2)
\ No newline at end of file
diff --git a/doc/Examples/Asiamodel.html b/doc/Examples/Asiamodel.html
new file mode 100755
index 0000000..5c07eae
--- /dev/null
+++ b/doc/Examples/Asiamodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Asiamodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">smoking ~ dcat(p.smoking[1:2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tuberculosis ~ dcat(p.tuberculosis[asia,1:2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">lung.cancer ~ dcat(p.lung.cancer[smoking,1:2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">bronchitis ~ dcat(p.bronchitis[smoking,1:2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">either <- max(tuberculosis,lung.cancer)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">xray ~ dcat(p.xray[either,1:2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">dyspnoea ~ dcat(p.dyspnoea[either,bronchitis,1:2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Asiamodel.txt b/doc/Examples/Asiamodel.txt
new file mode 100755
index 0000000..87c56f5
--- /dev/null
+++ b/doc/Examples/Asiamodel.txt
@@ -0,0 +1,10 @@
+ model
+ {
+ smoking ~ dcat(p.smoking[1:2])
+ tuberculosis ~ dcat(p.tuberculosis[asia,1:2])
+ lung.cancer ~ dcat(p.lung.cancer[smoking,1:2])
+ bronchitis ~ dcat(p.bronchitis[smoking,1:2])
+ either <- max(tuberculosis,lung.cancer)
+ xray ~ dcat(p.xray[either,1:2])
+ dyspnoea ~ dcat(p.dyspnoea[either,bronchitis,1:2])
+ }
diff --git a/doc/Examples/Beetles.html b/doc/Examples/Beetles.html
new file mode 100755
index 0000000..b48b7cb
--- /dev/null
+++ b/doc/Examples/Beetles.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Beetles</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="beetles0.bmp" alt="[beetles0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Beetles: choice of link function
</font><font face="Arial" color="#0000FF" size="5"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="3">Dobson (1983) analyses binary dose-response data published by Bliss (1935), in which the numbers of beetles killed after 5 hour exposure to carbon disulphide at N = 8 different concentrations are recorded:<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="beetles1.bmp" alt="[beetles1]"></center><br>
</font><font face="Arial" color="#000100" size="3">We assume that the observed number of deaths r
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> at each concentration x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is binomial with sample size n
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and true rate p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">. Plausible models for pi include the logistic, probit and extreme value (complimentary log-log) models, as follows
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br> p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = exp(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) / (1 + exp(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br> p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = Phi(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">+
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br> p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = 1 - exp(-exp(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)) <br><br>The corresponding graph is shown below:<br><center>
</font><font face="Arial" color="#0000FF" size="3"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Arial" color="#000100" size="1"><img src="beetles2.bmp" alt="[beetles2]"><br></center><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for( i in 1 : N ) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">r[i] ~ dbin(p[i],n[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">cloglog(p[i]) <- alpha.star + beta * (x[i] - mean(x[]))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">rhat[i] <- n[i] * p[i]<br> cumulative.r[i] <- cumulative(r[i], r[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha <- alpha.star - beta * mean(x[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta ~ dnorm(0.0,0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha.star ~ dnorm(0.0,0.001) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br> <br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Beetlesdata.html">Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Beetlesinits.html">Inits for chain 1</a> <a href="../Examples/Beetlesinits1.html">Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><br>Logit model<br><center><br><img src="beetles3.bmp" alt="[beetles3]">
</font><font face="Arial" color="#000000" size="2"><br></center>
</font><font face="Arial" color="#000000" size="3"><br>Probit model<br><center><img src="beetles4.bmp" alt="[beetles4]"><br>
</font><font face="Arial" color="#000100" size="1"><br></center>
</font><font face="Arial" color="#000100" size="3"><br>Extreme value (cloglog) model<br><center><br>
</font><font face="Arial" color="#000100" size="1"><br><img src="beetles5.bmp" alt="[beetles5]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Beetlesdata.html b/doc/Examples/Beetlesdata.html
new file mode 100755
index 0000000..758a643
--- /dev/null
+++ b/doc/Examples/Beetlesdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Beetlesdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list( x = c(1.6907, 1.7242, 1.7552, 1.7842, 1.8113, 1.8369, 1.8610, 1.8839),<br> n = c(59, 60, 62, 56, 63, 59, 62, 60),<br> r = c(6, 13, 18, 28, 52, 53, 61, 60), N = 8)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Beetlesdata.txt b/doc/Examples/Beetlesdata.txt
new file mode 100755
index 0000000..7d04ad3
--- /dev/null
+++ b/doc/Examples/Beetlesdata.txt
@@ -0,0 +1,3 @@
+list( x = c(1.6907, 1.7242, 1.7552, 1.7842, 1.8113, 1.8369, 1.8610, 1.8839),
+ n = c(59, 60, 62, 56, 63, 59, 62, 60),
+ r = c(6, 13, 18, 28, 52, 53, 61, 60), N = 8)
\ No newline at end of file
diff --git a/doc/Examples/Beetlesinits.html b/doc/Examples/Beetlesinits.html
new file mode 100755
index 0000000..26efe25
--- /dev/null
+++ b/doc/Examples/Beetlesinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Beetlesinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha.star=0, beta=0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Beetlesinits.txt b/doc/Examples/Beetlesinits.txt
new file mode 100755
index 0000000..44a7ed9
--- /dev/null
+++ b/doc/Examples/Beetlesinits.txt
@@ -0,0 +1 @@
+list(alpha.star=0, beta=0)
\ No newline at end of file
diff --git a/doc/Examples/Beetlesinits1.html b/doc/Examples/Beetlesinits1.html
new file mode 100755
index 0000000..4016b8a
--- /dev/null
+++ b/doc/Examples/Beetlesinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Beetlesinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha.star=1, beta=1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Beetlesinits1.txt b/doc/Examples/Beetlesinits1.txt
new file mode 100755
index 0000000..3781fa0
--- /dev/null
+++ b/doc/Examples/Beetlesinits1.txt
@@ -0,0 +1 @@
+list(alpha.star=1, beta=1)
\ No newline at end of file
diff --git a/doc/Examples/Beetlesmodel.html b/doc/Examples/Beetlesmodel.html
new file mode 100755
index 0000000..9679f76
--- /dev/null
+++ b/doc/Examples/Beetlesmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Beetlesmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for( i in 1 : N ) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">r[i] ~ dbin(p[i],n[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logit(p[i]) <- alpha.star + beta * (x[i] - mean(x[]))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">rhat[i] <- n[i] * p[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha <- alpha.star - beta * mean(x[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta ~ dnorm(0.0,0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha.star ~ dnorm(0.0,0.001) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Beetlesmodel.txt b/doc/Examples/Beetlesmodel.txt
new file mode 100755
index 0000000..17b01fb
--- /dev/null
+++ b/doc/Examples/Beetlesmodel.txt
@@ -0,0 +1,11 @@
+ model
+ {
+ for( i in 1 : N ) {
+ r[i] ~ dbin(p[i],n[i])
+ logit(p[i]) <- alpha.star + beta * (x[i] - mean(x[]))
+ rhat[i] <- n[i] * p[i]
+ }
+ alpha <- alpha.star - beta * mean(x[])
+ beta ~ dnorm(0.0,0.001)
+ alpha.star ~ dnorm(0.0,0.001)
+ }
diff --git a/doc/Examples/BiRats.html b/doc/Examples/BiRats.html
new file mode 100755
index 0000000..66901c5
--- /dev/null
+++ b/doc/Examples/BiRats.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BiRats</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="birats0.bmp" alt="[birats0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Birats: a bivariate normal<br> hierarchical model
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">We return to the Rats example, and illustrate the use of a multivariate Normal (MVN) population distribution for the regression coefficients of the growth curve for each rat. This is the model adopted by Gelfand etal (1990) for these data, and assumes
</font><font face="Arial" color="#000100" size="3"><em>a priori
</em></font><font face="Arial" color="#000100" size="3"> that the intercept and slope parameters for each rat are correlated. For example, positive correlation would imply that initially heavy rats (high intercept) tend to gain weight more rapidly (steeper slope) than lighter rats. The model is as follows<br><br> Y
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3"> x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ MVN(
</font><font face="Symbol" color="#000100" size="3"><strong>m
</strong></font><font face="Symbol" color="#000100" size="2"><sub>b
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3"><strong>W
</strong></font><font face="Arial" color="#000100" size="3">) <br><br>where Y
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> is the weight of the ith rat measured at age x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">, and
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> denotes the vector
</font><font face="Symbol" color="#000100" size="3">(b
</font><font face="Arial" color="#000100" size="2"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3">). We assume 'non-informative' independent univariate Normal priors for the separate components
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Symbol" color="#000100" size="2"><sub>b
</sub></font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Symbol" color="#000100" size="2"><sub>b
</sub></font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">. A Wishart(R,
</font><font face="Symbol" color="#000100" size="3">r
</font><font face="Arial" color="#000100" size="3">) prior was specified for
</font><font face="Symbol" color="#000100" size="3"><strong>W
</strong></font><font face="Arial" color="#000100" size="3">, the population precision matrix of the regression coefficients. To represent vague prior knowledge, we chose the the degrees of freedom
</font><font face="Symbol" color="#000100" size="3">r
</font><font face="Arial" color="#000100" size="3"> for this distribution to be as small as possible (i.e. 2, the rank of
</font><font face="Symbol" color="#000100" size="3"><strong>W
</strong></font><font face="Arial" color="#000100" size="3">). The scale matrix was specified as<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="birats1.bmp" alt="[birats1]">
</font><font face="Arial" color="#000100" size="3"><br></center>This represents our prior guess at the order of magnitude of the
</font><font face="Arial" color="#000100" size="3"><em>covariance
</em></font><font face="Arial" color="#000100" size="3"> matrix
</font><font face="Symbol" color="#000100" size="3"><strong>W
</strong></font><font face="Arial" color="#000100" size="2"><sup>-1
</sup></font><font face="Arial" color="#000100" size="3"> for
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> (see Classic BUGS manual (version 0.5) section on Multivariate normal models), and is equivalent to the prior specification used by Gelfand et al. Finally, a non-informative Gamma(0.001, 0.001) prior was assumed for the measurement precision
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3">.<br><center><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1"><img src="birats2.bmp" alt="[birats2]">
</font><font face="Arial" color="#000100" size="5"><strong><br></center><br>
</strong></font><font face="Arial" color="#000100" size="3"> model<br> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for( i in 1 : N ) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta[i , 1 : 2] ~ dmnorm(mu.beta[], R[ , ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for( j in 1 : T ) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Y[i, j] ~ dnorm(mu[i , j], tauC)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i, j] <- beta[i, 1] + beta[i, 2] * x[j]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu.beta[1 : 2] ~ dmnorm(mean[], prec[ , ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">R[1 : 2 , 1 : 2] ~ dwish(Omega[ , ], 2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tauC ~ dgamma(0.001, 0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma <- 1 / sqrt(tauC)<br> }<br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/BiRatsdata.html">Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/BiRatsinits.html">Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/BiRatsinits1.html">Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="2"><br> <br>
</font><font face="Arial" color="#0000FF" size="5">Results <br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center><br><img src="birats3.bmp" alt="[birats3]">
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/BiRatsdata.html b/doc/Examples/BiRatsdata.html
new file mode 100755
index 0000000..679b305
--- /dev/null
+++ b/doc/Examples/BiRatsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BiRatsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"> list(x = c(8.0, 15.0, 22.0, 29.0, 36.0), N = 30, T = 5,<br> Omega = structure(.Data = c(200, 0, 0, 0.2), .Dim = c(2, 2)), <br> mean = c(0,0),<br> prec = structure(.Data = c(1.0E-6, 0, 0, 1.0E-6), .Dim = c(2, 2)),<br> Y = structure(<br> &nb [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/BiRatsdata.txt b/doc/Examples/BiRatsdata.txt
new file mode 100755
index 0000000..3406cd5
--- /dev/null
+++ b/doc/Examples/BiRatsdata.txt
@@ -0,0 +1,36 @@
+ list(x = c(8.0, 15.0, 22.0, 29.0, 36.0), N = 30, T = 5,
+ Omega = structure(.Data = c(200, 0, 0, 0.2), .Dim = c(2, 2)),
+ mean = c(0,0),
+ prec = structure(.Data = c(1.0E-6, 0, 0, 1.0E-6), .Dim = c(2, 2)),
+ Y = structure(
+ .Data = c(151, 199, 246, 283, 320,
+ 145, 199, 249, 293, 354,
+ 147, 214, 263, 312, 328,
+ 155, 200, 237, 272, 297,
+ 135, 188, 230, 280, 323,
+ 159, 210, 252, 298, 331,
+ 141, 189, 231, 275, 305,
+ 159, 201, 248, 297, 338,
+ 177, 236, 285, 350, 376,
+ 134, 182, 220, 260, 296,
+ 160, 208, 261, 313, 352,
+ 143, 188, 220, 273, 314,
+ 154, 200, 244, 289, 325,
+ 171, 221, 270, 326, 358,
+ 163, 216, 242, 281, 312,
+ 160, 207, 248, 288, 324,
+ 142, 187, 234, 280, 316,
+ 156, 203, 243, 283, 317,
+ 157, 212, 259, 307, 336,
+ 152, 203, 246, 286, 321,
+ 154, 205, 253, 298, 334,
+ 139, 190, 225, 267, 302,
+ 146, 191, 229, 272, 302,
+ 157, 211, 250, 285, 323,
+ 132, 185, 237, 286, 331,
+ 160, 207, 257, 303, 345,
+ 169, 216, 261, 295, 333,
+ 157, 205, 248, 289, 316,
+ 137, 180, 219, 258, 291,
+ 153, 200, 244, 286, 324),
+ .Dim = c(30,5)))
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diff --git a/doc/Examples/BiRatsinits.html b/doc/Examples/BiRatsinits.html
new file mode 100755
index 0000000..6b0e927
--- /dev/null
+++ b/doc/Examples/BiRatsinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BiRatsinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"> list(mu.beta = c(0,0), tauC = 1,<br> beta = structure(<br> .Data = c(100,6,100,6,100,6,100,6,100,6,<br> 100,6,100,6,100,6,100,6,100,6,<br> 100,6,100,6,100,6,100,6,100,6,<br> 100,6,100,6,100,6,100,6,100,6,<br> [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/BiRatsinits.txt b/doc/Examples/BiRatsinits.txt
new file mode 100755
index 0000000..2858af9
--- /dev/null
+++ b/doc/Examples/BiRatsinits.txt
@@ -0,0 +1,10 @@
+ list(mu.beta = c(0,0), tauC = 1,
+ beta = structure(
+ .Data = c(100,6,100,6,100,6,100,6,100,6,
+ 100,6,100,6,100,6,100,6,100,6,
+ 100,6,100,6,100,6,100,6,100,6,
+ 100,6,100,6,100,6,100,6,100,6,
+ 100,6,100,6,100,6,100,6,100,6,
+ 100,6,100,6,100,6,100,6,100,6),
+ .Dim = c(30, 2)),
+ R = structure(.Data = c(1,0,0,1), .Dim = c(2, 2)))
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diff --git a/doc/Examples/BiRatsinits1.html b/doc/Examples/BiRatsinits1.html
new file mode 100755
index 0000000..bf8d5ac
--- /dev/null
+++ b/doc/Examples/BiRatsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BiRatsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(mu.beta = c(10,10), tauC = 0.1,<br> beta = structure(<br> .Data = c(50,3,50,3,50,3,50,3,50,3,<br> 50,3,50,3,50,3,50,3,50,3,<br> 50,3,50,3,50,3,50,3,50,3,<br> 50,3,50,3,50,3,50,3,50,3,<br> 50,3,50,3, [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/BiRatsinits1.txt b/doc/Examples/BiRatsinits1.txt
new file mode 100755
index 0000000..32bf4f1
--- /dev/null
+++ b/doc/Examples/BiRatsinits1.txt
@@ -0,0 +1,10 @@
+list(mu.beta = c(10,10), tauC = 0.1,
+ beta = structure(
+ .Data = c(50,3,50,3,50,3,50,3,50,3,
+ 50,3,50,3,50,3,50,3,50,3,
+ 50,3,50,3,50,3,50,3,50,3,
+ 50,3,50,3,50,3,50,3,50,3,
+ 50,3,50,3,50,3,50,3,50,3,
+ 50,3,50,3,50,3,50,3,50,3),
+ .Dim = c(30, 2)),
+ R = structure(.Data = c(3,0,0,3), .Dim = c(2, 2)))
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diff --git a/doc/Examples/BiRatsmodel.html b/doc/Examples/BiRatsmodel.html
new file mode 100755
index 0000000..5207645
--- /dev/null
+++ b/doc/Examples/BiRatsmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BiRatsmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for( i in 1 : N ) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta[i , 1 : 2] ~ dmnorm(mu.beta[], R[ , ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for( j in 1 : T ) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Y[i, j] ~ dnorm(mu[i , j], tauC)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i, j] <- beta[i, 1] + beta[i, 2] * x[j]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu.beta[1 : 2] ~ dmnorm(mean[], prec[ , ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">R[1 : 2 , 1 : 2] ~ dwish(Omega[ , ], 2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tauC ~ dgamma(0.001, 0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma <- 1 / sqrt(tauC)<br> }<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/BiRatsmodel.txt b/doc/Examples/BiRatsmodel.txt
new file mode 100755
index 0000000..8f0c48b
--- /dev/null
+++ b/doc/Examples/BiRatsmodel.txt
@@ -0,0 +1,15 @@
+ model
+ {
+ for( i in 1 : N ) {
+ beta[i , 1 : 2] ~ dmnorm(mu.beta[], R[ , ])
+ for( j in 1 : T ) {
+ Y[i, j] ~ dnorm(mu[i , j], tauC)
+ mu[i, j] <- beta[i, 1] + beta[i, 2] * x[j]
+ }
+ }
+
+ mu.beta[1 : 2] ~ dmnorm(mean[], prec[ , ])
+ R[1 : 2 , 1 : 2] ~ dwish(Omega[ , ], 2)
+ tauC ~ dgamma(0.001, 0.001)
+ sigma <- 1 / sqrt(tauC)
+ }
diff --git a/doc/Examples/Biopsies.html b/doc/Examples/Biopsies.html
new file mode 100755
index 0000000..6708616
--- /dev/null
+++ b/doc/Examples/Biopsies.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Biopsies</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="biopsies0.bmp" alt="[biopsies0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Biopsies: discrete variable<br> latent class model
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">Spiegelhalter and Stovin (1983) presented data on repeated biopsies of transplanted hearts, in which a total of 414 biopsies had been taken at 157 sessions. Each biopsy was graded on evidence of rejection using a 4 category scale of none (O), minimal (M), mild (+) and moderate-severe (++). Part of the data is shown below.<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="biopsies1.bmp" alt="[biopsies1]"><br></center>
</font><font face="Arial" color="#000100" size="3">The sampling procedure may not detect the area of maximum rejection, which is considered the true underlying state at the time of the session and denoted t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> --- the underlying probability distribution of the four true states is denoted by the vector p. It is then assumed that each of the observed biopsies are conditionally independent given this truestate with the restriction that there are no`false positives': i.e. one cannot observe a biopsy worse than the true state. We then have the sampling model <br><br> b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Multinomial(e
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br><br> t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Categorical(p)<br><br><br>where b
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> denotes the multinomial response at session
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> where n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> biopsies have been taken, and e
</font><font face="Arial" color="#000100" size="3"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3"> is the probability that a true state t
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = j generates a biopsy in state k.The no-false-positive restriction means that e
</font><font face="Arial" color="#000100" size="2"><sub>12
</sub></font><font face="Arial" color="#000100" size="3"> = e
</font><font face="Arial" color="#000100" size="2"><sub>13
</sub></font><font face="Arial" color="#000100" size="3"> = e
</font><font face="Arial" color="#000100" size="2"><sub>14
</sub></font><font face="Arial" color="#000100" size="3"> = e
</font><font face="Arial" color="#000100" size="2"><sub>23
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">= e
</font><font face="Arial" color="#000100" size="2"><sub>24
</sub></font><font face="Arial" color="#000100" size="3"> = e
</font><font face="Arial" color="#000100" size="2"><sub>34
</sub></font><font face="Arial" color="#000100" size="3"> = 0. Spiegelhalter and Stovin (1983) estimated the parameters e
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> and p using the EM algorithm, with some smoothing to avoid zero estimates.<br><br>The appropriate graph is shown below, where the role of the true state t
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is simply to pick the appropriate row from the 4 x 4 error matrix e. Here the probability vectors e
</font><font face="Arial" color="#000100" size="2">j
</font><font face="Arial" color="#000100" size="3"> (j = 1,...,4) and p are assumed to have uniform priors on the unit simplex, which correspond to Dirichlet priors with all parameters being 1.<br><br>The BUGS code for this model is given below. No initial values are provided for the latent states, since the forward sampling procedure will find a configuration of starting values that is compatible with the expressed constraints. We also note the apparent ``cycle'' in the graph created by [...]
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1 : ns){<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">nbiops[i] <- sum(biopsies[i, ]) <br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">true[i] ~ dcat(p[])<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">biopsies[i, 1 : 4] ~ dmulti(error[true[i], ], nbiops[i])<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">error[2,1 : 2] ~ ddirich(prior[1 : 2])<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">error[3,1 : 3] ~ ddirich(prior[1 : 3])<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">error[4,1 : 4] ~ ddirich(prior[1 : 4])<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">p[1 : 4] ~ ddirich(prior[]); # prior for p<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Biopsiesdata.html">Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Biopsiesinits.html">Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Biopsiesinits1.html">Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center><br><img src="biopsies2.bmp" alt="[biopsies2]">
</font><font face="Arial" color="#000000" size="2"><br>
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Biopsiesdata.html b/doc/Examples/Biopsiesdata.html
new file mode 100755
index 0000000..689447b
--- /dev/null
+++ b/doc/Examples/Biopsiesdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Biopsiesdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(ns = 157,<br> error = structure(.Data = c(1, 0, 0, 0,<br>NA, NA, 0, 0,<br> NA, NA, NA, 0,<br> NA, NA, NA, NA), .Dim = c(4, 4)),<br> prior = c(1, 1, 1, 1), [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Biopsiesdata.txt b/doc/Examples/Biopsiesdata.txt
new file mode 100755
index 0000000..4f9d57e
--- /dev/null
+++ b/doc/Examples/Biopsiesdata.txt
@@ -0,0 +1,165 @@
+list(ns = 157,
+ error = structure(.Data = c(1, 0, 0, 0,
+ NA, NA, 0, 0,
+ NA, NA, NA, 0,
+ NA, NA, NA, NA), .Dim = c(4, 4)),
+ prior = c(1, 1, 1, 1),
+ biopsies = structure(.Data = c(
+ 2,0,0,0,
+ 2,0,0,0,
+ 2,0,0,0,
+ 2,0,0,0,
+ 2,0,0,0,
+ 2,0,0,0,
+ 2,0,0,0,
+ 2,0,0,0,
+ 2,0,0,0,
+ 2,0,0,0,
+ 2,0,0,0,
+ 2,0,0,0,
+ 1,1,0,0,
+ 1,1,0,0,
+ 1,1,0,0,
+ 1,1,0,0,
+ 1,1,0,0,
+ 1,1,0,0,
+ 1,1,0,0,
+ 1,1,0,0,
+ 1,1,0,0,
+ 1,1,0,0,
+ 0,2,0,0,
+ 0,2,0,0,
+ 0,2,0,0,
+ 0,2,0,0,
+ 1,0,1,0,
+ 1,0,1,0,
+ 1,0,1,0,
+ 1,0,1,0,
+ 1,0,1,0,
+ 1,0,1,0,
+ 1,0,1,0,
+ 1,0,1,0,
+ 1,0,1,0,
+ 0,0,2,0,
+ 0,0,2,0,
+ 0,0,2,0,
+ 0,0,2,0,
+ 0,0,2,0,
+ 0,0,2,0,
+ 0,0,2,0,
+ 0,0,2,0,
+ 0,0,2,0,
+ 0,0,2,0,
+ 0,0,2,0,
+ 0,0,2,0,
+ 1,0,0,1,
+ 0,0,1,1,
+ 0,0,1,1,
+ 0,0,1,1,
+ 0,0,0,2,
+ 0,0,0,2,
+ 0,0,0,2,
+ 0,0,0,2,
+ 0,0,0,2,
+ 0,0,0,2,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 3,0,0,0,
+ 2,1,0,0,
+ 2,1,0,0,
+ 2,1,0,0,
+ 2,1,0,0,
+ 2,1,0,0,
+ 2,1,0,0,
+ 2,1,0,0,
+ 2,1,0,0,
+ 2,1,0,0,
+ 2,1,0,0,
+ 2,1,0,0,
+ 2,1,0,0,
+ 2,1,0,0,
+ 1,2,0,0,
+ 1,2,0,0,
+ 1,2,0,0,
+ 1,2,0,0,
+ 1,2,0,0,
+ 1,2,0,0,
+ 1,2,0,0,
+ 1,2,0,0,
+ 1,2,0,0,
+ 1,2,0,0,
+ 0,3,0,0,
+ 2,0,1,0,
+ 2,0,1,0,
+ 2,0,1,0,
+ 2,0,1,0,
+ 2,0,1,0,
+ 2,0,1,0,
+ 2,0,1,0,
+ 2,0,1,0,
+ 2,0,1,0,
+ 1,1,1,0,
+ 0,2,1,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 1,0,2,0,
+ 0,1,2,0,
+ 0,0,3,0,
+ 0,0,3,0,
+ 0,0,3,0,
+ 0,0,3,0,
+ 0,0,3,0,
+ 0,0,3,0,
+ 0,0,3,0,
+ 0,0,3,0,
+ 2,0,0,1,
+ 1,0,1,1,
+ 0,0,2,1,
+ 0,0,1,2,
+ 0,0,1,2,
+ 0,0,1,2,
+ 0,0,0,3,
+ 0,0,0,3,
+ 0,0,0,3,
+ 0,0,0,3,
+ 0,0,0,3
+ ), .Dim = c(157, 4)))
diff --git a/doc/Examples/Biopsiesinits.html b/doc/Examples/Biopsiesinits.html
new file mode 100755
index 0000000..3c8a061
--- /dev/null
+++ b/doc/Examples/Biopsiesinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Biopsiesinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(p = c(0.25, 0.25, 0.25, 0.25),<br>error = structure(.Data = c(NA, NA, NA, NA,<br>0.5, 0.5, NA, NA,<br> 0.33333333, 0.33333333,0.33333333, NA,<br> [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Biopsiesinits.txt b/doc/Examples/Biopsiesinits.txt
new file mode 100755
index 0000000..399575e
--- /dev/null
+++ b/doc/Examples/Biopsiesinits.txt
@@ -0,0 +1,5 @@
+list(p = c(0.25, 0.25, 0.25, 0.25),
+ error = structure(.Data = c(NA, NA, NA, NA,
+ 0.5, 0.5, NA, NA,
+ 0.33333333, 0.33333333,0.33333333, NA,
+ 0.25, 0.25, 0.25, 0.25), .Dim = c(4, 4)))
\ No newline at end of file
diff --git a/doc/Examples/Biopsiesinits1.html b/doc/Examples/Biopsiesinits1.html
new file mode 100755
index 0000000..a0865fe
--- /dev/null
+++ b/doc/Examples/Biopsiesinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Biopsiesinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(p = c(0.4, 0.1, 0.1, 0.4),<br>error = structure(.Data = c(NA, NA, NA, NA,<br>0.7, 0.3, NA, NA,<br> 0.2, 0.3,0.5, NA,<br> 0 [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Biopsiesinits1.txt b/doc/Examples/Biopsiesinits1.txt
new file mode 100755
index 0000000..44002ce
--- /dev/null
+++ b/doc/Examples/Biopsiesinits1.txt
@@ -0,0 +1,5 @@
+list(p = c(0.4, 0.1, 0.1, 0.4),
+ error = structure(.Data = c(NA, NA, NA, NA,
+ 0.7, 0.3, NA, NA,
+ 0.2, 0.3,0.5, NA,
+ 0.1, 0.1, 0.1, 0.7), .Dim = c(4, 4)))
\ No newline at end of file
diff --git a/doc/Examples/Biopsiesmodel.html b/doc/Examples/Biopsiesmodel.html
new file mode 100755
index 0000000..1f5dffb
--- /dev/null
+++ b/doc/Examples/Biopsiesmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Biopsiesmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1 : ns){<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">nbiops[i] <- sum(biopsies[i, ]) <br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">true[i] ~ dcat(p[])<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">biopsies[i, 1 : 4] ~ dmulti(error[true[i], ], nbiops[i])<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">error[2,1 : 2] ~ ddirich(prior[1 : 2])<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">error[3,1 : 3] ~ ddirich(prior[1 : 3])<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">error[4,1 : 4] ~ ddirich(prior[1 : 4])<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">p[1 : 4] ~ ddirich(prior[]); # prior for p<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">}<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Biopsiesmodel.txt b/doc/Examples/Biopsiesmodel.txt
new file mode 100755
index 0000000..1577dab
--- /dev/null
+++ b/doc/Examples/Biopsiesmodel.txt
@@ -0,0 +1,12 @@
+ model
+ {
+ for (i in 1 : ns){
+ nbiops[i] <- sum(biopsies[i, ])
+ true[i] ~ dcat(p[])
+ biopsies[i, 1 : 4] ~ dmulti(error[true[i], ], nbiops[i])
+ }
+ error[2,1 : 2] ~ ddirich(prior[1 : 2])
+ error[3,1 : 3] ~ ddirich(prior[1 : 3])
+ error[4,1 : 4] ~ ddirich(prior[1 : 4])
+ p[1 : 4] ~ ddirich(prior[]); # prior for p
+ }
diff --git a/doc/Examples/Birds.html b/doc/Examples/Birds.html
new file mode 100755
index 0000000..5c3b7af
--- /dev/null
+++ b/doc/Examples/Birds.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Birds</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><strong><img src="birds0.bmp" alt="[birds0]">
</strong></font><font face="Courier New" color="#000100" size="6"> Birds: species richness,estimating<br> the size of a Closed "Population"<br> with individual heterogeneity in<br>detection probability
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#000100" size="6"> <br> (contributed by Marc Kery)<br>
</font><font face="Arial" color="#000100" size="3"><br>This example expands on the previous example of estimating the size of a closed population by allowing for each individual to have its own detection probability. Let J denote the number of sample occasions. The observations are the number of encounters (out of J samples) on each of n individuals, y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> for i =1, 2,...,nind. We suppose that, for each individual in the population, <br><br> logit(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) ~ Normal(mu, tau) for i = 1, 2, ...., N <br><br>where N is the total number of individuals in the population. This model is sometimes referred to as a "Model Mh" in the jargon of capture-recapture. A large number of mixture models have been suggested for this situation (see Pledger 2000; Coull and Agresti 1999; Dorazio and Royle 2003). See Link (2003) for additional context. One area of widespread use f [...]
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, J)<br> logit(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) ~Normal(mu, tau) for i = 1, 2, ...., N <br> <br>However, N is unknown, so that the number of y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = 0 "observations", that is, the number of species that are present in the community but were not detected, is also unknown. As in the closed population size estimation example, we deal with unknown-N by data augmentation. Data augmentation -- For analysis by data augmentation, we introduce excess zero "observations" y
</font><font face="Arial" color="#000100" size="2"><sub>n +1
</sub></font><font face="Arial" color="#000100" size="3">= 0,...,y
</font><font face="Arial" color="#000100" size="2"><sub>M
</sub></font><font face="Arial" color="#000100" size="3"> = 0, and a set of latent indicator variables z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">; i = 1,2,...,M with <br><br> z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli(psi). <br><br>If z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = 1, then element i of the list corresponds to a member of the population of size N, and if <br>z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = 0, it is an excess 0 relative to the binomial model. M is set arbitrarily large. It can be motivated as the upper limit of a discrete uniform prior for N. That is, <br><br> N ~ dunif(0 ,M). <br> <br>The model for the augmented data is: <br><br> z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli(psi) <br> y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">* p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, J) # zero-inflation accomplished by z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> * p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> <br> logit(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) ~ Normal(mu, tau) for i = 1, 2, ...., M # note upper bound here is M not N <br> <br>Prior distributions are: <br><br> psi ~ unif(0, 1) <br> mu ~ dnorm(0, 0.001) <br> tau ~ dgamma(0.001, 0.001) <br> <br>Comments: <br>(1) The population size parameter is a derived parameter: N =
</font><font face="Symbol" color="#000100" size="5">S
</font><font face="Arial" color="#000100" size="3"> z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">. <br>(2) This model is precisely a zero-inflated binomial mixture model. Likelihood analysis of this model is also straightforward (Coull and Agresti 1999; Royle 2006). <br>(3) We have assumed here that individual detection probabilities do not vary over time, but the example here can be easily modified to allow such generality, by formulating the binomial observation model in terms of its individual Bernoulli components. In the su [...]
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = 0 individuals. <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># prior distributions <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">psi~dunif(0,1) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu~dnorm(0,0.001) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau~dgamma(.001,.001) # zero-inflated binomial mixture model for <br> # the augmented data <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(i in 1: nind + nz){ <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">z[i] ~ dbern(psi) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">eta[i]~ dnorm(mu, tau) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logit(p[i])<- eta[i] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">muy[i]<-p[i] * z[i] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">y[i] ~ dbin(muy[i], J) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Derived parameters <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">N<-sum(z[1 : nind + nz]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma<-sqrt(1 / tau) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Birdsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Birdsinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="3"> </a>
</font><font face="Arial" color="#0000FF" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Birdsinits2.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u><br>
</u></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="3"> <br>Two chains were run for 11000 iterations which produced the following estimates: <br><center><br><img src="birds1.bmp" alt="[birds1]"><br></center><br>The posterior distribution of N is shown below. We see that M was probably excessive and we could save some computational effort by reducing the number of zero observations added to the data set. <br><br><img src="birds2.bmp" alt="[birds2]">
</font>
</p>
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diff --git a/doc/Examples/Birdsdata.html b/doc/Examples/Birdsdata.html
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+++ b/doc/Examples/Birdsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Birdsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(y= c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 7, 7, 7, 8, 8, 9, 10, 10, 11, 11, 11, 11, 12, 12, 12, 12, 14, 16, 16, 17, 17, 17, 18, 19, 20, 21, 25, 26, 28, 30, 36, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Birdsdata.txt b/doc/Examples/Birdsdata.txt
new file mode 100755
index 0000000..23e8adf
--- /dev/null
+++ b/doc/Examples/Birdsdata.txt
@@ -0,0 +1 @@
+list(y= c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 7, 7, 7, 8, 8, 9, 10, 10, 11, 11, 11, 11, 12, 12, 12, 12, 14, 16, 16, 17, 17, 17, 18, 19, 20, 21, 25, 26, 28, 30, 36, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 [...]
diff --git a/doc/Examples/Birdsinits1.html b/doc/Examples/Birdsinits1.html
new file mode 100755
index 0000000..770dcfd
--- /dev/null
+++ b/doc/Examples/Birdsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Birdsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(mu = 0, tau = 1, psi = 0.5,<br>z = c(1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1,1, 1, 1, 1, 1, 1,<br>0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,<br>0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,<br>0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,<br>0, 0, 0, 0, [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Birdsinits1.txt b/doc/Examples/Birdsinits1.txt
new file mode 100755
index 0000000..9890c20
--- /dev/null
+++ b/doc/Examples/Birdsinits1.txt
@@ -0,0 +1,18 @@
+list(mu = 0, tau = 1, psi = 0.5,
+z = c(1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,
+1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,
+1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,
+1, 1, 1, 1, 1,1, 1, 1, 1, 1, 1,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0))
diff --git a/doc/Examples/Birdsinits2.html b/doc/Examples/Birdsinits2.html
new file mode 100755
index 0000000..f778210
--- /dev/null
+++ b/doc/Examples/Birdsinits2.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Birdsinits2</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(mu = 2, tau = 0.1, psi = 0.9,<br>z = c(1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1,1, 1, 1, 1, 1, 1,<br>0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,<br>0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,<br>0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,<br>0, 0, 0, 0 [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Birdsinits2.txt b/doc/Examples/Birdsinits2.txt
new file mode 100755
index 0000000..df1e540
--- /dev/null
+++ b/doc/Examples/Birdsinits2.txt
@@ -0,0 +1,18 @@
+list(mu = 2, tau = 0.1, psi = 0.9,
+z = c(1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,
+1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,
+1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,1, 1, 1, 1, 1,
+1, 1, 1, 1, 1,1, 1, 1, 1, 1, 1,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,0, 0, 0, 0, 0,
+0, 0, 0, 0, 0,0, 0, 0, 0, 0))
diff --git a/doc/Examples/Birdsmodel.html b/doc/Examples/Birdsmodel.html
new file mode 100755
index 0000000..fd7279b
--- /dev/null
+++ b/doc/Examples/Birdsmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Birdsmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># prior distributions <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">psi~dunif(0,1) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu~dnorm(0,0.001) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau~dgamma(.001,.001) # zero-inflated binomial mixture model for <br> # the augmented data <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(i in 1: nind + nz){ <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">z[i] ~ dbin(psi,1) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">eta[i]~ dnorm(mu, tau) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logit(p[i])<- eta[i] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">muy[i]<-p[i] * z[i] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">y[i] ~ dbin(muy[i], J) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Derived parameters <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">N<-sum(z[1 : nind+nz]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma<-sqrt(1 /tau) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br>
</font>
</p>
</body>
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diff --git a/doc/Examples/Birdsmodel.txt b/doc/Examples/Birdsmodel.txt
new file mode 100755
index 0000000..0d3a647
--- /dev/null
+++ b/doc/Examples/Birdsmodel.txt
@@ -0,0 +1,18 @@
+
+ model {
+ # prior distributions
+ psi~dunif(0,1)
+ mu~dnorm(0,0.001)
+ tau~dgamma(.001,.001) # zero-inflated binomial mixture model for
+ # the augmented data
+ for(i in 1: nind + nz){
+ z[i] ~ dbin(psi,1)
+ eta[i]~ dnorm(mu, tau)
+ logit(p[i])<- eta[i]
+ muy[i]<-p[i] * z[i]
+ y[i] ~ dbin(muy[i], J)
+ }
+ # Derived parameters
+ N<-sum(z[1 : nind+nz])
+ sigma<-sqrt(1 /tau)
+ }
diff --git a/doc/Examples/Blockers.html b/doc/Examples/Blockers.html
new file mode 100755
index 0000000..f2ad72c
--- /dev/null
+++ b/doc/Examples/Blockers.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Blockers</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="blockers0.bmp" alt="[blockers0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Blocker: random effects <br> meta-analysis of clinical<br> trials
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">Carlin (1992) considers a Bayesian approach to meta-analysis, and includes the following examples of 22 trials of beta-blockers to prevent mortality after myocardial infarction.<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="blockers1.bmp" alt="[blockers1]"></center>
</font><font face="Arial" color="#000100" size="3"><br>In a random effects meta-analysis we assume the true effect (on a log-odds scale)
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> in a trial
</font><font face="Arial" color="#000100" size="3"><em> i
</em></font><font face="Arial" color="#000100" size="3">is drawn from some population distribution.Let r
</font><font face="Arial" color="#000100" size="2"><sup>C
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> denote number of events in the control group in trial
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">, and r
</font><font face="Arial" color="#000100" size="2"><sup>T
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> denote events under active treatment in trial
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">. Our model is:<br> <br> r
</font><font face="Arial" color="#000100" size="2"><sup>C
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(p
</font><font face="Arial" color="#000100" size="2"><sup>C
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, n
</font><font face="Arial" color="#000100" size="2"><sup>C
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br> r
</font><font face="Arial" color="#000100" size="2"><sup>T
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(p
</font><font face="Arial" color="#000100" size="2"><sup>T
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, n
</font><font face="Arial" color="#000100" size="2"><sup>T
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br> logit(p
</font><font face="Arial" color="#000100" size="2"><sup>C
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub><br> <br>
</sub></font><font face="Arial" color="#000100" size="3">logit(p
</font><font face="Arial" color="#000100" size="2"><sup>T
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub><br> <br>
</sub></font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Normal(d,
</font><font face="Symbol" color="#000100" size="3"> t
</font><font face="Arial" color="#000100" size="3">)<br><br>``Noninformative'' priors are given for the
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">'s.
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> and d. The graph for this model is shown in below. We want to make inferences about the population effect d, and the predictive distribution for the effect
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>new
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">in a new trial.
</font><font face="Arial" color="#000100" size="3"><em>Empirical Bayes
</em></font><font face="Arial" color="#000100" size="3">methods estimate d and
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> by maximum likelihood and use these estimates to form the predictive distribution p(
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>new
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">| d
</font><font face="Arial" color="#000100" size="2"><sub>hat
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>hat
</sub></font><font face="Arial" color="#000100" size="3"> ).
</font><font face="Arial" color="#000100" size="3"><em>Full Bayes
</em></font><font face="Arial" color="#000100" size="3"> allows for the uncertainty concerning d and
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">. <br><br>
</font><font face="Arial" color="#0000FF" size="5"><strong><center>
</strong></font><font face="Arial" color="#000100" size="3"><em>Graphical model for blocker example:<br>
</em></font><font face="Arial" color="#0000FF" size="3"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="5"><strong><img src="blockers2.bmp" alt="[blockers2]">
</strong></font><font face="Arial" color="#000100" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><br>BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for blocker example:
</em></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1"><br><br><br></center><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for( i in 1 : Num ) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">rc[i] ~ dbin(pc[i], nc[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">rt[i] ~ dbin(pt[i], nt[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logit(pc[i]) <- mu[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logit(pt[i]) <- mu[i] + delta[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i] ~ dnorm(0.0,1.0E-5)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">delta[i] ~ dnorm(d, tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">d ~ dnorm(0.0,1.0E-6)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau ~ dgamma(0.001,0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">delta.new ~ dnorm(d, tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma <- 1 / sqrt(tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Blockersdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#000100" size="3"></a> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Blockersinits.html">Inits for chain 1 </a> <a href="../Examples/Blockersinits1.html">Inits for chain 2 </a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center><br><img src="blockers3.bmp" alt="[blockers3]"><br>
</font><font face="Arial" color="#000100" size="1"><br></center>
</font><font face="Arial" color="#000100" size="3">Our estimates are lower and with tighter precision - in fact similar to the values obtained by Carlin for the empirical Bayes estimator. The discrepancy appears to be due to Carlin's use of a uniform prior for
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> in his analysis, which will lead to increased posterior mean and standard deviation for d, as compared to our (approximate) use of p(
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">) ~ 1 /
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"><sup>
</sup></font><font face="Arial" color="#000100" size="3">(see his Figure 1).<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3">In some circumstances it might be reasonable to assume that the population distribution has heavier tails, for example a t distribution with low degrees of freedom. This is easily accomplished in
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> by using the dt distribution function instead of dnorm for
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="3"><sub>new
</sub></font><font face="Arial" color="#000100" size="3">.
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1"><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Blockersdata.html b/doc/Examples/Blockersdata.html
new file mode 100755
index 0000000..fc50dab
--- /dev/null
+++ b/doc/Examples/Blockersdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Blockersdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(rt = c(3, 7, 5, 102, 28, 4, 98, 60, 25, 138, 64, 45, 9, 57, 25, 33, 28, 8, 6, 32, 27, 22 ),<br> nt = c(38, 114, 69, 1533, 355, 59, 945, 632, 278,1916, 873, 263, 291, 858, 154, 207, 251, 151, 174, 209, 391, 680),<br> rc = c(3, 14, 11, 127, 27, 6, 152, 48, 37, 188, 52, 47, 16, 45, 31, 38, 12, 6, 3, 40, 43, 39),<br> nc = c(39, 116, 93, 1520 [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Blockersdata.txt b/doc/Examples/Blockersdata.txt
new file mode 100755
index 0000000..45cea22
--- /dev/null
+++ b/doc/Examples/Blockersdata.txt
@@ -0,0 +1,5 @@
+list(rt = c(3, 7, 5, 102, 28, 4, 98, 60, 25, 138, 64, 45, 9, 57, 25, 33, 28, 8, 6, 32, 27, 22 ),
+ nt = c(38, 114, 69, 1533, 355, 59, 945, 632, 278,1916, 873, 263, 291, 858, 154, 207, 251, 151, 174, 209, 391, 680),
+ rc = c(3, 14, 11, 127, 27, 6, 152, 48, 37, 188, 52, 47, 16, 45, 31, 38, 12, 6, 3, 40, 43, 39),
+ nc = c(39, 116, 93, 1520, 365, 52, 939, 471, 282, 1921, 583, 266, 293, 883, 147, 213, 122, 154, 134, 218, 364, 674),
+ Num = 22)
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diff --git a/doc/Examples/Blockersinits.html b/doc/Examples/Blockersinits.html
new file mode 100755
index 0000000..7bea02b
--- /dev/null
+++ b/doc/Examples/Blockersinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Blockersinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list
</font><font face="Arial" color="#000100" size="1">(d = 0, delta.new = 0, tau=1, mu = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),<br> delta = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Blockersinits.txt b/doc/Examples/Blockersinits.txt
new file mode 100755
index 0000000..63733fb
--- /dev/null
+++ b/doc/Examples/Blockersinits.txt
@@ -0,0 +1,2 @@
+list(d = 0, delta.new = 0, tau=1, mu = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
+ delta = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
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diff --git a/doc/Examples/Blockersinits1.html b/doc/Examples/Blockersinits1.html
new file mode 100755
index 0000000..83759cd
--- /dev/null
+++ b/doc/Examples/Blockersinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Blockersinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list
</font><font face="Arial" color="#000100" size="1">(d = 2, delta.new = 2, tau=0.1, mu = c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2),<br> delta = c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2))
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Blockersinits1.txt b/doc/Examples/Blockersinits1.txt
new file mode 100755
index 0000000..94bb709
--- /dev/null
+++ b/doc/Examples/Blockersinits1.txt
@@ -0,0 +1,2 @@
+list(d = 2, delta.new = 2, tau=0.1, mu = c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2),
+ delta = c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2))
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diff --git a/doc/Examples/Blockersmodel.html b/doc/Examples/Blockersmodel.html
new file mode 100755
index 0000000..2a42329
--- /dev/null
+++ b/doc/Examples/Blockersmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Blockersmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for( i in 1 : Num ) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">rc[i] ~ dbin(pc[i], nc[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">rt[i] ~ dbin(pt[i], nt[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logit(pc[i]) <- mu[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logit(pt[i]) <- mu[i] + delta[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i] ~ dnorm(0.0,1.0E-5)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">delta[i] ~ dt(d, tau, 4)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">d ~ dnorm(0.0,1.0E-6)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau ~ dgamma(0.001,0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">delta.new ~ dt(d, tau, 4)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma <- 1 / sqrt(tau)<br>}
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Blockersmodel.txt b/doc/Examples/Blockersmodel.txt
new file mode 100755
index 0000000..96dafa8
--- /dev/null
+++ b/doc/Examples/Blockersmodel.txt
@@ -0,0 +1,15 @@
+ model
+ {
+ for( i in 1 : Num ) {
+ rc[i] ~ dbin(pc[i], nc[i])
+ rt[i] ~ dbin(pt[i], nt[i])
+ logit(pc[i]) <- mu[i]
+ logit(pt[i]) <- mu[i] + delta[i]
+ mu[i] ~ dnorm(0.0,1.0E-5)
+ delta[i] ~ dt(d, tau, 4)
+ }
+ d ~ dnorm(0.0,1.0E-6)
+ tau ~ dgamma(0.001,0.001)
+ delta.new ~ dt(d, tau, 4)
+ sigma <- 1 / sqrt(tau)
+}
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diff --git a/doc/Examples/Bones.html b/doc/Examples/Bones.html
new file mode 100755
index 0000000..7ea9555
--- /dev/null
+++ b/doc/Examples/Bones.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Bones</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="bones0.bmp" alt="[bones0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Bones: latent trait model <br> for multiple ordered<br> categorical responses
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>The concept of skeletal age (SA) arises from the idea that individuals mature at different rates: for any given chronological age (CA), the
</font><font face="Arial" color="#000100" size="3"><em>average
</em></font><font face="Arial" color="#000100" size="3"> SA in a sample of individuals should equal their CA, but with an inter-individual spread which reflects the differential rate of maturation. Roche et al (1975) have developed a model for predicting SA by calibrating 34 indicators (items) of skeletal maturity which may be observed in a radiograph. Each indicator is categorized with respect to its degree of maturity: 19 are binary items (i.e. 0 = immature or 1 = mature); 8 items have [...]
</font><font face="Arial" color="#000100" size="3"><em>et al.
</em></font><font face="Arial" color="#000100" size="3"> calculated threshold parameters for the boundarys between grades for each indicator. For the binary items, there is a single threshold representing the CA at which 50% of individuals are mature for the indicator. Three-category items have 2 threshold parameters: the first corresponds to the CA at which 50% of individuals are either partially or fully mature for the indicator; the second is the CA at which 50% of individuals are full [...]
</font><font face="Arial" color="#000100" size="3"><em>et al.
</em></font><font face="Arial" color="#000100" size="3">calculated a discriminability (slope) parameter for each item which reflects its rate of maturation. Part of this data is shown below. Columns 1--4 represent the threshold parameters (note the use of the missing value code NA to `fill in' the columns for items with fewer than 4 thresholds); column 5 is the discriminability parameter; column 6 gives the number of grades per item.<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="bones1.bmp" alt="[bones1]">
</font><font face="Arial" color="#000100" size="3"> <br></center>Thissen (1986) (p.71) presents the following graded radiograph data on 13 boys whose chronological ages range from 6 months to 18 years. (Note that for ease of implementation in
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> we have listed the items in a different order to that used by Thissen):<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="bones2.bmp" alt="[bones2]">
</font><font face="Arial" color="#000100" size="3"><br></center>Some items have missing data (represented by the code NA in the table above). This does not present a problem for
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3">: the missing grades are simply treated as unknown parameters to be estimated along with the other parameters of interest such as the SA for each boy.<br><br>Thissen models the above data using the logistic function. For each item
</font><font face="Arial" color="#000100" size="3"><em>j
</em></font><font face="Arial" color="#000100" size="3"> and each grade
</font><font face="Arial" color="#000100" size="3"><em>k
</em></font><font face="Arial" color="#000100" size="3">, the cumulative probability Q
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3"> that a boy with skeletal age
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3"> is assigned a more mature grade than
</font><font face="Arial" color="#000100" size="3"><em>k
</em></font><font face="Arial" color="#000100" size="3"> is given by<br><br> logitQ
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">(
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3"> -
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br>where
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> is the discriminability parameter and the
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3"> are the threshold parameters for item
</font><font face="Arial" color="#000100" size="3"><em>j
</em></font><font face="Arial" color="#000100" size="3">. Hence the probability of observing an immature grade (i.e. k =1) for a particular skeletal age
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3"> is p
</font><font face="Arial" color="#000100" size="2"><sub>j,1
</sub></font><font face="Arial" color="#000100" size="3"> = 1 - Q
</font><font face="Arial" color="#000100" size="2"><sub>j,1
</sub></font><font face="Arial" color="#000100" size="3">. The probability of observing a fully mature grade (i.e.k = K
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">, where K
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> is the number of grades for item
</font><font face="Arial" color="#000100" size="3"><em>j
</em></font><font face="Arial" color="#000100" size="3">is p
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>,K
</sub></font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> = Q
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>,K
</sub></font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="2"><sub> -1
</sub></font><font face="Arial" color="#000100" size="3">. For items with 3 or more categories, the probability of observing an itermediate grade is p
</font><font face="Arial" color="#000100" size="2"><sub>j,k
</sub></font><font face="Arial" color="#000100" size="3"> = Q
</font><font face="Arial" color="#000100" size="2"><sub>j,k-1
</sub></font><font face="Arial" color="#000100" size="3"> - Q
</font><font face="Arial" color="#000100" size="2"><sub>j,k
</sub></font><font face="Arial" color="#000100" size="3"> (i.e. the difference between the cumulative probability of being assigned grade
</font><font face="Arial" color="#000100" size="3"><em>k
</em></font><font face="Arial" color="#000100" size="3"> or more, and of being assigned grade
</font><font face="Arial" color="#000100" size="3"><em>k+1
</em></font><font face="Arial" color="#000100" size="3"> or more). <br><br>The
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language for this model is given below. Note that the
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> for each boy
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> is assigned a vague, independent normal prior theta[i] ~ dnorm(0.0, 0.001). That is, each boy is treated as a separate problem with is no `learning' or `borrowing strength' across individuals, and hence no hierachical structure on the
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">'s.<br><center><br><br>BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for bones example
</em></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2"></center>
</font><font face="Arial" color="#000100" size="3"> model<br> {<br> for (i in 1 : nChild) {<br> theta[i] ~ dnorm(0.0, 0.001)<br> for (j in 1 : nInd) { <br> # Cumulative probability of > grade k given theta<br> for (k in 1: ncat [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Bonesdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#000100" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Bonesinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Bonesinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>We note a couple of tricks used in the above code. Firstly, the variable p has been declared as a 3-way rectangular array with the size of the third dimension equal to the maximum number of possible grades (i.e.5) for all items (even though items 1--28 have fewer than 5 categories). The statement <br><br> grade[i, j] ~ dcat(p[i, j, 1 :ngrade[j]])<br><br>is then used to select the relevant elements of p[i,j, ] for item
</font><font face="Arial" color="#000100" size="3"><em>j
</em></font><font face="Arial" color="#000100" size="3">, thus ignoring any `empty' spaces in the array for items with fewer than the maximum number of grades. Secondly, the final section of the above code includes a loop indexed as follows <br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3">A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center><br><img src="bones3.bmp" alt="[bones3]">
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Bonesdata.html b/doc/Examples/Bonesdata.html
new file mode 100755
index 0000000..93a925b
--- /dev/null
+++ b/doc/Examples/Bonesdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Bonesdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(nChild = 13, nInd = 34,<br> gamma = structure(<br> .Data = c(0.7425, NA, NA, NA,<br>10.2670, NA, NA, NA,<br>10.5215, NA, NA, NA,<br>9.3877, NA, NA, NA,<br>0.2593, NA, NA, NA,<br>-0.5998, NA, NA, NA,<br>10.5891, NA, NA, NA,<br>6.6701, NA, NA, NA,<br>8.8921, NA, NA, NA,<br>12.4275, NA, NA, NA,<br>12.4788, NA, NA, NA,<br>13.7778, NA, NA, NA,<br>5.8374, NA, NA, NA,<br>6.9485, NA, NA, NA,<br>13.7184, NA, NA, NA, [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Bonesdata.txt b/doc/Examples/Bonesdata.txt
new file mode 100755
index 0000000..0e0915a
--- /dev/null
+++ b/doc/Examples/Bonesdata.txt
@@ -0,0 +1,59 @@
+list(nChild = 13, nInd = 34,
+ gamma = structure(
+ .Data = c(0.7425, NA, NA, NA,
+ 10.2670, NA, NA, NA,
+ 10.5215, NA, NA, NA,
+ 9.3877, NA, NA, NA,
+ 0.2593, NA, NA, NA,
+ -0.5998, NA, NA, NA,
+ 10.5891, NA, NA, NA,
+ 6.6701, NA, NA, NA,
+ 8.8921, NA, NA, NA,
+ 12.4275, NA, NA, NA,
+ 12.4788, NA, NA, NA,
+ 13.7778, NA, NA, NA,
+ 5.8374, NA, NA, NA,
+ 6.9485, NA, NA, NA,
+ 13.7184, NA, NA, NA,
+ 14.3476, NA, NA, NA,
+ 4.8066, NA, NA, NA,
+ 9.1037, NA, NA, NA,
+ 10.7483, NA, NA, NA,
+ 0.3887, 1.0153, NA, NA,
+ 3.2573, 7.0421, NA, NA,
+ 11.6273, 14.4242, NA, NA,
+ 15.8842, 17.4685, NA, NA,
+ 14.8926, 16.7409, NA, NA,
+ 15.5487, 16.8720, NA, NA,
+ 15.4091, 17.0061, NA, NA,
+ 3.9216, 5.2099, NA, NA,
+ 15.4750, 16.9406, 17.4944, NA,
+ 0.4927, 1.3556, 2.3016, 3.2535,
+ 1.3059, 1.8793, 2.4970, 3.2306,
+ 1.5012, 1.8902, 2.3689, 2.9495,
+ 0.8021, 2.3873, 3.9525, 5.3198,
+ 5.0022, 6.3704, 8.2832, 10.4988,
+ 4.0168, 5.1537, 7.1053, 10.3038), .Dim = c(34, 4)),
+ delta = c(2.9541, 0.6603, 0.7965, 1.0495, 5.7874, 3.8376, 0.6324,
+ 0.8272, 0.6968, 0.8747, 0.8136, 0.8246, 0.6711, 0.978,
+ 1.1528, 1.6923, 1.0331, 0.5381, 1.0688, 8.1123, 0.9974,
+ 1.2656, 1.1802, 1.368, 1.5435, 1.5006, 1.6766, 1.4297,
+ 3.385, 3.3085, 3.4007, 2.0906, 1.0954, 1.5329),
+ ncat = c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
+ 3, 3, 3, 3, 3, 3, 3, 3, 4, 5, 5, 5, 5, 5, 5),
+grade = structure(
+.Data = c(
+1,1,1, 1,1,1,1, 1,1,1, 1, 1, 1, 1,1, 1, 1,1, 1,2,1,1, 1, 1, 1, 1,1,1,2,1,1,2,1,1,
+2,1,1, 1,2,2,1, 1,1,1, 1, 1, 1, 1,1, 1, 1,1, 1,3,1,1, 1, 1, 1, 1,1,1,3,1,1,2,1,1,
+2,1,1, 1,2,2,1, 1,1,1, 1, 1, 1, 1,1, 1, 1,1, 1,3,1,1, 1, 1, 1, 1,1,1,4,3,3,3,1,1,
+2,1,1, 1,2,2,1, 1,1,1, 1, 1, NA,1,1, 1, 1,1, 1,3,1,1, 1, 1, 1, 1,1,1,4,5,4,3,1,1,
+2,1,1, 1,2,2,1, 1,2,1, 1, 1, 1, 1,1, 1, 2,1, 1,3,2,1, 1, 1, 1, 1,3,1,5,5,5,4,2,3,
+2,1,1, 1,2,2,1, 2,1,1, 1, 1, 1, 2,1, 1, 2,NA,1,3,2,1, 1, 1, 1, 1,3,1,5,5,5,5,3,3,
+2,1,1, 1,2,2,1, 1,1,NA,NA,1, 1, 1,1, 1, 2,NA,1,3,3,1, 1, 1, 1, 1,3,1,5,5,5,5,3,3,
+2,1,2, 2,2,2,2, 2,1,NA,NA,1, 2, 2,1, 1, 2,2, 1,3,2,1, 1, 1, 1, 1,3,1,5,5,5,5,3,4,
+2,1,1, 2,2,2,2, 2,2,1, 1, 1, 2, 1,1, 1, 2,1, 1,3,3,1, 1, 1, 1, 1,3,1,5,5,5,5,4,4,
+2,1,2, 2,2,2,2, 2,2,1, 1, 1, 2, 2,2, 1, 2,NA,2,3,3,1, 1, 1, 1, 1,3,1,5,5,5,5,5,5,
+2,1,NA,2,2,2,NA,2,2,1, NA,NA,2, 2,NA,NA,2,1, 2,3,3,NA,1, NA,1, 1,3,1,5,5,5,5,5,5,
+2,2,2, 2,2,2,2, 2,2,2, 2, 2, 2, 2,2, 2, 2,2, 2,3,3,3, 1, NA,2, 1,3,2,5,5,5,5,5,5,
+2,2,2, 2,2,2,2, 2,2,2, NA,2, 2, 2,2, 2, 2,2, 2,3,3,3, NA,2, NA,2,3,4,5,5,5,5,5,5), .Dim = c(13, 34))
+)
diff --git a/doc/Examples/Bonesinits.html b/doc/Examples/Bonesinits.html
new file mode 100755
index 0000000..9a069e7
--- /dev/null
+++ b/doc/Examples/Bonesinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Bonesinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(theta = c(0.5,1,2,3,5,6,7,8,9,12,13,16,18),<br>grade = structure(<br>.Data = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, <br> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, <br> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, <br> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, <br>&nb [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Bonesinits.txt b/doc/Examples/Bonesinits.txt
new file mode 100755
index 0000000..43f5715
--- /dev/null
+++ b/doc/Examples/Bonesinits.txt
@@ -0,0 +1,28 @@
+list(theta = c(0.5,1,2,3,5,6,7,8,9,12,13,16,18),
+ grade = structure(
+ .Data = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, 1, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, 1, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1, 1, NA, NA,
+ NA, NA, NA, NA, 1, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1, 1, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1,
+ NA, NA, NA, 1, NA, NA, NA, 1, 1, NA, NA, 1, 1, NA, NA, NA, NA, NA, 1,
+ NA, 1, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, 1, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1, NA, 1, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA), .Dim = c(13, 34))
+ )
diff --git a/doc/Examples/Bonesinits1.html b/doc/Examples/Bonesinits1.html
new file mode 100755
index 0000000..a6ed957
--- /dev/null
+++ b/doc/Examples/Bonesinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Bonesinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(theta = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13),<br>grade = structure(<br>.Data = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, <br> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, <br> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, <br> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Bonesinits1.txt b/doc/Examples/Bonesinits1.txt
new file mode 100755
index 0000000..d9783ed
--- /dev/null
+++ b/doc/Examples/Bonesinits1.txt
@@ -0,0 +1,28 @@
+list(theta = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13),
+ grade = structure(
+ .Data = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, 1, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, 1, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1, 1, NA, NA,
+ NA, NA, NA, NA, 1, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1, 1, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1,
+ NA, NA, NA, 1, NA, NA, NA, 1, 1, NA, NA, 1, 1, NA, NA, NA, NA, NA, 1,
+ NA, 1, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, 1, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1, NA, 1, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA), .Dim = c(13, 34))
+ )
diff --git a/doc/Examples/Bonesmodel.html b/doc/Examples/Bonesmodel.html
new file mode 100755
index 0000000..feccd29
--- /dev/null
+++ b/doc/Examples/Bonesmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Bonesmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for (i in 1 : nChild) {<br> theta[i] ~ dnorm(0.0, 0.001)<br> for (j in 1 : nInd) { <br> # Cumulative probability of > grade k given theta<br> for (k in 1: ncat[j] - 1 [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Bonesmodel.txt b/doc/Examples/Bonesmodel.txt
new file mode 100755
index 0000000..49b9f56
--- /dev/null
+++ b/doc/Examples/Bonesmodel.txt
@@ -0,0 +1,22 @@
+ model
+ {
+ for (i in 1 : nChild) {
+ theta[i] ~ dnorm(0.0, 0.001)
+ for (j in 1 : nInd) {
+ # Cumulative probability of > grade k given theta
+ for (k in 1: ncat[j] - 1) {
+ logit(Q[i, j, k]) <- delta[j] * (theta[i] - gamma[j, k])
+ }
+ }
+
+ # Probability of observing grade k given theta
+ for (j in 1 : nInd) {
+ p[i, j, 1] <- 1 - Q[i, j, 1]
+ for (k in 2 : ncat[j] - 1) {
+ p[i, j, k] <- Q[i, j, k - 1] - Q[i, j, k]
+ }
+ p[i, j, ncat[j]] <- Q[i, j, ncat[j] - 1]
+ grade[i, j] ~ dcat(p[i, j, 1 : ncat[j]])
+ }
+ }
+ }
diff --git a/doc/Examples/Camel.html b/doc/Examples/Camel.html
new file mode 100755
index 0000000..b8e521b
--- /dev/null
+++ b/doc/Examples/Camel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Camel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"><strong><img src="camel0.bmp" alt="[camel0]">
</strong></font><font face="Arial" color="#000100" size="1"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Camel: Multivariate normal with<br> structured missing data
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#000000" size="3">Tanner and Wong present a data set with missing values modeled as a bivariate normal. No closed form for the deviance of the model can be found and so no deviance node is created by the BUGS compiler. For the same reason the DIC menu is greyed-out <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> model<br> {<br> for (i in 1 : N){<br> Y[i, 1 : 2] ~ dmnorm(mu[], tau[ , ])<br> }<br> mu[1] <- 0<br> mu[2] <- 0<br> tau[1 : 2,1 : 2] ~ dwish(R[ , ], 2)<br> & [...]
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Cameldata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="5">
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Camelinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Camelinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br><center>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br><br><img src="camel1.bmp" alt="[camel1]"><br><br><br><br><img src="camel2.bmp" alt="[camel2]"><br> </center><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Cameldata.html b/doc/Examples/Cameldata.html
new file mode 100755
index 0000000..6ffc621
--- /dev/null
+++ b/doc/Examples/Cameldata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Cameldata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(N= 12,<br> Y = structure(<br> .Data = c(1,1,<br> 1,-1,<br> -1,1,<br> -1, -1,<br> &nb [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Cameldata.txt b/doc/Examples/Cameldata.txt
new file mode 100755
index 0000000..788319f
--- /dev/null
+++ b/doc/Examples/Cameldata.txt
@@ -0,0 +1,15 @@
+list(N= 12,
+ Y = structure(
+ .Data = c(1,1,
+ 1,-1,
+ -1,1,
+ -1, -1,
+ 2, NA,
+ 2, NA,
+ -2, NA,
+ -2, NA,
+ NA, 2,
+ NA, 2,
+ NA, -2,
+ NA, -2),
+ .Dim = c(12, 2)))
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diff --git a/doc/Examples/Camelinits.html b/doc/Examples/Camelinits.html
new file mode 100755
index 0000000..cc4a8ff
--- /dev/null
+++ b/doc/Examples/Camelinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Camelinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(tau = structure(.Data = c(0.1,0,0,0.1), .Dim = c(2,2)),<br> Y = structure(<br> .Data = c(NA,NA,<br> NA,NA,<br> NA,NA,<br> NA, [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Camelinits.txt b/doc/Examples/Camelinits.txt
new file mode 100755
index 0000000..adc00d0
--- /dev/null
+++ b/doc/Examples/Camelinits.txt
@@ -0,0 +1,15 @@
+list(tau = structure(.Data = c(0.1,0,0,0.1), .Dim = c(2,2)),
+ Y = structure(
+ .Data = c(NA,NA,
+ NA,NA,
+ NA,NA,
+ NA, NA,
+ NA, 1,
+ NA, 1,
+ NA, 1,
+ NA, 1,
+ 1, NA,
+ 1, NA,
+ 1, NA,
+ 1, NA),
+ .Dim = c(12, 2)))
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diff --git a/doc/Examples/Camelinits1.html b/doc/Examples/Camelinits1.html
new file mode 100755
index 0000000..48f25f2
--- /dev/null
+++ b/doc/Examples/Camelinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Camelinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(tau = structure(.Data = c(0.5,0,0,0.5), .Dim = c(2,2)),<br> Y = structure(<br> .Data = c(NA,NA,<br> NA,NA,<br> NA,NA,<br> NA, [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Camelinits1.txt b/doc/Examples/Camelinits1.txt
new file mode 100755
index 0000000..45774b7
--- /dev/null
+++ b/doc/Examples/Camelinits1.txt
@@ -0,0 +1,15 @@
+list(tau = structure(.Data = c(0.5,0,0,0.5), .Dim = c(2,2)),
+ Y = structure(
+ .Data = c(NA,NA,
+ NA,NA,
+ NA,NA,
+ NA, NA,
+ NA, 2,
+ NA, 2,
+ NA, 2,
+ NA, 2,
+ 3, NA,
+ 3, NA,
+ 3, NA,
+ 3, NA),
+ .Dim = c(12, 2)))
\ No newline at end of file
diff --git a/doc/Examples/Camelmodel.html b/doc/Examples/Camelmodel.html
new file mode 100755
index 0000000..6b08240
--- /dev/null
+++ b/doc/Examples/Camelmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Camelmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for (i in 1 : N){<br> Y[i, 1 : 2] ~ dmnorm(mu[], tau[ , ])<br> }<br> mu[1] <- 0<br> mu[2] <- 0<br> tau[1 : 2,1 : 2] ~ dwish(R[ , ], 2)<br> &n [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Camelmodel.txt b/doc/Examples/Camelmodel.txt
new file mode 100755
index 0000000..8390c09
--- /dev/null
+++ b/doc/Examples/Camelmodel.txt
@@ -0,0 +1,15 @@
+ model
+ {
+ for (i in 1 : N){
+ Y[i, 1 : 2] ~ dmnorm(mu[], tau[ , ])
+ }
+ mu[1] <- 0
+ mu[2] <- 0
+ tau[1 : 2,1 : 2] ~ dwish(R[ , ], 2)
+ R[1, 1] <- 0.001
+ R[1, 2] <- 0
+ R[2, 1] <- 0;
+ R[2, 2] <- 0.001
+ Sigma2[1 : 2,1 : 2] <- inverse(tau[ , ])
+ rho <- Sigma2[1, 2] / sqrt(Sigma2[1, 1] * Sigma2[2, 2])
+ }
diff --git a/doc/Examples/Cervix.html b/doc/Examples/Cervix.html
new file mode 100755
index 0000000..c18c48b
--- /dev/null
+++ b/doc/Examples/Cervix.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Cervix</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="cervix0.bmp" alt="[cervix0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Cervix: case - control study <br> with errors in covariates
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">Carroll, Gail and Lubin (1993) consider the problem of estimating the odds ratio of a disease d in a case-control study where the binary exposure variable is measured with error. Their example concerns exposure to herpes simplex virus (HSV) in women with invasive cervical cancer (d=1) and in controls (d=0). Exposure to HSV is measured by a relatively inaccurate western blot procedure w for 1929 of the 2044 women, whilst for 115 women, it [...]
</font><font face="Arial" color="#000100" size="2"><img src="cervix1.bmp" alt="[cervix1]"><br></center>
</font><font face="Arial" color="#000100" size="3"><br>They fitted a prospective logistic model to the case-control data as follows<br><br> d
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) i = 1,...,2044 <br> logit(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>0C
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> i = 1,...,2044 <br><br>where
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> is the log odds ratio of disease. Since the relationship between d and x is only directly observable in the 115 women with "complete'' data, and because there is evidence of differential measurement error, the following parameters are required in order to estimate the logistic model<br><br>
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>1,1
</sub></font><font face="Arial" color="#000100" size="3"> = P(w=1 | x=0, d=0)<br>
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>1,2
</sub></font><font face="Arial" color="#000100" size="3"> = P(w=1 | x=0, d=1)<br>
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>2,1
</sub></font><font face="Arial" color="#000100" size="3"> = P(w=1 | x=1, d=0)<br>
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>2,2
</sub></font><font face="Arial" color="#000100" size="3"> = P(w=1 | x=1, d=1)<br> q = P(x=1)<br><br><br>The differential probability of being exposed to HSV (x=1) for cases and controls is calculated as follows<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="cervix2.bmp" alt="[cervix2]">
</font><font face="Arial" color="#000100" size="3"><br></center>The BUGS code is given below.
</font><font face="Arial" color="#000100" size="3">The role of the variables
</font><font face="Courier" color="#000100" size="3">x
</font><font face="Courier" color="#000100" size="2">1
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Courier" color="#000100" size="3">d
</font><font face="Courier" color="#000100" size="2">1
</font><font face="Arial" color="#000100" size="3"> is to pick the appropriate value of
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> (the incidence of w) for any given true exposure status x and disease status d. Since x and d take the values 0 or 1, and the subscripts for
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> take values 1 or 2, we must first add 1 to each
</font><font face="Courier" color="#000100" size="3">x[i]
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Courier" color="#000100" size="3">d[i]
</font><font face="Arial" color="#000100" size="3"> in the BUGS code before using them as index values for
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3">. BUGS does not allow subscripts to be functions of variable quantities --- hence the need to create
</font><font face="Courier" color="#000100" size="3">x1
</font><font face="Arial" color="#000100" size="3">and
</font><font face="Courier" color="#000100" size="3">d1
</font><font face="Arial" color="#000100" size="3"> for use as subscripts. In addition, note that
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> were not simulated directly in BUGS, but were calculated as functions of other parameters. This is because the dependence of
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> on d would have led to a cycle in the graphical model which would no longer define a probability distribution. <br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">x[i] ~ dbern(q) # incidence of HSV<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logit(p[i]) <- beta0C + beta * x[i] # logistic model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">d[i] ~ dbern(p[i]) # incidence of cancer<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">x1[i] <- x[i] + 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">d1[i] <- d[i] + 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">w[i] ~ dbern(phi[x1[i], d1[i]]) # incidence of w<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">q ~ dunif(0.0, 1.0) # prior distributions<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta0C ~ dnorm(0.0, 0.00001);<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta ~ dnorm(0.0, 0.00001);<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(j in 1 : 2) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(k in 1 : 2){<br> phi[j, k] ~ dunif(0.0, 1.0)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># calculate gamma1 = P(x=1|d=0) and gamma2 = P(x=1|d=1) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma1 <- 1 / (1 + (1 + exp(beta0C + beta)) / (1 + exp(beta0C)) * (1 - q) / q)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma2 <- 1 / (1 + (1 + exp(-beta0C - beta)) / (1 + exp(-beta0C)) * (1 - q) / q)<br> }<br><br>
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Cervixdata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Examples/Cervixinits.html">Inits for chain 1</a> <a href="../Examples/Cervixinits1.html">Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="5"> <br>
</font><font face="Arial" color="#000100" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates <br><center><br><img src="cervix3.bmp" alt="[cervix3]">
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Cervixdata.html b/doc/Examples/Cervixdata.html
new file mode 100755
index 0000000..4617feb
--- /dev/null
+++ b/doc/Examples/Cervixdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Cervixdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 2044,<br> d = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, <br> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, <br> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, <br> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, <br> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Cervixdata.txt b/doc/Examples/Cervixdata.txt
new file mode 100755
index 0000000..b4e8752
--- /dev/null
+++ b/doc/Examples/Cervixdata.txt
@@ -0,0 +1,284 @@
+list(N = 2044,
+ d = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
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+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA), w = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
+ 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
\ No newline at end of file
diff --git a/doc/Examples/Cervixinits.html b/doc/Examples/Cervixinits.html
new file mode 100755
index 0000000..c31a03b
--- /dev/null
+++ b/doc/Examples/Cervixinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Cervixinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"> list(beta0C = 0, beta = 0, q = .5, phi = structure(.Data = c(.5,.5,.5,.5), .Dim = c(2, 2)))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Cervixinits.txt b/doc/Examples/Cervixinits.txt
new file mode 100755
index 0000000..7a4daf8
--- /dev/null
+++ b/doc/Examples/Cervixinits.txt
@@ -0,0 +1 @@
+ list(beta0C = 0, beta = 0, q = .5, phi = structure(.Data = c(.5,.5,.5,.5), .Dim = c(2, 2)))
\ No newline at end of file
diff --git a/doc/Examples/Cervixinits1.html b/doc/Examples/Cervixinits1.html
new file mode 100755
index 0000000..cad1523
--- /dev/null
+++ b/doc/Examples/Cervixinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Cervixinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(beta0C = 1.0, beta = 1.0, q = 0.75, phi = structure(.Data = c(0.15,0.15,0.15,0.15), .Dim = c(2, 2)))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Cervixinits1.txt b/doc/Examples/Cervixinits1.txt
new file mode 100755
index 0000000..fe074be
--- /dev/null
+++ b/doc/Examples/Cervixinits1.txt
@@ -0,0 +1 @@
+list(beta0C = 1.0, beta = 1.0, q = 0.75, phi = structure(.Data = c(0.15,0.15,0.15,0.15), .Dim = c(2, 2)))
\ No newline at end of file
diff --git a/doc/Examples/Cervixmodel.html b/doc/Examples/Cervixmodel.html
new file mode 100755
index 0000000..c0cabd3
--- /dev/null
+++ b/doc/Examples/Cervixmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Cervixmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">x[i] ~ dbern(q) # incidence of HSV<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logit(p[i]) <- beta0C + beta * x[i] # logistic model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">d[i] ~ dbern(p[i]) # incidence of cancer<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">x1[i] <- x[i] + 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">d1[i] <- d[i] + 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">w[i] ~ dbern(phi[x1[i], d1[i]]) # incidence of w<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">q ~ dunif(0.0, 1.0) # prior distributions<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta0C ~ dnorm(0.0, 0.00001);<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta ~ dnorm(0.0, 0.00001);<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(j in 1 : 2) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(k in 1 : 2){<br> phi[j, k] ~ dunif(0.0, 1.0)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># calculate gamma1 = P(x=1|d=0) and gamma2 = P(x=1|d=1) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma1 <- 1 / (1 + (1 + exp(beta0C + beta)) / (1 + exp(beta0C)) * (1 - q) / q)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma2 <- 1 / (1 + (1 + exp(-beta0C - beta)) / (1 + exp(-beta0C)) * (1 - q) / q)<br> }<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Cervixmodel.txt b/doc/Examples/Cervixmodel.txt
new file mode 100755
index 0000000..51cb8b3
--- /dev/null
+++ b/doc/Examples/Cervixmodel.txt
@@ -0,0 +1,22 @@
+ model
+ {
+ for (i in 1 : N) {
+ x[i] ~ dbern(q) # incidence of HSV
+ logit(p[i]) <- beta0C + beta * x[i] # logistic model
+ d[i] ~ dbern(p[i]) # incidence of cancer
+ x1[i] <- x[i] + 1
+ d1[i] <- d[i] + 1
+ w[i] ~ dbern(phi[x1[i], d1[i]]) # incidence of w
+ }
+ q ~ dunif(0.0, 1.0) # prior distributions
+ beta0C ~ dnorm(0.0, 0.00001);
+ beta ~ dnorm(0.0, 0.00001);
+ for(j in 1 : 2) {
+ for(k in 1 : 2){
+ phi[j, k] ~ dunif(0.0, 1.0)
+ }
+ }
+ # calculate gamma1 = P(x=1|d=0) and gamma2 = P(x=1|d=1)
+ gamma1 <- 1 / (1 + (1 + exp(beta0C + beta)) / (1 + exp(beta0C)) * (1 - q) / q)
+ gamma2 <- 1 / (1 + (1 + exp(-beta0C - beta)) / (1 + exp(-beta0C)) * (1 - q) / q)
+ }
diff --git a/doc/Examples/DataCloning.html b/doc/Examples/DataCloning.html
new file mode 100755
index 0000000..25e6fad
--- /dev/null
+++ b/doc/Examples/DataCloning.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>DataCloning</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="datacloning0.bmp" alt="[datacloning0]">
</font><font face="Courier New" color="#000100" size="6">Using Data Cloning to Calculate <br> MLEs for the Seeds Model
</font><font face="Arial" color="#000100" size="3"><br><br><br> model<br> {<br> for( i in 1 : N ) {<br> for(k in 1 : K){ # replicate data and random effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> r.rep[i, k] <- r[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> r.rep[i, k] ~ dbin(p[i, k],n[i])<br> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> b[i, k] ~ dnorm(0.0,tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> logit(p[i, k]) <- alpha0 + alpha1 * x1[i] + alpha2 * x2[i] + <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha12 * x1[i] * x2[i] + b[i, k]<br> } <br> }<br> alpha0 ~ dnorm(0.0,1.0E-6)<br> alpha1 ~ dnorm(0.0,1.0E [...]
</font><font face="Arial" color="#000100" size="1"><sup>1/2
</sup></font><font face="Arial" color="#000100" size="3">.Note<br>that Monte Carlo errors will be magnified by this scaling so accurate estimates of the MLE SE will need both large K and long MCMC runs.<br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Seedsdataclone.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><a href="../Examples/Seedsinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000000" size="3"> <br><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd sd*K^0.5 MC_error val2.5pc median val97.5pc start sample<br> K = 1 <br>
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="2">alpha0 -0.5485 0.196 0.196 0.007577 -0.9406 -0.549 -0.1511 1001 10000<br> alpha1 0.07439 0.3178 0.3178 0.01159 -0.5561 0.08066 0.6841 10 [...]
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><strong>K = 2
</strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"> alpha0 -0.5456 0.1258 0.1779 0.005102 -0.7946 -0.5452 -0.2963 1001 10000<br> alpha1 0.08221 0.21 0.2970 0.008157 -0.3328 0.08527 0.4923 [...]
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="2"><strong>K = 4
</strong></font><font face="Arial" color="#000100" size="2"><br> alpha0 -0.5486 0.08535 0.1707 0.002859 -0.7156 -0.5473 -0.3819 1001 10000<br> alpha1 0.09523 0.1402 0.2804 0.004785 -0.192 0.09921 &nb [...]
</font><font face="Arial" color="#000100" size="2"><strong>K = 8
</strong></font><font face="Arial" color="#000100" size="2"><br> alpha0 -0.5516 0.06062 0.1715 0.002096 -0.6734 -0.5513 -0.4327 1001 10000<br> alpha1 0.1017 0.1008 0.2851 0.003262 -0.09649 0.1012 &nb [...]
</font><font face="Arial" color="#000100" size="2"><strong>K = 16
</strong></font><font face="Arial" color="#000100" size="2"><br> alpha0 -0.5493 0.04149 0.1660 0.001354 -0.6305 -0.5499 -0.4681 1001 10000<br> alpha1 0.09651 0.06921 0.2768 0.002323 -0.03731 0.09542 [...]
</font><font face="Arial" color="#000100" size="2"><strong>K = 32<br>
</strong></font><font face="Arial" color="#000100" size="2"> alpha0 -0.5503 0.03028 0.1713 0.001039 -0.6097 -0.5509 -0.4898 1001 10000<br> alpha1 0.09915 0.0504 0.2851 0.00159 9.589E-4 0.09946 [...]
</font><font face="Arial" color="#000100" size="2"><strong>K = 64<br>
</strong></font><font face="Arial" color="#000100" size="2"> alpha0 -0.5488 0.02058 0.1646 6.559E-4 -0.5891 -0.5487 -0.5088 1001 10000<br> alpha1 0.0981 0.03465 0.2768 0.001063 0.0299 0.09791 & [...]
</font><font face="Arial" color="#000100" size="2"><strong><br>K = 128<br>
</strong></font><font face="Arial" color="#000100" size="2"> alpha0 -0.5483 0.01477 0.1671 5.063E-4 -0.5777 -0.548 -0.5198 1001 10000<br> alpha1 0.09684 0.02418 0.2736 8.603E-4 0.04867 0.09703 [...]
</font><font face="Arial" color="#000100" size="2"><strong>K = 256<br>
</strong></font><font face="Arial" color="#000100" size="2"> alpha0 -0.5489 0.01018 0.1629 3.314E-4 -0.5692 -0.5486 -0.5293 1001 10000<br> alpha1 0.0972 0.01707 0.2731 5.336E-4 0.06356 0.09732 [...]
</font><font face="Arial" color="#000100" size="3">We may compare simple logistic, maximum likelihood (from EGRET), penalized quasi-likelihood (PQL) Breslow and Clayton (1993) with the
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> results<br><center>
</font><font face="Arial" color="#000100" size="2"><br><img src="datacloning1.bmp" alt="[datacloning1]"><br></center>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Dogs.html b/doc/Examples/Dogs.html
new file mode 100755
index 0000000..a38f5f0
--- /dev/null
+++ b/doc/Examples/Dogs.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dogs</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><strong><img src="dogs0.bmp" alt="[dogs0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Dogs: loglinear model for<br> binary data
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="3">Lindley (19??) analyses data from Kalbfleisch (1985) on the Solomon-Wynne experiment on dogs, whereby they learn to avoid an electric shock. A dog is put in a compartment, the lights are turned out and a barrier is raised, and 10 seconds later an electric shock is applied. The results are recorded as success (Y = 1 ) if the dog jumps the barrier before the shock occurs, or failure (Y = 0) otherwise. <br><br>Thirty [...]
</font><font face="Symbol" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> = A
</font><font face="Arial" color="#000100" size="2"><sup>x
</sup></font><font face="Arial" color="#000100" size="2"><sup>j
</sup></font><font face="Arial" color="#000100" size="3"> B
</font><font face="Arial" color="#000100" size="2"><sup>j-x
</sup></font><font face="Arial" color="#000100" size="2"><sup>j
</sup></font><font face="Arial" color="#000100" size="3"><br><br>for the probability of a shock (failure) at trial j, where x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">= number of success (avoidances) before trial j and j - x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">= number of previous failures (shocks). This is equivalent to the following log linear model<br><br> log
</font><font face="Symbol" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">+ b
</font><font face="Arial" color="#000100" size="3">( j-x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>Hence we have a generalised linear model for binary data, but with a log-link function rather than the canonical logit link. This is trivial to implement in BUGS:<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">model<br> {<br> for (i in 1 : Dogs) {<br> xa[i, 1] <- 0; xs[i, 1] <- 0 p[i, 1] <- 0 <br> for (j in 2 : Trials) {<br> xa[i, j] <- sum(Y[i, 1 : j - 1])<br> [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha ~ dflat()T(, -0.00001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta ~ dflat()T(, -0.00001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> A <- exp(alpha)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> B <- exp(beta)<br> }
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Dogsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#000100" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Dogsinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Dogsinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><center><br><img src="dogs1.bmp" alt="[dogs1]"><br>
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Dogsdata.html b/doc/Examples/Dogsdata.html
new file mode 100755
index 0000000..7d464b0
--- /dev/null
+++ b/doc/Examples/Dogsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dogsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(Dogs = 30, Trials = 25,<br> Y = structure(.Data = c(0, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,<br> 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,<br> &nb [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Dogsdata.txt b/doc/Examples/Dogsdata.txt
new file mode 100755
index 0000000..0b204c4
--- /dev/null
+++ b/doc/Examples/Dogsdata.txt
@@ -0,0 +1,32 @@
+list(Dogs = 30, Trials = 25,
+ Y = structure(.Data = c(0, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 1, 0,
+ 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 1, 1, 0, 1, 0, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 1, 0, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 1, 0, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1,
+ 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
+ .Dim = c(30, 25)))
diff --git a/doc/Examples/Dogsinits.html b/doc/Examples/Dogsinits.html
new file mode 100755
index 0000000..9da6c03
--- /dev/null
+++ b/doc/Examples/Dogsinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dogsinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = -1, beta = -1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Dogsinits.txt b/doc/Examples/Dogsinits.txt
new file mode 100755
index 0000000..1545c97
--- /dev/null
+++ b/doc/Examples/Dogsinits.txt
@@ -0,0 +1 @@
+list(alpha = -1, beta = -1)
\ No newline at end of file
diff --git a/doc/Examples/Dogsinits1.html b/doc/Examples/Dogsinits1.html
new file mode 100755
index 0000000..c77da75
--- /dev/null
+++ b/doc/Examples/Dogsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dogsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = -2, beta = -2)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Dogsinits1.txt b/doc/Examples/Dogsinits1.txt
new file mode 100755
index 0000000..f1ace45
--- /dev/null
+++ b/doc/Examples/Dogsinits1.txt
@@ -0,0 +1 @@
+list(alpha = -2, beta = -2)
\ No newline at end of file
diff --git a/doc/Examples/Dogsmodel.html b/doc/Examples/Dogsmodel.html
new file mode 100755
index 0000000..fbdf3c2
--- /dev/null
+++ b/doc/Examples/Dogsmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dogsmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">model<br> {<br> for (i in 1 : Dogs) {<br> xa[i, 1] <- 0; xs[i, 1] <- 0 p[i, 1] <- 0 <br> for (j in 2 : Trials) {<br> xa[i, j] <- sum(Y[i, 1 : j - 1])<br> [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha ~ dflat()T(, -0.00001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta ~ dflat()T(, -0.00001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> A <- exp(alpha)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> B <- exp(beta)<br> }
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Dogsmodel.txt b/doc/Examples/Dogsmodel.txt
new file mode 100755
index 0000000..e19fea4
--- /dev/null
+++ b/doc/Examples/Dogsmodel.txt
@@ -0,0 +1,17 @@
+ model
+ {
+ for (i in 1 : Dogs) {
+ xa[i, 1] <- 0; xs[i, 1] <- 0 p[i, 1] <- 0
+ for (j in 2 : Trials) {
+ xa[i, j] <- sum(Y[i, 1 : j - 1])
+ xs[i, j] <- j - 1 - xa[i, j]
+ log(p[i, j]) <- alpha * xa[i, j] + beta * xs[i, j]
+ y[i, j] <- 1 - Y[i, j]
+ y[i, j] ~ dbern(p[i, j])
+ }
+ }
+ alpha ~ dflat()T(, -0.00001)
+ beta ~ dflat()T(, -0.00001)
+ A <- exp(alpha)
+ B <- exp(beta)
+ }
diff --git a/doc/Examples/Dugongs.html b/doc/Examples/Dugongs.html
new file mode 100755
index 0000000..c37a77f
--- /dev/null
+++ b/doc/Examples/Dugongs.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dugongs</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="dugongs0.bmp" alt="[dugongs0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Dugongs: nonlinear growth curve
</font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Arial" color="#000000" size="5"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">Carlin and Gelfand (1991) present a nonconjugate Bayesian analysis of the following data set from Ratkowsky (1983):<br>
</font><font face="Arial" color="#000100" size="2"><img src="dugongs1.bmp" alt="[dugongs1]">
</font><font face="Arial" color="#000000" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">The data are length and age measurements for 27 captured dugongs (sea cows). Carlin and Gelfand (1991) model this data using a nonlinear growth curve with no inflection point and an asymptote as X
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> tends to infinity:<br><br> Y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">), i = 1,...,27<br> <br>
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> -
</font><font face="Symbol" color="#000100" size="3">bg
</font><font face="Arial" color="#000100" size="2"><sup>Xi
</sup></font><font face="Arial" color="#000100" size="3"><sup>
</sup></font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> > 0; 0 <
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"> < 1<br><br>Standard noninformative priors are adopted for
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">, and a uniform prior on (0,1) is assumed for
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3">. However, this specification leads to a non conjugate full conditional distribution for
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"> which is also non log-concave. The graph and corresponding BUGS code is given below
</font><font face="Arial" color="#000000" size="3"><strong><br><center>
</strong></font><font face="Arial" color="#000100" size="5"><strong><br><img src="dugongs2.bmp" alt="[dugongs2]"><br><br>
</strong></font><font face="Arial" color="#000100" size="2"><br></center>
</font><font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : N ) {<br> Y[i] ~ dnorm(mu[i], tau)<br> mu[i] <- alpha - beta * pow(gamma,x[i]) <br> }<br> alpha ~ dflat()T(0,)<br> &n [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Dugongsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Dugongsinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Dugongsinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates <br><center><br><img src="dugongs3.bmp" alt="[dugongs3]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Dugongsdata.html b/doc/Examples/Dugongsdata.html
new file mode 100755
index 0000000..70538a0
--- /dev/null
+++ b/doc/Examples/Dugongsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dugongsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"> list(x = c( 1.0, 1.5, 1.5, 1.5, 2.5, 4.0, 5.0, 5.0, 7.0,<br> 8.0, 8.5, 9.0, 9.5, 9.5, 10.0, 12.0, 12.0, 13.0,<br> 13.0, 14.5, 15.5, 15.5, 16.5, 17.0, 22.5, 29.0, 31.5),<br> Y = c(1.80, 1.85, 1.87, 1.77, 2.02, 2.27, 2.15, 2.26, 2.47,<br> 2.19, 2.26, 2.40, 2.39, 2.41, 2.50, 2.32, 2.32, 2.43,<br> 2.47, 2.56, 2.65, 2.47, 2.64, 2.56, 2.70, 2.72, 2.5 [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Dugongsdata.txt b/doc/Examples/Dugongsdata.txt
new file mode 100755
index 0000000..e2ead5a
--- /dev/null
+++ b/doc/Examples/Dugongsdata.txt
@@ -0,0 +1,6 @@
+ list(x = c( 1.0, 1.5, 1.5, 1.5, 2.5, 4.0, 5.0, 5.0, 7.0,
+ 8.0, 8.5, 9.0, 9.5, 9.5, 10.0, 12.0, 12.0, 13.0,
+ 13.0, 14.5, 15.5, 15.5, 16.5, 17.0, 22.5, 29.0, 31.5),
+ Y = c(1.80, 1.85, 1.87, 1.77, 2.02, 2.27, 2.15, 2.26, 2.47,
+ 2.19, 2.26, 2.40, 2.39, 2.41, 2.50, 2.32, 2.32, 2.43,
+ 2.47, 2.56, 2.65, 2.47, 2.64, 2.56, 2.70, 2.72, 2.57), N = 27)
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diff --git a/doc/Examples/Dugongsinits.html b/doc/Examples/Dugongsinits.html
new file mode 100755
index 0000000..4fbad2e
--- /dev/null
+++ b/doc/Examples/Dugongsinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dugongsinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list
</font><font face="Arial" color="#000100" size="2">(alpha = 1, beta = 1, tau = 1, gamma = 0.9)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Dugongsinits.txt b/doc/Examples/Dugongsinits.txt
new file mode 100755
index 0000000..73132d5
--- /dev/null
+++ b/doc/Examples/Dugongsinits.txt
@@ -0,0 +1 @@
+list(alpha = 1, beta = 1, tau = 1, gamma = 0.9)
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diff --git a/doc/Examples/Dugongsinits1.html b/doc/Examples/Dugongsinits1.html
new file mode 100755
index 0000000..9dd9787
--- /dev/null
+++ b/doc/Examples/Dugongsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dugongsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list
</font><font face="Arial" color="#000100" size="2">(alpha = 0.1, beta = 0.1, tau = 0.1, gamma = 0.5)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Dugongsinits1.txt b/doc/Examples/Dugongsinits1.txt
new file mode 100755
index 0000000..150bdd4
--- /dev/null
+++ b/doc/Examples/Dugongsinits1.txt
@@ -0,0 +1 @@
+list(alpha = 0.1, beta = 0.1, tau = 0.1, gamma = 0.5)
\ No newline at end of file
diff --git a/doc/Examples/Dugongsmodel.html b/doc/Examples/Dugongsmodel.html
new file mode 100755
index 0000000..4f296d8
--- /dev/null
+++ b/doc/Examples/Dugongsmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dugongsmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : N ) {<br> Y[i] ~ dnorm(mu[i], tau)<br> mu[i] <- alpha - beta * pow(gamma,x[i]) <br> }<br> alpha ~ dflat()T(0,)<br>&nb [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Dugongsmodel.txt b/doc/Examples/Dugongsmodel.txt
new file mode 100755
index 0000000..c0450b4
--- /dev/null
+++ b/doc/Examples/Dugongsmodel.txt
@@ -0,0 +1,13 @@
+ model
+ {
+ for( i in 1 : N ) {
+ Y[i] ~ dnorm(mu[i], tau)
+ mu[i] <- alpha - beta * pow(gamma,x[i])
+ }
+ alpha ~ dflat()T(0,)
+ beta ~ dflat()T(0,)
+ gamma ~ dunif(0.5, 1.0)
+ tau ~ dgamma(0.001, 0.001)
+ sigma <- 1 / sqrt(tau)
+ U3 <- logit(gamma)
+ }
diff --git a/doc/Examples/Dyes.html b/doc/Examples/Dyes.html
new file mode 100755
index 0000000..a512cf2
--- /dev/null
+++ b/doc/Examples/Dyes.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dyes</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><strong><img src="dyes0.bmp" alt="[dyes0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Dyes: variance components model
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><br>Box and Tiao (1973) analyse data first presented by Davies (1967) concerning batch to batch variation in yields of dyestuff. The data (shown below) arise from a balanced experiment whereby the total product yield was determined for 5 samples from each of 6 randomly chosen batches of raw material.<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="dyes1.bmp" alt="[dyes1]"></center><br>
</font><font face="Arial" color="#000100" size="3">The object of the study was to determine the relative importance of between batch variation versus variation due to sampling and analytic errors. On the assumption that the batches and samples vary independently, and contribute additively to the total error variance, we may assume the following model for dyestuff yield:<br><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">y
</font><font face="Arial" color="#000100" size="1"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="1"><sub>within
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br>
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3"> t
</font><font face="Arial" color="#000100" size="1"><sub>between
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br>where y
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> is the yield for sample
</font><font face="Arial" color="#000100" size="3"><em>j
</em></font><font face="Arial" color="#000100" size="3"> of batch
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is the true yield for batch
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>within
</sub></font><font face="Arial" color="#000100" size="3"> is the inverse of the within-batch variance
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>within
</sub></font><font face="Arial" color="#000100" size="3"> (
</font><font face="Arial" color="#000100" size="3"><em>i.e.
</em></font><font face="Arial" color="#000100" size="3"> the variation due to sampling and analytic error),
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3"> is the true average yield for all batches and
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>between
</sub></font><font face="Arial" color="#000100" size="3"> is the inverse of the between-batch variance s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>between
</sub></font><font face="Arial" color="#000100" size="3">. The total variation in product yield is thus
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>total
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>within
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>between
</sub></font><font face="Arial" color="#000100" size="3"> and the relative contributions of each component to the total variance are f
</font><font face="Arial" color="#000100" size="2"><sub>within
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>within
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">/
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>total
</sub></font><font face="Arial" color="#000100" size="3"> and f
</font><font face="Arial" color="#000100" size="2"><sub>between
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>between
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">/
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>total
</sub></font><font face="Arial" color="#000100" size="3"> . We assume standard non-informative priors for
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>within
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>between
</sub></font><font face="Arial" color="#000100" size="3">.<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><strong><center>
</strong></font><font face="Arial" color="#000100" size="3"><em>Graphical model for dyes example
</em></font><font face="Arial" color="#0000FF" size="5"><strong><br><img src="dyes2.bmp" alt="[dyes2]">
</strong></font><font face="Arial" color="#000100" size="5"><strong><br><br><br>
</strong></font><font face="Arial" color="#000100" size="3"><em>Bugs
</em></font><font face="Arial" color="#000100" size="3"> language for dyes example<br>
</font><font face="Arial" color="#000100" size="5"><strong></center>
</strong></font><font face="Arial" color="#000100" size="3"> <br> model<br> {<br> for(i in 1 : batches) {<br> mu[i] ~ dnorm(theta, tau.btw)<br> for(j in 1 : samples) {<br> y[i , j] ~ dnorm(mu[i], tau.with)<br> &nb [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Dyesdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Dyesinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Dyesinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>A 25000 update burn in followed by a further 100000 updates gave the parameter estimates<br><center>
</font><font face="Arial" color="#000100" size="3"><br><img src="dyes3.bmp" alt="[dyes3]"><br>
</font><font face="Arial" color="#000100" size="3"><br>Note that a relatively long run was required because of the high autocorrelation between successively sampled values of some parameters. Such correlations reduce the 'effective' size of the posterior sample, and hence a longer run is needed to ensure sufficient precision of the posterior estimates. Note that the posterior distribution for
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"><sub>between
</sub></font><font face="Arial" color="#000100" size="3"> has a very long upper tail: hence the posterior mean is considerably larger than the median. Box and Tiao estimate
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>within
</sub></font><font face="Arial" color="#000100" size="3"> = 2451 and
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>between
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">= 1764 by classical analysis of variance. Here,
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>between
</sub></font><font face="Arial" color="#000100" size="3"> is estimated by the difference of the between- and within-batch mean squares divided by the number of batches - 1. In cases where the between-batch mean square within-batch mean square, this leads to the unsatisfactory situation of a
</font><font face="Arial" color="#000100" size="3"><em>negative
</em></font><font face="Arial" color="#000100" size="3"> variance estimate. Computing a confidence interval for
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>between
</sub></font><font face="Arial" color="#000100" size="3"> is also difficult using the classical approach due to its complicated sampling distribution<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Dyesdata.html b/doc/Examples/Dyesdata.html
new file mode 100755
index 0000000..97727bf
--- /dev/null
+++ b/doc/Examples/Dyesdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dyesdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(batches = 6, samples = 5,<br> y = structure(<br> .Data = c(1545, 1440, 1440, 1520, 1580,<br>1540, 1555, 1490, 1560, 1495,<br>1595, 1550, 1605, 1510, 1560,<br>1445, 1440, 1595, 1465, 1545,<br>1595, 1630, 1515, 1635, 1625,<br>1520, 1455, 1450, 1480, 1445), .Dim = c(6, 5)))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Dyesdata.txt b/doc/Examples/Dyesdata.txt
new file mode 100755
index 0000000..2d499f3
--- /dev/null
+++ b/doc/Examples/Dyesdata.txt
@@ -0,0 +1,8 @@
+list(batches = 6, samples = 5,
+ y = structure(
+ .Data = c(1545, 1440, 1440, 1520, 1580,
+ 1540, 1555, 1490, 1560, 1495,
+ 1595, 1550, 1605, 1510, 1560,
+ 1445, 1440, 1595, 1465, 1545,
+ 1595, 1630, 1515, 1635, 1625,
+ 1520, 1455, 1450, 1480, 1445), .Dim = c(6, 5)))
\ No newline at end of file
diff --git a/doc/Examples/Dyesinits.html b/doc/Examples/Dyesinits.html
new file mode 100755
index 0000000..067defc
--- /dev/null
+++ b/doc/Examples/Dyesinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dyesinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(theta=1500, tau.with=1, tau.btw=1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Dyesinits.txt b/doc/Examples/Dyesinits.txt
new file mode 100755
index 0000000..6842ebf
--- /dev/null
+++ b/doc/Examples/Dyesinits.txt
@@ -0,0 +1 @@
+list(theta=1500, tau.with=1, tau.btw=1)
\ No newline at end of file
diff --git a/doc/Examples/Dyesinits1.html b/doc/Examples/Dyesinits1.html
new file mode 100755
index 0000000..44b33da
--- /dev/null
+++ b/doc/Examples/Dyesinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dyesinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(theta=3000, tau.with=0.1, tau.btw=0.1)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Dyesinits1.txt b/doc/Examples/Dyesinits1.txt
new file mode 100755
index 0000000..7382e0f
--- /dev/null
+++ b/doc/Examples/Dyesinits1.txt
@@ -0,0 +1 @@
+list(theta=3000, tau.with=0.1, tau.btw=0.1)
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diff --git a/doc/Examples/Dyesmodel.html b/doc/Examples/Dyesmodel.html
new file mode 100755
index 0000000..f3ca177
--- /dev/null
+++ b/doc/Examples/Dyesmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Dyesmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for(i in 1 : batches) {<br> mu[i] ~ dnorm(theta, tau.btw)<br> for(j in 1 : samples) {<br> y[i , j] ~ dnorm(mu[i], tau.with)<br> }<br> [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Dyesmodel.txt b/doc/Examples/Dyesmodel.txt
new file mode 100755
index 0000000..4520251
--- /dev/null
+++ b/doc/Examples/Dyesmodel.txt
@@ -0,0 +1,14 @@
+ model
+ {
+ for(i in 1 : batches) {
+ mu[i] ~ dnorm(theta, tau.btw)
+ for(j in 1 : samples) {
+ y[i , j] ~ dnorm(mu[i], tau.with)
+ }
+ }
+ sigma2.with <- 1 / tau.with
+ sigma2.btw <- 1 / tau.btw
+ tau.with ~ dgamma(0.001, 0.001)
+ tau.btw ~ dgamma(0.001, 0.001)
+ theta ~ dnorm(0.0, 1.0E-10)
+ }
diff --git a/doc/Examples/Endo.html b/doc/Examples/Endo.html
new file mode 100755
index 0000000..e7b3841
--- /dev/null
+++ b/doc/Examples/Endo.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Endo</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="endo0.bmp" alt="[endo0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Endo: conditional inference in<br> case-control studies
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">Breslow and Day (1980) analyse a set of data from a case-control study relating endometrial cancer with exposure to estrogens. 183 pairs of cases and controls were studied, and the full data is shown below.<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="endo1.bmp" alt="[endo1]"><br>
</font><font face="Arial" color="#000100" size="3"></center>We denote estrogen exposure as x
</font><font face="Arial" color="#000100" size="3"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> for the ith case-control pair, where j=1 for a case and j=2 for a control. The conditional likelihood for the log (odds ratio)
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> is then given by
</font><font face="Symbol" color="#000100" size="3">P
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> exp
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>i1
</sub></font><font face="Arial" color="#000100" size="3"> / (exp
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>i1
</sub></font><font face="Arial" color="#000100" size="3"> + exp
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>i2
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>We shall illustrate three methods of fitting this model. It is convenient to denote the fixed disease status as a variable Y
</font><font face="Arial" color="#000100" size="2"><sub>i1
</sub></font><font face="Arial" color="#000100" size="3"> = 1, Y
</font><font face="Arial" color="#000100" size="2"><sub>i2
</sub></font><font face="Arial" color="#000100" size="3"> = 0.<br><br>First, Breslow and Day point out that for case-control studies with a single control per case, we may obtain this likelihood by using unconditional logistic regression for each case-control pair. That is<br><br> Y
</font><font face="Arial" color="#000100" size="2"><sub>i1
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">,2)<br> logit p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> (x
</font><font face="Arial" color="#000100" size="2"><sub>i1
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3"> x
</font><font face="Arial" color="#000100" size="2"><sub>i2
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>Second, the Classic BUGS manual (version 0.5) section on
</font><font face="Arial" color="#000100" size="3"><em>Conditional likelihoods in case-control studies
</em></font><font face="Arial" color="#000100" size="3"> discusses fitting this likelihood directly by assuming the model <br><br> Y
</font><font face="Arial" color="#000100" size="2"><sub>i.
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Multinomial(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>.
</sub></font><font face="Arial" color="#000100" size="3">, 1)<br> p
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = e
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> /
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> e
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><br> log e
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> x
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><br><br>Finally, the Classic BUGS manual (version 0.5) shows how the multinomial-Poisson transformation can be used. In general, this will be more efficient than using the multinomial-logistic parameterisation above, since it avoids the time-consuming evaluation of
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> e
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">. However, in the present example this summation is only over J=2 elements, whilst the multinomial-Poisson parameterisation involves estimation of an additional intercept parameter for each of the 183 strata. Consequently the latter is
</font><font face="Arial" color="#000100" size="3"><em>less
</em></font><font face="Arial" color="#000100" size="3"> efficient than the multinomial-logistic in this case.<br><br>We note that all these formulations may be easily extended to include additional subject-specific covariates, and that the second and third methods can handle arbitrary numbers of controls per case. In addition, the Bayesian approach allows the incorporation of hierarchical structure, measurement error, missing data and so on.<br><br>All these techniques are illustrated in [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br><br> model<br> {<br> # transform collapsed data into full<br> for (i in 1 : I){<br> Y[i,1] <- 1 <br> Y[i,2] <- 0<br> }<br> # loop around strata with case exposed, control [...]
</font><font face="Arial" color="#000100" size="3"># METHOD 1 - logistic regression<br> # Y[i,1] ~ dbin( p[i,1], 1) <br> # logit(p[i,1]) <- beta * (est[i,1] - est[i,J]) <br> <br> # METHOD 2 - conditional likelihoods<br>
</font><font face="Arial" color="#000100" size="3"> Y[i, 1 : J] ~ dmulti( p[i, 1 : J],1)<br> for (j in 1:2){<br> p[i, j] <- e[i, j] / sum(e[i, ])<br> log( e[i, j] ) <- beta * est[i, j] <br> }
</font><font face="Arial" color="#000100" size="3"><br> # METHOD 3 fit standard Poisson regressions relative to baseline<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">#for (j in 1:J) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Y[i, j] ~ dpois(mu[i, j]);<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># log(mu[i, j]) <- beta0[i] + beta*est[i, j]; <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">#beta0[i] ~ dnorm(0, 1.0E-6)
</font><font face="Arial" color="#000100" size="3"><br> }<br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Endodata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( cklick to open )
</font><font face="Arial" color="#000100" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Endoinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Endoinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3">( cklick to open )
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br>
</font><font face="Arial" color="#000000" size="3"><br>A 5000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center><br><img src="endo2.bmp" alt="[endo2]">
</font>
</center>
</p>
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diff --git a/doc/Examples/Endodata.html b/doc/Examples/Endodata.html
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+++ b/doc/Examples/Endodata.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Endodata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(n10=43, n01=7, n11=12, I = 183, J=2)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Endodata.txt b/doc/Examples/Endodata.txt
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index 0000000..009ae30
--- /dev/null
+++ b/doc/Examples/Endodata.txt
@@ -0,0 +1 @@
+list(n10=43, n01=7, n11=12, I = 183, J=2)
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diff --git a/doc/Examples/Endoinits.html b/doc/Examples/Endoinits.html
new file mode 100755
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--- /dev/null
+++ b/doc/Examples/Endoinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Endoinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(beta = 2)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Endoinits.txt b/doc/Examples/Endoinits.txt
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+++ b/doc/Examples/Endoinits.txt
@@ -0,0 +1 @@
+list(beta = 2)
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diff --git a/doc/Examples/Endoinits1.html b/doc/Examples/Endoinits1.html
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--- /dev/null
+++ b/doc/Examples/Endoinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Endoinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(beta = 0.1)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Endoinits1.txt b/doc/Examples/Endoinits1.txt
new file mode 100755
index 0000000..886cd20
--- /dev/null
+++ b/doc/Examples/Endoinits1.txt
@@ -0,0 +1 @@
+list(beta = 0.1)
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diff --git a/doc/Examples/Endomodel.html b/doc/Examples/Endomodel.html
new file mode 100755
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--- /dev/null
+++ b/doc/Examples/Endomodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Endomodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> # transform collapsed data into full<br> for (i in 1 : I){<br> Y[i,1] <- 1 <br> Y[i,2] <- 0<br> }<br> # loop around strata with case exposed, control not exposed (n10)<br>   [...]
</font><font face="Arial" color="#000100" size="3"># METHOD 1 - logistic regression<br> # Y[i,1] ~ dbin( p[i,1], 1) <br> # logit(p[i,1]) <- beta * (est[i,1] - est[i,J]) <br> <br> # METHOD 2 - conditional likelihoods<br>
</font><font face="Arial" color="#000100" size="3"> Y[i, 1 : J] ~ dmulti( p[i, 1 : J],1)<br> for (j in 1:2){<br> p[i, j] <- e[i, j] / sum(e[i, ])<br> log( e[i, j] ) <- beta * est[i, j] <br> }
</font><font face="Arial" color="#000100" size="3"><br> # METHOD 3 fit standard Poisson regressions relative to baseline<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">#for (j in 1:J) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Y[i, j] ~ dpois(mu[i, j]);<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># log(mu[i, j]) <- beta0[i] + beta*est[i, j]; <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">#beta0[i] ~ dnorm(0, 1.0E-6)
</font><font face="Arial" color="#000100" size="3"><br> }<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Endomodel.txt b/doc/Examples/Endomodel.txt
new file mode 100755
index 0000000..bc6223b
--- /dev/null
+++ b/doc/Examples/Endomodel.txt
@@ -0,0 +1,50 @@
+ model
+ {
+ # transform collapsed data into full
+ for (i in 1 : I){
+ Y[i,1] <- 1
+ Y[i,2] <- 0
+ }
+ # loop around strata with case exposed, control not exposed (n10)
+ for (i in 1 : n10){
+ est[i,1] <- 1
+ est[i,2] <- 0
+ }
+ # loop around strata with case not exposed, control exposed (n01)
+ for (i in (n10+1) : (n10+n01)){
+ est[i,1] <- 0
+ est[i,2] <- 1
+ }
+ # loop around strata with case exposed, control exposed (n11)
+ for (i in (n10+n01+1) : (n10+n01+n11)){
+ est[i,1] <- 1
+ est[i,2] <- 1
+ }
+ # loop around strata with case not exposed, control not exposed (n00)
+ for (i in (n10+n01+n11+1) :I ){
+ est[i,1] <- 0
+ est[i,2] <- 0
+ }
+
+ # PRIORS
+ beta ~ dnorm(0,1.0E-6) ;
+
+ # LIKELIHOOD
+ for (i in 1 : I) { # loop around strata
+ # METHOD 1 - logistic regression
+ # Y[i,1] ~ dbin( p[i,1], 1)
+ # logit(p[i,1]) <- beta * (est[i,1] - est[i,J])
+
+ # METHOD 2 - conditional likelihoods
+ Y[i, 1 : J] ~ dmulti( p[i, 1 : J],1)
+ for (j in 1:2){
+ p[i, j] <- e[i, j] / sum(e[i, ])
+ log( e[i, j] ) <- beta * est[i, j]
+ }
+ # METHOD 3 fit standard Poisson regressions relative to baseline
+ #for (j in 1:J) {
+ # Y[i, j] ~ dpois(mu[i, j]);
+ # log(mu[i, j]) <- beta0[i] + beta*est[i, j];
+ }
+ #beta0[i] ~ dnorm(0, 1.0E-6)
+ }
diff --git a/doc/Examples/Epil.html b/doc/Examples/Epil.html
new file mode 100755
index 0000000..d08612d
--- /dev/null
+++ b/doc/Examples/Epil.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Epil</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="epil0.bmp" alt="[epil0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Epilepsy: repeated measures on<br> Poisson counts
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3">Breslow and Clayton (1993) analyse data initially provided by Thall and Vail (1990) concerning seizure counts in a randomised trial of anti-convulsant therpay in epilepsy. The table below shows the successive seizure counts for 59 patients. Covariates are treatment (0,1), 8-week baseline seizure counts, and age in years. The structure of this data is shown below<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="epil1.bmp" alt="[epil1]"></center>
</font><font face="Arial" color="#000100" size="3"><br>We consider model
</font><font face="Arial" color="#000100" size="3"><em>III
</em></font><font face="Arial" color="#000100" size="3"> of Breslow and Clayton (1993), in which Base is transformed to log(Base/4) and Age to log(Age), and a Treatment by log(Base/4) interaction is included. Also present are random effects for both individual subjects b
</font><font face="Arial" color="#000100" size="2">1
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> and also subject by visit random effects b
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">to model extra-Poisson variability within subjects. V
</font><font face="Arial" color="#000100" size="2">4
</font><font face="Arial" color="#000100" size="3"> is an indicator variable for the 4th visit.<br><br> <br> y
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3"> ~ Poisson(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br> log
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>Base
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">log(Base
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">/ 4) +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>Trt
</sub></font><font face="Arial" color="#000100" size="3">Trt
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>BT
</sub></font><font face="Arial" color="#000100" size="3">Trt
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">log(Base
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">/ 4) +<br>
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>Age
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">Age
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>V4
</sub></font><font face="Arial" color="#000100" size="3">V
</font><font face="Arial" color="#000100" size="2"><sub>4
</sub></font><font face="Arial" color="#000100" size="3"> + b1
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> + b
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3"><br> <br> b1
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(0,
</font><font face="Symbol" color="#000100" size="3"> t
</font><font face="Arial" color="#000100" size="2"><sub>b1
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br> b
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(0,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>b
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>Coefficients and precisions are given independent "noninformative'' priors. <br><br>The graphical model is below<br><center>
</font><font face="Arial" color="#000100" size="2"><br><img src="epil2.bmp" alt="[epil2]"><br></center><br>
</font><font face="Arial" color="#000100" size="3">The model shown above leads to a Markov chain that is highly correlated with poor convergence properties. This can be overcome by standardizing each covariate about its mean to ensure approximate prior independence between the regression coefficients as show below:<br><center>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for epil example model III with covariate centering<br>(centering interaction term BT about mean(BT)):
</em></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2"><br></center>
</font><font face="Arial" color="#000100" size="3"> model <br> {<br> for(j in 1 : N) {<br> for(k in 1 : T) {<br> log(mu[j, k]) <- a0 + alpha.Base * (log.Base4[j] - log.Base4.bar) <br> + alpha.Trt * (Trt[j] - Trt.bar) <br> + alpha.BT * (BT[j] - BT.bar) <br> & [...]
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Epildata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#000100" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Epilinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Epilinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>A burn in of 5000 updates followed by a further 10000 updates gave the following parameter estimates <br><center><br><img src="epil3.bmp" alt="[epil3]"><br><br>These estimates can be compared with those of Breslow and Clayton (1993) who reported<br>
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000000" size="2"><sub>0
</sub></font><font face="Arial" color="#000000" size="3"> = -1.27 +/- 1.2,
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000000" size="2"><sub>Base
</sub></font><font face="Arial" color="#000000" size="3"> = 0.86 +/- 0.13,
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000000" size="2"><sub>Trt
</sub></font><font face="Arial" color="#000000" size="3"> = -0.93 +/- 0.40,
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000000" size="2"><sub>BT
</sub></font><font face="Arial" color="#000000" size="3"> = 0.34 +/- 0.21,
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000000" size="2"><sub>Age
</sub></font><font face="Arial" color="#000000" size="3"> = 0.47 +/- 0.35,
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000000" size="2"><sub>V4
</sub></font><font face="Arial" color="#000000" size="3"> = -0.10 +/- 0.90
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000000" size="2"><sub>b1
</sub></font><font face="Arial" color="#000000" size="3"> = 0.48 +/- 0.06
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000000" size="2"><sub>b
</sub></font><font face="Arial" color="#000000" size="3"> = 0.36+/0.04.<br><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Epildata.html b/doc/Examples/Epildata.html
new file mode 100755
index 0000000..c685b2d
--- /dev/null
+++ b/doc/Examples/Epildata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Epildata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"> list(N = 59, T = 4,<br> y = structure(.Data = c( 5, 3, 3, 3,<br>3, 5, 3, 3,<br>2, 4, 0, 5,<br>4, 4, 1, 4,<br>7, 18, 9, 21,<br>5, 2, 8, 7,<br>6, 4, 0, 2,<br>40, 20, 21, 12,<br>5, 6, 6, 5,<br>14, 13, 6, 0,<br>26, 12, 6, 22,<br>12, 6, 8, 4,<br>4, 4, 6, 2,<br>7, 9, 12, 14,<br>16, 24, 10, 9,<br>11, 0, 0, 5,<br>0, 0, 3, 3,<br>37, 29, 28, 29,<br>3, 5, 2, 5,<br>3, 0, 6, 7,<br>3, 4, 3, 4,<br>3, 4, 3, 4,<br>2, 3, 3, 5,<br>8, 12, 2, 8,<br [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Epildata.txt b/doc/Examples/Epildata.txt
new file mode 100755
index 0000000..5052e7a
--- /dev/null
+++ b/doc/Examples/Epildata.txt
@@ -0,0 +1,79 @@
+ list(N = 59, T = 4,
+ y = structure(.Data = c( 5, 3, 3, 3,
+ 3, 5, 3, 3,
+ 2, 4, 0, 5,
+ 4, 4, 1, 4,
+ 7, 18, 9, 21,
+ 5, 2, 8, 7,
+ 6, 4, 0, 2,
+ 40, 20, 21, 12,
+ 5, 6, 6, 5,
+ 14, 13, 6, 0,
+ 26, 12, 6, 22,
+ 12, 6, 8, 4,
+ 4, 4, 6, 2,
+ 7, 9, 12, 14,
+ 16, 24, 10, 9,
+ 11, 0, 0, 5,
+ 0, 0, 3, 3,
+ 37, 29, 28, 29,
+ 3, 5, 2, 5,
+ 3, 0, 6, 7,
+ 3, 4, 3, 4,
+ 3, 4, 3, 4,
+ 2, 3, 3, 5,
+ 8, 12, 2, 8,
+ 18, 24, 76, 25,
+ 2, 1, 2, 1,
+ 3, 1, 4, 2,
+ 13, 15, 13, 12,
+ 11, 14, 9, 8,
+ 8, 7, 9, 4,
+ 0, 4, 3, 0,
+ 3, 6, 1, 3,
+ 2, 6, 7, 4,
+ 4, 3, 1, 3,
+ 22, 17, 19, 16,
+ 5, 4, 7, 4,
+ 2, 4, 0, 4,
+ 3, 7, 7, 7,
+ 4, 18, 2, 5,
+ 2, 1, 1, 0,
+ 0, 2, 4, 0,
+ 5, 4, 0, 3,
+ 11, 14, 25, 15,
+ 10, 5, 3, 8,
+ 19, 7, 6, 7,
+ 1, 1, 2, 3,
+ 6, 10, 8, 8,
+ 2, 1, 0, 0,
+ 102, 65, 72, 63,
+ 4, 3, 2, 4,
+ 8, 6, 5, 7,
+ 1, 3, 1, 5,
+ 18, 11, 28, 13,
+ 6, 3, 4, 0,
+ 3, 5, 4, 3,
+ 1, 23, 19, 8,
+ 2, 3, 0, 1,
+ 0, 0, 0, 0,
+ 1, 4, 3, 2), .Dim = c(59, 4)),
+ Trt = c( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 1),
+ Base = c( 11, 11, 6, 8, 66, 27, 12, 52, 23, 10,
+ 52, 33, 18, 42, 87, 50, 18,111, 18, 20,
+ 12, 9, 17, 28, 55, 9, 10, 47, 76, 38,
+ 19, 10, 19, 24, 31, 14, 11, 67, 41, 7,
+ 22, 13, 46, 36, 38, 7, 36, 11,151, 22,
+ 41, 32, 56, 24, 16, 22, 25, 13, 12),
+ Age = c(31,30,25,36,22,29,31,42,37,28,
+ 36,24,23,36,26,26,28,31,32,21,
+ 29,21,32,25,30,40,19,22,18,32,
+ 20,30,18,24,30,35,27,20,22,28,
+ 23,40,33,21,35,25,26,25,22,32,
+ 25,35,21,41,32,26,21,36,37),
+ V4 = c(0, 0, 0, 1))
diff --git a/doc/Examples/Epilinits.html b/doc/Examples/Epilinits.html
new file mode 100755
index 0000000..968449d
--- /dev/null
+++ b/doc/Examples/Epilinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Epilinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"> list(a0 = 1, alpha.Base = 0, alpha.Trt = 0, alpha.BT = 0, <br>alpha.Age = 0, alpha.V4 = 0, tau.b1 = 1, tau.b =1)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Epilinits.txt b/doc/Examples/Epilinits.txt
new file mode 100755
index 0000000..563b139
--- /dev/null
+++ b/doc/Examples/Epilinits.txt
@@ -0,0 +1,2 @@
+ list(a0 = 1, alpha.Base = 0, alpha.Trt = 0, alpha.BT = 0,
+ alpha.Age = 0, alpha.V4 = 0, tau.b1 = 1, tau.b =1)
\ No newline at end of file
diff --git a/doc/Examples/Epilinits1.html b/doc/Examples/Epilinits1.html
new file mode 100755
index 0000000..42fbef5
--- /dev/null
+++ b/doc/Examples/Epilinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Epilinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(a0 = 1, alpha.Base = 1, alpha.Trt = 1, alpha.BT = 1, <br>alpha.Age = 1, alpha.V4 = 1, tau.b1 = 0.1, tau.b =0.1)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Epilinits1.txt b/doc/Examples/Epilinits1.txt
new file mode 100755
index 0000000..9ab441d
--- /dev/null
+++ b/doc/Examples/Epilinits1.txt
@@ -0,0 +1,2 @@
+list(a0 = 1, alpha.Base = 1, alpha.Trt = 1, alpha.BT = 1,
+ alpha.Age = 1, alpha.V4 = 1, tau.b1 = 0.1, tau.b =0.1)
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diff --git a/doc/Examples/Epilmodel.html b/doc/Examples/Epilmodel.html
new file mode 100755
index 0000000..471cfa5
--- /dev/null
+++ b/doc/Examples/Epilmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Epilmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model <br> {<br> for(j in 1 : N) {<br> for(k in 1 : T) {<br> log(mu[j, k]) <- a0 + alpha.Base * (log.Base4[j] - log.Base4.bar) <br> + alpha.Trt * (Trt[j] - Trt.bar) <br> + alpha.BT * (BT[j] - BT.bar) <br> &n [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Epilmodel.txt b/doc/Examples/Epilmodel.txt
new file mode 100755
index 0000000..551f1c5
--- /dev/null
+++ b/doc/Examples/Epilmodel.txt
@@ -0,0 +1,39 @@
+ model
+ {
+ for(j in 1 : N) {
+ for(k in 1 : T) {
+ log(mu[j, k]) <- a0 + alpha.Base * (log.Base4[j] - log.Base4.bar)
+ + alpha.Trt * (Trt[j] - Trt.bar)
+ + alpha.BT * (BT[j] - BT.bar)
+ + alpha.Age * (log.Age[j] - log.Age.bar)
+ + alpha.V4 * (V4[k] - V4.bar)
+ + b1[j] + b[j, k]
+ y[j, k] ~ dpois(mu[j, k])
+ b[j, k] ~ dnorm(0.0, tau.b); # subject*visit random effects
+ }
+ b1[j] ~ dnorm(0.0, tau.b1) # subject random effects
+ BT[j] <- Trt[j] * log.Base4[j] # interaction
+ log.Base4[j] <- log(Base[j] / 4) log.Age[j] <- log(Age[j])
+ }
+
+ # covariate means:
+ log.Age.bar <- mean(log.Age[])
+ Trt.bar <- mean(Trt[])
+ BT.bar <- mean(BT[])
+ log.Base4.bar <- mean(log.Base4[])
+ V4.bar <- mean(V4[])
+ # priors:
+
+ a0 ~ dnorm(0.0,1.0E-4)
+ alpha.Base ~ dnorm(0.0,1.0E-4)
+ alpha.Trt ~ dnorm(0.0,1.0E-4);
+ alpha.BT ~ dnorm(0.0,1.0E-4)
+ alpha.Age ~ dnorm(0.0,1.0E-4)
+ alpha.V4 ~ dnorm(0.0,1.0E-4)
+ tau.b1 ~ dgamma(1.0E-3,1.0E-3); sigma.b1 <- 1.0 / sqrt(tau.b1)
+ tau.b ~ dgamma(1.0E-3,1.0E-3); sigma.b <- 1.0/ sqrt(tau.b)
+
+ # re-calculate intercept on original scale:
+ alpha0 <- a0 - alpha.Base * log.Base4.bar - alpha.Trt * Trt.bar
+ - alpha.BT * BT.bar - alpha.Age * log.Age.bar - alpha.V4 * V4.bar
+ }
diff --git a/doc/Examples/Equiv.html b/doc/Examples/Equiv.html
new file mode 100755
index 0000000..2de1f7e
--- /dev/null
+++ b/doc/Examples/Equiv.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Equiv</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="equiv0.bmp" alt="[equiv0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Equiv: bioequivalence in a <br> cross-over trial
</font><font face="Arial" color="#000100" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><br>The table below shows some data from a two-treatment, two-period crossover trial to compare 2 tablets A and B, as reported by Gelfand
</font><font face="Arial" color="#000100" size="3"><em>et al
</em></font><font face="Arial" color="#000100" size="3">(1990).<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="equiv1.bmp" alt="[equiv1]">
</font><font face="Arial" color="#000100" size="3"><br></center><br>The response Y
</font><font face="Arial" color="#000100" size="3"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"> from the
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">th subject (
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">= 1,...,10) in the
</font><font face="Arial" color="#000100" size="3"><em>k
</em></font><font face="Arial" color="#000100" size="3">th period (
</font><font face="Arial" color="#000100" size="3"><em>k
</em></font><font face="Arial" color="#000100" size="3"> = 1,2) is assumed to be of the form<br><br> Y
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(m
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">)<br><br> m
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="3"> + (-1)
</font><font face="Arial" color="#000100" size="3"><sup>T
</sup></font><font face="Arial" color="#000100" size="2"><sup>ik
</sup></font><font face="Arial" color="#000100" size="3"><sup>
</sup></font><font face="Arial" color="#000100" size="2"><sup>- 1
</sup></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3">/ 2 + (-1)
</font><font face="Arial" color="#000100" size="2"><sup>k - 1
</sup></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="3"> / 2 +
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(0,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>where T
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3">= 1,2 denotes the treatment given to subject
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">in period
</font><font face="Arial" color="#000100" size="3"><em>k
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">m, f, p
</font><font face="Arial" color="#000100" size="3"> are the overall mean, treatment and period effects respectively, and
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> represents the random effect for subject
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">. The graph of this model and its
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language description are shown below <br><br><br><center>
</font><font face="Arial" color="#000100" size="3"><em>Graphical model for equiv example
</em></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><img src="equiv2.bmp" alt="[equiv2]"><br><br><br><br>BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for equiv example
</em></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"><br></center> model<br> {<br> for( k in 1 : P ) {<br> for( i in 1 : N ) {<br> Y[i , k] ~ dnorm(m[i , k], tau1)<br> m[i , k] <- mu + sign[T[i , k]] * phi / 2 + sign[k] * pi / 2 [...]
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3"> = e
</font><font face="Symbol" color="#000100" size="2"><sup>f
</sup></font><font face="Arial" color="#000100" size="3"> lies between 0.8 and 1.2 which traditionally determines bioequivelence.<br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Equivdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Equivinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Equivinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )<br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3">A 1000 update burn in followed by a further 10000 updates gave the parameteres estimates<br><center><br><img src="equiv3.bmp" alt="[equiv3]">
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Equivdata.html b/doc/Examples/Equivdata.html
new file mode 100755
index 0000000..40c9e8d
--- /dev/null
+++ b/doc/Examples/Equivdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Equivdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 10, P = 2,<br> group = c(1, 1, -1, -1, -1, 1, 1, 1, -1, -1),<br> Y = structure(.Data = c(1.40, 1.65,<br> 1.64, 1.57,<br>   [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Equivdata.txt b/doc/Examples/Equivdata.txt
new file mode 100755
index 0000000..5a27e09
--- /dev/null
+++ b/doc/Examples/Equivdata.txt
@@ -0,0 +1,13 @@
+list(N = 10, P = 2,
+ group = c(1, 1, -1, -1, -1, 1, 1, 1, -1, -1),
+ Y = structure(.Data = c(1.40, 1.65,
+ 1.64, 1.57,
+ 1.44, 1.58,
+ 1.36, 1.68,
+ 1.65, 1.69,
+ 1.08, 1.31,
+ 1.09, 1.43,
+ 1.25, 1.44,
+ 1.25, 1.39,
+ 1.30, 1.52), .Dim = c(10, 2)),
+ sign = c(1, -1))
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diff --git a/doc/Examples/Equivinits.html b/doc/Examples/Equivinits.html
new file mode 100755
index 0000000..5c5018b
--- /dev/null
+++ b/doc/Examples/Equivinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Equivinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(mu=0, phi=0, pi=0, tau1= 1, tau2 = 1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Equivinits.txt b/doc/Examples/Equivinits.txt
new file mode 100755
index 0000000..93759ff
--- /dev/null
+++ b/doc/Examples/Equivinits.txt
@@ -0,0 +1 @@
+list(mu=0, phi=0, pi=0, tau1= 1, tau2 = 1)
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diff --git a/doc/Examples/Equivinits1.html b/doc/Examples/Equivinits1.html
new file mode 100755
index 0000000..6d878d4
--- /dev/null
+++ b/doc/Examples/Equivinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Equivinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(mu=10, phi=10, pi=10, tau1= 0.1, tau2 = 0.1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Equivinits1.txt b/doc/Examples/Equivinits1.txt
new file mode 100755
index 0000000..a0e40a7
--- /dev/null
+++ b/doc/Examples/Equivinits1.txt
@@ -0,0 +1 @@
+list(mu=10, phi=10, pi=10, tau1= 0.1, tau2 = 0.1)
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diff --git a/doc/Examples/Equivmodel.html b/doc/Examples/Equivmodel.html
new file mode 100755
index 0000000..8c115c0
--- /dev/null
+++ b/doc/Examples/Equivmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Equivmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for( k in 1 : P ) {<br> for( i in 1 : N ) {<br> Y[i , k] ~ dnorm(m[i , k], tau1)<br> m[i , k] <- mu + sign[T[i , k]] * phi / 2 + sign[k] * pi / 2 + delta[i]<br>  [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Equivmodel.txt b/doc/Examples/Equivmodel.txt
new file mode 100755
index 0000000..e8eed76
--- /dev/null
+++ b/doc/Examples/Equivmodel.txt
@@ -0,0 +1,20 @@
+ model
+ {
+ for( k in 1 : P ) {
+ for( i in 1 : N ) {
+ Y[i , k] ~ dnorm(m[i , k], tau1)
+ m[i , k] <- mu + sign[T[i , k]] * phi / 2 + sign[k] * pi / 2 + delta[i]
+ T[i , k] <- group[i] * (k - 1.5) + 1.5
+ }
+ }
+ for( i in 1 : N ) {
+ delta[i] ~ dnorm(0.0, tau2)
+ }
+ tau1 ~ dgamma(0.001, 0.001) sigma1 <- 1 / sqrt(tau1)
+ tau2 ~ dgamma(0.001, 0.001) sigma2 <- 1 / sqrt(tau2)
+ mu ~ dnorm(0.0, 1.0E-6)
+ phi ~ dnorm(0.0, 1.0E-6)
+ pi ~ dnorm(0.0, 1.0E-6)
+ theta <- exp(phi)
+ equiv <- step(theta - 0.8) - step(theta - 1.2)
+ }
diff --git a/doc/Examples/Eye-tracking.html b/doc/Examples/Eye-tracking.html
new file mode 100755
index 0000000..8e36ea4
--- /dev/null
+++ b/doc/Examples/Eye-tracking.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Eye-tracking</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><img src="eye-tracking0.bmp" alt="[eye-tracking0]">
</font><font face="Arial" color="#0000FF" size="6">
</font><font face="Courier New" color="#000100" size="6">Eye Tracking: dirichlet process<br> prior
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="6"><br>
</font><font face="Arial" color="#000000" size="3">Adapted from Congdon (2001), example 6.27, page 263.<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"> model{ <br> for( i in 1 : N ) {<br> S[i] ~ dcat(pi[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i] <- theta[S[i]]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">x[i] ~ dpois(mu[i])<br> for (j in 1 : C) {<br> SC[i, j] <- equals(j, S[i])<br> }<br> }<br> # Precision Parameter <br> alpha <- 1<br> # alpha~ dgamma(0.1,0. [...]
</font><font face="Arial" color="#000100" size="3"> p[1] <- r[1]<br> for (j in 2 : C) {<br> p[j] <- r[j] * (1 - r[j - 1]) * p[j -1 ] / r[j - 1]<br> }<br>
</font><font face="Arial" color="#000100" size="3"> p.sum <- sum(p[])
</font><font face="Arial" color="#000100" size="3"><br> for (j in 1:C){ <br>
</font><font face="Arial" color="#000100" size="3">theta[j] ~ dgamma(A, B)
</font><font face="Arial" color="#000100" size="3"><br> r[j] ~ dbeta(1, alpha)<br> # scaling to ensure sum to 1 <br> pi[j] <- p[j] / p.sum <br> }<br>
</font><font face="Arial" color="#000100" size="3"> # hierarchical prior on theta[i] or preset parameters<br> A ~ dexp(0.1) B ~dgamma(0.1, 0.1)<br> # A <- 1 B <- 1<br> # total clusters<br> K <- sum(cl[])<br> for (j in 1 : C) {<br> sumSC[j] <- sum(SC[ , j] [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Eyetrackingdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br><br>
</font><font face="Arial" color="#000000" size="3">a) fixed A and B, fixed alpha=1, C=10 (max catgeories)<br><center><br><img src="eye-tracking1.bmp" alt="[eye-tracking1]">
</font><font face="Arial" color="#000100" size="2"><br><br><img src="eye-tracking2.bmp" alt="[eye-tracking2]"><br></center>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">Notice prior and data conflict.
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#000000" size="3">b) variable A and B, fixed alpha=1, C=10 (max catgeories)<br><center>
</font><font face="Arial" color="#000100" size="2"><br><img src="eye-tracking3.bmp" alt="[eye-tracking3]"><br> <br><img src="eye-tracking4.bmp" alt="[eye-tracking4]"><br></center>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Eyes.html b/doc/Examples/Eyes.html
new file mode 100755
index 0000000..7985e38
--- /dev/null
+++ b/doc/Examples/Eyes.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Eyes</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="eyes0.bmp" alt="[eyes0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Eyes: Normal Mixture Model
</font><font face="Arial" color="#000100" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Bowmaker et al (1985) analyse data on the peak sensitivity wavelengths for individual microspectrophotometric records on a small set of monkey's eyes. Data for one monkey (S14 in the paper) are given below (500 has been subtracted from each of the 48 measurements).
</font><font face="Arial" color="#000100" size="2"><br><center><img src="eyes1.bmp" alt="[eyes1]">
</font><font face="Arial" color="#000100" size="1"><br></center>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Part of the analysis involves fitting a mixture of two normal distributions with common variance to this distribution, so that each observation y
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">is assumed drawn from one of two groups. T
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">= 1, 2 be the true group of the
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">th observation, where group j has a normal distribution with mean
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> and precision
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">. We assume an unknown fraction P of observations are in group 2, 1 - P in group 1. The model is thus <br><br><br> y
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="3"><sub>T
</sub></font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">)<br> <br> T
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Categorical(P).<br><br><br>We note that this formulation easily generalises to additional components to the mixture, although for identifiability an order constraint must be put onto the group means.<br><br>Robert (1994) points out that when using this model, there is a danger that at some iteration,
</font><font face="Arial" color="#000100" size="3"><em>all
</em></font><font face="Arial" color="#000100" size="3"> the data will go into one component of themixture, and this state will be difficult to escape from --- this matches our experience. obert suggests a re-parameterisation, a simplified version of which is to assume <br><br>
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">+
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3"> > 0.<br> <br>
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3"> t
</font><font face="Arial" color="#000100" size="3">, P, are given independent ``noninformative" priors, including a uniform prior for P on (0,1). The appropriate graph and the BUGS code are given below.<br>
</font><font face="Arial" color="#000100" size="2"><br><center><img src="eyes2.bmp" alt="[eyes2]"><br><br><br>
</font><font face="Arial" color="#000100" size="1"></center>
</font><font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : N ) {<br> y[i] ~ dnorm(mu[i], tau)<br> mu[i] <- lambda[T[i]]<br> T[i] ~ dcat(P[])<br> } <br> [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Eyesdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#000100" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="2"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Eyesinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Eyesinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u> Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )<br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center><br><br><img src="eyes3.bmp" alt="[eyes3]">
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Eyesdata.html b/doc/Examples/Eyesdata.html
new file mode 100755
index 0000000..0645f8d
--- /dev/null
+++ b/doc/Examples/Eyesdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Eyesdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">list(y = c(529.0, 530.0, 532.0, 533.1, 533.4, 533.6, 533.7, 534.1, 534.8, 535.3,<br> 535.4, 535.9, 536.1, 536.3, 536.4, 536.6, 537.0, 537.4, 537.5, 538.3,<br> 538.5, 538.6, 539.4, 539.6, 540.4, 540.8, 542.0, 542.8, 543.0, 543.5,<br> 543.8, 543.9, 545.3, 546.2, 548.8, 548.7, 548.9, 549.0, 5 [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Eyesdata.txt b/doc/Examples/Eyesdata.txt
new file mode 100755
index 0000000..db42f94
--- /dev/null
+++ b/doc/Examples/Eyesdata.txt
@@ -0,0 +1,10 @@
+list(y = c(529.0, 530.0, 532.0, 533.1, 533.4, 533.6, 533.7, 534.1, 534.8, 535.3,
+ 535.4, 535.9, 536.1, 536.3, 536.4, 536.6, 537.0, 537.4, 537.5, 538.3,
+ 538.5, 538.6, 539.4, 539.6, 540.4, 540.8, 542.0, 542.8, 543.0, 543.5,
+ 543.8, 543.9, 545.3, 546.2, 548.8, 548.7, 548.9, 549.0, 549.4, 549.9,
+ 550.6, 551.2, 551.4, 551.5, 551.6, 552.8, 552.9,553.2), N = 48, alpha = c(1, 1),
+ T = c(1, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+ NA, NA, NA, NA, NA, NA, NA, 2))
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diff --git a/doc/Examples/Eyesinits.html b/doc/Examples/Eyesinits.html
new file mode 100755
index 0000000..0196b4f
--- /dev/null
+++ b/doc/Examples/Eyesinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Eyesinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">list(lambda = c(535, NA), theta = 5, tau = 0.1)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Eyesinits.txt b/doc/Examples/Eyesinits.txt
new file mode 100755
index 0000000..bca2dde
--- /dev/null
+++ b/doc/Examples/Eyesinits.txt
@@ -0,0 +1 @@
+list(lambda = c(535, NA), theta = 5, tau = 0.1)
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diff --git a/doc/Examples/Eyesinits1.html b/doc/Examples/Eyesinits1.html
new file mode 100755
index 0000000..a736639
--- /dev/null
+++ b/doc/Examples/Eyesinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Eyesinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">list(lambda = c(100, NA), theta = 50, tau = 1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Eyesinits1.txt b/doc/Examples/Eyesinits1.txt
new file mode 100755
index 0000000..30c1c34
--- /dev/null
+++ b/doc/Examples/Eyesinits1.txt
@@ -0,0 +1 @@
+list(lambda = c(100, NA), theta = 50, tau = 1)
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diff --git a/doc/Examples/Eyesmodel.html b/doc/Examples/Eyesmodel.html
new file mode 100755
index 0000000..a513114
--- /dev/null
+++ b/doc/Examples/Eyesmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Eyesmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : N ) {<br> y[i] ~ dnorm(mu[i], tau)<br> mu[i] <- lambda[T[i]]<br> T[i] ~ dcat(P[])<br> } <br> P[1:2] [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Eyesmodel.txt b/doc/Examples/Eyesmodel.txt
new file mode 100755
index 0000000..91761ab
--- /dev/null
+++ b/doc/Examples/Eyesmodel.txt
@@ -0,0 +1,13 @@
+ model
+ {
+ for( i in 1 : N ) {
+ y[i] ~ dnorm(mu[i], tau)
+ mu[i] <- lambda[T[i]]
+ T[i] ~ dcat(P[])
+ }
+ P[1:2] ~ ddirich(alpha[])
+ theta ~ dunif(0.0, 1000)
+ lambda[2] <- lambda[1] + theta
+ lambda[1] ~ dnorm(0.0, 1.0E-6)
+ tau ~ dgamma(0.001, 0.001) sigma <- 1 / sqrt(tau)
+ }
diff --git a/doc/Examples/Eyetracking.html b/doc/Examples/Eyetracking.html
new file mode 100755
index 0000000..27b9780
--- /dev/null
+++ b/doc/Examples/Eyetracking.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Eyetracking</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><img src="eyetracking0.bmp" alt="[eyetracking0]">
</font><font face="Arial" color="#0000FF" size="6">
</font><font face="Courier New" color="#000100" size="6">Eye Tracking: dirichlet process<br> prior
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="6"><br>
</font><font face="Arial" color="#000000" size="3">Adapted from Congdon (2001), example 6.27, page 263.<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"> model{ <br> for( i in 1 : N ) {<br> S[i] ~ dcat(pi[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i] <- theta[S[i]]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">x[i] ~ dpois(mu[i])<br> for (j in 1 : C) {<br> SC[i, j] <- equals(j, S[i])<br> }<br> }<br> # Precision Parameter <br> alpha <- 1<br> # alpha~ dgamma(0.1,0. [...]
</font><font face="Arial" color="#000100" size="3"> p[1] <- r[1]<br> for (j in 2 : C) {<br> p[j] <- r[j] * (1 - r[j - 1]) * p[j -1 ] / r[j - 1]<br> }<br>
</font><font face="Arial" color="#000100" size="3"> p.sum <- sum(p[])
</font><font face="Arial" color="#000100" size="3"><br> for (j in 1:C){ <br>
</font><font face="Arial" color="#000100" size="3">theta[j] ~ dgamma(A, B)
</font><font face="Arial" color="#000100" size="3"><br> r[j] ~ dbeta(1, alpha)<br> # scaling to ensure sum to 1 <br> pi[j] <- p[j] / p.sum <br> }<br>
</font><font face="Arial" color="#000100" size="3"> # hierarchical prior on theta[i] or preset parameters<br> A ~ dexp(0.1) B ~dgamma(0.1, 0.1)<br> # A <- 1 B <- 1<br> # total clusters<br> K <- sum(cl[])<br> for (j in 1 : C) {<br> sumSC[j] <- sum(SC[ , j] [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Eyetrackingdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br><br>
</font><font face="Arial" color="#000000" size="3">a) fixed A and B, fixed alpha=1, C=10 (max catgeories)<br><center><br><img src="eyetracking1.bmp" alt="[eyetracking1]"><br><br><br><img src="eyetracking2.bmp" alt="[eyetracking2]">
</font><font face="Arial" color="#000100" size="2"><br></center>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">Notice prior and data conflict.
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#000000" size="3">b) variable A and B, fixed alpha=1, C=10 (max catgeories)<br><center><br><br><img src="eyetracking3.bmp" alt="[eyetracking3]">
</font><font face="Arial" color="#000100" size="2"><br><br><br><img src="eyetracking4.bmp" alt="[eyetracking4]"><br>
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Eyetrackingdata.html b/doc/Examples/Eyetrackingdata.html
new file mode 100755
index 0000000..2029e3e
--- /dev/null
+++ b/doc/Examples/Eyetrackingdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Eyetrackingdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(x=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,<br>2,3, 3, 3, 3, 4, 4, 5, 5, 5, 6, 6, 6,7,7,7,8,9,9,10, 10,<br>11, 11, 12, 12, 14, 15, 15, 17, 17, 22, 24, 34), N=101, C=10)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Eyetrackingdata.txt b/doc/Examples/Eyetrackingdata.txt
new file mode 100755
index 0000000..2133737
--- /dev/null
+++ b/doc/Examples/Eyetrackingdata.txt
@@ -0,0 +1,4 @@
+list(x=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,
+2,3, 3, 3, 3, 4, 4, 5, 5, 5, 6, 6, 6,7,7,7,8,9,9,10, 10,
+11, 11, 12, 12, 14, 15, 15, 17, 17, 22, 24, 34), N=101, C=10)
\ No newline at end of file
diff --git a/doc/Examples/Eyetrackingmodel.html b/doc/Examples/Eyetrackingmodel.html
new file mode 100755
index 0000000..9c1ec79
--- /dev/null
+++ b/doc/Examples/Eyetrackingmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Eyetrackingmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model{ <br> for( i in 1 : N ) {<br> S[i] ~ dcat(pi[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i] <- theta[S[i]]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">x[i] ~ dpois(mu[i]) <br> for (j in 1 : C) {<br> SC[i, j] <- equals(j, S[i])<br> }<br> }<br> # Precision Parameter <br> alp [...]
</font><font face="Arial" color="#000100" size="3"> p[1] <- r[1]<br> for (j in 2 : C) {<br> p[j] <- r[j] * (1 - r[j - 1]) * p[j -1 ] / r[j - 1]<br> }<br>
</font><font face="Arial" color="#000100" size="3"> p.sum <- sum(p[])
</font><font face="Arial" color="#000100" size="3"> <br> for (j in 1:C){ <br>
</font><font face="Arial" color="#000100" size="3">theta[j] ~ dgamma(A, B)
</font><font face="Arial" color="#000100" size="3"><br> r[j] ~ dbeta(1, alpha) <br> # scaling to ensure sum to 1 <br> pi[j] <- p[j] / p.sum <br> }<br>
</font><font face="Arial" color="#000100" size="3"> # hierarchical prior on theta[i] or preset parameters<br> A ~ dexp(0.1) B ~dgamma(0.1, 0.1)<br> # A <- 1 B <- 1<br> # total clusters <br> K <- sum(cl[])<br> for (j in 1 : C) {<br> &nb [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Eyetrackingmodel.txt b/doc/Examples/Eyetrackingmodel.txt
new file mode 100755
index 0000000..5f755f6
--- /dev/null
+++ b/doc/Examples/Eyetrackingmodel.txt
@@ -0,0 +1,34 @@
+ model{
+ for( i in 1 : N ) {
+ S[i] ~ dcat(pi[])
+ mu[i] <- theta[S[i]]
+ x[i] ~ dpois(mu[i])
+ for (j in 1 : C) {
+ SC[i, j] <- equals(j, S[i])
+ }
+ }
+ # Precision Parameter
+ alpha <- 1
+ # alpha~ dgamma(0.1,0.1)
+ # Constructive DPP
+ p[1] <- r[1]
+ for (j in 2 : C) {
+ p[j] <- r[j] * (1 - r[j - 1]) * p[j -1 ] / r[j - 1]
+ }
+ p.sum <- sum(p[])
+ for (j in 1:C){
+ theta[j] ~ dgamma(A, B)
+ r[j] ~ dbeta(1, alpha)
+ # scaling to ensure sum to 1
+ pi[j] <- p[j] / p.sum
+ }
+ # hierarchical prior on theta[i] or preset parameters
+ A ~ dexp(0.1) B ~dgamma(0.1, 0.1)
+ # A <- 1 B <- 1
+ # total clusters
+ K <- sum(cl[])
+ for (j in 1 : C) {
+ sumSC[j] <- sum(SC[ , j])
+ cl[j] <- step(sumSC[j] -1)
+ }
+ }
diff --git a/doc/Examples/Fire.html b/doc/Examples/Fire.html
new file mode 100755
index 0000000..2c2a82f
--- /dev/null
+++ b/doc/Examples/Fire.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Fire</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">This example is taken from Section 5 of<br><br>Scollnik, David P. M. , 'On composite lognormal-Pareto models', Scandinavian Actuarial Journal, 2007:1, pages 20 - 33 <br><br>using the lognormal-pareto II model.<br><br>The data are fire insurance losses (in Danish Krone). The model is lognormal with mean mu and variance sigma when the losses (X) are less than an unknown parameter, theta, and pareto with parameter alpha when X is greater than theta [...]
</font><font face="Arial" color="#000100" size="3"><strong><br>log(r/phi(alpha * sigma)) * ( 1 - stepxtheta[i] ) + log(1-r) * stepxtheta[i] +
</strong></font><font face="Arial" color="#000100" size="3"><br>( -0.5 * log(2 * pi) - log( x[i] ) - log( sigma ) - 0.5 * pow( (log(x[i])- mu)/ sigma, 2) ) * <br>( 1 - stepxtheta[i] ) + <br>( log(alpha) + alpha * log(theta) - (alpha+1)* log( x[i]) ) * stepxtheta[i]<br><br>stepxtheta[i] <- step( x[i] - theta )<br><br>}<br><br>theta ~ dgamma( 0.001, 0.001) # dexp( 0.5 ) #<br>alpha ~dgamma( 0.001, 0.001) # dexp( 0.5 ) #<br>sigma ~ dgamma(0.001, 0.001) # dexp( 0.5 ) #<br><br>r <- (sqrt( [...]
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Firedata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )<br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Fireinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits</a>
</u></font><font face="Arial" color="#000000" size="3"> <br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3">A 1000 update burn in followed by a further 10000 updates gave the parameter estimates:<br><br>
</font><font face="Arial" color="#000100" size="2"><img src="fire0.bmp" alt="[fire0]"><img src="fire1.bmp" alt="[fire1]"><img src="fire2.bmp" alt="[fire2]"><br><br><br>
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> alpha 1.328 0.03179 7.257E-4 1.267 1.328 1.392 1001 10000<br> sigma 0.1971 0.01209 5.755E-4 0.1745 0.1966 0.2219 1001 10000<br [...]
</font><font face="Arial" color="#000000" size="3"><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Firedata.html b/doc/Examples/Firedata.html
new file mode 100755
index 0000000..c5ad9f8
--- /dev/null
+++ b/doc/Examples/Firedata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Firedata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(x=c(1.6837482, 2.0937042, 1.7325813, 1.7797540, 4.6120059,<br>8.7252738, 7.8989751, 2.2080454, 1.4860908, 2.7961713,<br>7.3206442, 3.3674963, 1.4641288, 1.7222225, 11.3748170,<br>2.4827394, 26.2146413, 2.0024305, 4.5300146, 1.8417526,<br>3.8067350, 14.1220761, 5.4242533, 11.7130307, 1.5153734,<br>2.5385886, 2.0497804, 12.4655930, 1.7354451, 1.6837482,<br>3.3238521, 1.8210249, 2.4158126, 1.4641288, 5.8759019,<br>1.7924392, 3.3382138, 1.58448 [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Firedata.txt b/doc/Examples/Firedata.txt
new file mode 100755
index 0000000..0204910
--- /dev/null
+++ b/doc/Examples/Firedata.txt
@@ -0,0 +1,499 @@
+list(x=c(1.6837482, 2.0937042, 1.7325813, 1.7797540, 4.6120059,
+8.7252738, 7.8989751, 2.2080454, 1.4860908, 2.7961713,
+7.3206442, 3.3674963, 1.4641288, 1.7222225, 11.3748170,
+2.4827394, 26.2146413, 2.0024305, 4.5300146, 1.8417526,
+3.8067350, 14.1220761, 5.4242533, 11.7130307, 1.5153734,
+2.5385886, 2.0497804, 12.4655930, 1.7354451, 1.6837482,
+3.3238521, 1.8210249, 2.4158126, 1.4641288, 5.8759019,
+1.7924392, 3.3382138, 1.5844876, 1.9313206, 2.0497804,
+1.5737584, 1.7569546, 4.9311859, 5.4172767, 1.5373353,
+17.5695461, 1.6911230, 1.5816120, 1.4671157, 2.0497804,
+1.9287116, 3.2631537, 1.7042460, 2.0746076, 3.2942899,
+1.8399751, 7.3206442, 7.3206442, 1.5762152, 4.8560981,
+1.5422753, 13.6207906, 1.7569546, 1.6398243, 2.0363777,
+21.9619327, 1.7990264, 2.4524158, 2.6691069, 2.0241464,
+1.7247438, 1.6438638, 1.9619327, 4.6266471, 1.4641288,
+3.9632504, 5.5638521, 4.3923865, 3.6403133, 1.6778917,
+1.4494876, 263.2503660, 2.5007321, 1.8257687, 9.8828697,
+2.1466179, 2.8702592, 6.3199136, 2.1234612, 2.9238653,
+2.0363763, 1.7364568, 2.0497804, 1.9033675, 1.6105417,
+1.7174231, 3.1294378, 2.0519575, 1.9675183, 2.1024890,
+3.2591508, 1.9985359, 5.4172767, 2.8198360, 3.6970835,
+2.0453880, 2.6793558, 3.4262240, 1.5885798, 4.2628712,
+1.7558594, 1.9870059, 1.6619253, 7.6134700, 1.7948785,
+6.6748170, 2.1859444, 3.8550512, 3.2210835, 2.1229868,
+1.7602914, 2.0416530, 3.7559385, 2.2421113, 1.7211127,
+1.4641288, 4.7118917, 2.1538243, 3.8748126, 19.0702782,
+1.8872621, 1.4641288, 1.5361640, 2.5600659, 2.7997072,
+2.0131772, 1.4641288, 6.3250366, 1.5673001, 2.1961933,
+2.3352855, 2.1156662, 1.4695447, 5.4026354, 5.3147877,
+2.8726208, 2.7818448, 2.5768214, 3.1010249, 1.4641288,
+2.0497804, 1.9619327, 1.4641288, 2.6354319, 1.4641288,
+5.8565154, 3.2942899, 2.5208565, 19.4729136, 1.8354627,
+2.0497804, 2.7833089, 2.7818448, 1.7569546, 2.8404100,
+2.3308931, 1.7562254, 1.3145478, 2.4039712, 6.9156304,
+1.4918768, 1.5323958, 1.8738611, 1.8152031, 8.2568807,
+1.4102045, 2.2066252, 34.1415465, 2.4433106, 3.5943696,
+2.3722149, 3.6697248, 6.8884535, 1.8020970, 1.4416776,
+9.1743119, 2.0969856, 2.8145478, 1.6849030, 2.0996068,
+2.6212320, 1.3761468, 1.6644823, 2.3591088, 4.1364875,
+1.3943958, 1.8020970, 1.8191350, 1.5137615, 3.0807733,
+20.9698558, 4.1939712, 1.8616435, 2.4967235, 2.2137811,
+5.2424640, 1.3222543, 8.5517693, 1.9659240, 12.8951507,
+1.7889908, 2.1768270, 8.7776278, 1.8152031, 1.6831402,
+3.6435125, 1.6133683, 1.4678899, 1.4056042, 3.1208034,
+1.5981809, 3.8007864, 1.5100891, 1.5727392, 1.8300524,
+2.6212320, 2.8064810, 1.3577982, 1.6186107, 1.9659240,
+3.0222805, 56.2254260, 4.9803408, 1.9871625, 1.9659240,
+2.7112923, 1.9003932, 1.7234600, 1.5727392, 1.7038008,
+3.0196592, 1.8348624, 1.4193971, 4.3905636, 7.8636959,
+1.5727392, 1.3366134, 1.7038008, 2.6356225, 1.8647182,
+1.4577549, 7.5583224, 2.0313971, 1.3499345, 1.4748624,
+5.1114024, 5.2424640, 1.4416776, 3.9361389, 4.0629096,
+1.3761468, 1.6841415, 1.4406199, 1.3645491, 1.5727392,
+2.1854220, 3.2813460, 1.3631009, 2.1231979, 2.6343381,
+2.0982962, 3.4343526, 1.4787955, 2.6212320, 3.0013106,
+1.4297339, 10.2228047, 2.5793958, 1.7553591, 1.4734050,
+1.9528178, 1.7798689, 1.9868624, 1.9397117, 1.6759004,
+1.5727392, 2.5249017, 14.6788991, 3.0340760, 1.9790301,
+5.9377588, 1.4416776, 2.6212320, 2.0380079, 3.7549148,
+2.4377457, 1.7020315, 7.1098702, 2.0196592, 1.8504902,
+1.4159502, 7.6933159, 3.0144168, 2.3591088, 1.5923159,
+1.3892529, 1.3329685, 1.4233290, 2.9775714, 1.3873552,
+1.4049803, 2.6212320, 4.2791612, 1.6055046, 2.0117955,
+2.2673657, 1.4646501, 3.3740655, 1.4907995, 2.0969856,
+1.5701664, 1.3761468, 3.1454784, 8.4537353, 3.0332831,
+2.0642202, 6.4220183, 1.8987877, 1.4901704, 50.0655308,
+1.5596330, 1.9659240, 1.8000524, 2.4246396, 1.3106160,
+1.6120577, 4.2211653, 1.2604043, 1.4036932, 1.2972652,
+1.9274923, 1.9154578, 1.2074518, 5.6985826, 1.9024970,
+1.1891344, 10.1780238, 1.6020797, 4.1617122, 2.3630499,
+1.9650440, 1.9459822, 2.8537455, 1.2024400, 10.8204518,
+1.5887634, 2.0963496, 5.4696790, 1.8929845, 2.0332937,
+1.6052319, 1.4030916, 1.1950059, 3.2461356, 1.2631225,
+2.9726516, 1.2049501, 1.8812735, 1.7835910, 3.9239001,
+1.9024970, 1.6646849, 4.4528252, 1.3236207, 1.6052319,
+24.9702735, 2.7348395, 1.7835910, 1.8109394, 2.1141498,
+1.3912010, 1.3460166, 1.5073841, 1.9404875, 2.5697979,
+1.5807658, 1.4875149, 1.5219976, 1.6908442, 1.7835910,
+1.2588656, 1.5737479, 1.4673008, 2.7137051, 2.7360285,
+1.4565993, 2.1374316, 2.4790904, 2.3781213, 4.6373365, # )) ,
+1.1890606, 1.5457788, 2.3424495, 2.3376932, 1.3971463,
+4.2211653, 1.6399524, 1.2187872, 3.6860880, 2.4970273,
+2.4970273, 5.2318668, 1.3079667, 1.2681249, 2.1652794,
+4.6401926, 2.9726516, 1.6646849, 1.1890606, 11.8906064,
+2.8656361, 1.2443674, 1.7241379, 5.6956005, 1.3595696,
+7.0749108, 1.4034756, 1.4024185, 1.3198573, 4.3205886,
+1.8430440, 1.4149822, 1.4863258, 4.9460321, 1.9131986,
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diff --git a/doc/Examples/Fireinits.html b/doc/Examples/Fireinits.html
new file mode 100755
index 0000000..dbdade7
--- /dev/null
+++ b/doc/Examples/Fireinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Fireinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(alpha=1, sigma = 0.1, theta=1) # MLEs are 1.3234, 0.1927, 1.1969 <br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Fireinits.txt b/doc/Examples/Fireinits.txt
new file mode 100755
index 0000000..0b436ab
--- /dev/null
+++ b/doc/Examples/Fireinits.txt
@@ -0,0 +1 @@
+list(alpha=1, sigma = 0.1, theta=1) # MLEs are 1.3234, 0.1927, 1.1969
diff --git a/doc/Examples/Firemodel.html b/doc/Examples/Firemodel.html
new file mode 100755
index 0000000..503bee7
--- /dev/null
+++ b/doc/Examples/Firemodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Firemodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">model{<br><br>for ( i in 1 : 2492){<br><br>dummy[i] <- 0<br>dummy[i] ~ dloglik(logLike[i])<br>logLike[i] <-
</font><font face="Arial" color="#000100" size="3"><strong><br>log(r/phi(alpha * sigma)) * ( 1 - stepxtheta[i] ) + log(1-r) * stepxtheta[i] +
</strong></font><font face="Arial" color="#000100" size="3"><br>( -0.5 * log(2 * pi) - log( x[i] ) - log( sigma ) - 0.5 * pow( (log(x[i])- mu)/ sigma, 2) ) * <br>( 1 - stepxtheta[i] ) + <br>( log(alpha) + alpha * log(theta) - (alpha+1)* log( x[i]) ) * stepxtheta[i]<br><br>stepxtheta[i] <- step( x[i] - theta )<br><br>}<br><br>theta ~ dgamma( 0.001, 0.001) # dexp( 0.5 ) #<br>alpha ~dgamma( 0.001, 0.001) # dexp( 0.5 ) #<br>sigma ~ dgamma(0.001, 0.001) # dexp( 0.5 ) #<br><br>r <- (sqrt( [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Firemodel.txt b/doc/Examples/Firemodel.txt
new file mode 100755
index 0000000..ceef20f
--- /dev/null
+++ b/doc/Examples/Firemodel.txt
@@ -0,0 +1,35 @@
+model{
+
+for ( i in 1 : 2492){
+
+ dummy[i] <- 0
+ dummy[i] ~ dloglik(logLike[i])
+ logLike[i] <-
+ log(r/phi(alpha * sigma)) * ( 1 - stepxtheta[i] ) + log(1-r) * stepxtheta[i] +
+ ( -0.5 * log(2 * pi) - log( x[i] ) - log( sigma ) - 0.5 * pow( (log(x[i])- mu)/ sigma, 2) ) *
+ ( 1 - stepxtheta[i] ) +
+ ( log(alpha) + alpha * log(theta) - (alpha+1)* log( x[i]) ) * stepxtheta[i]
+
+ stepxtheta[i] <- step( x[i] - theta )
+
+}
+
+theta ~ dgamma( 0.001, 0.001) # dexp( 0.5 ) #
+alpha ~dgamma( 0.001, 0.001) # dexp( 0.5 ) #
+sigma ~ dgamma(0.001, 0.001) # dexp( 0.5 ) #
+
+r <- (sqrt(2*pi)*alpha*sigma*phi(alpha*sigma))
+ /(sqrt(2*pi)*alpha*sigma*phi(alpha*sigma)+exp(-0.5* pow(alpha* sigma,2)))
+mu <- log(theta)- alpha*pow(sigma,2)
+pi <-3.14159565
+
+
+xf <- xa * delta + xb * ( 1 - delta )
+xa ~ dlnorm( mu, tau ) I( , theta )
+xb ~ dpar( alpha, theta )
+
+delta ~ dbern( r )
+tau <- 1/pow(sigma,2)
+
+
+}
diff --git a/doc/Examples/FunShapesinits1.html b/doc/Examples/FunShapesinits1.html
new file mode 100755
index 0000000..8508991
--- /dev/null
+++ b/doc/Examples/FunShapesinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>FunShapesinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(x = 0, y = 0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/FunShapesinits1.txt b/doc/Examples/FunShapesinits1.txt
new file mode 100755
index 0000000..5d3f23f
--- /dev/null
+++ b/doc/Examples/FunShapesinits1.txt
@@ -0,0 +1 @@
+list(x = 0, y = 0)
\ No newline at end of file
diff --git a/doc/Examples/Functionals.html b/doc/Examples/Functionals.html
new file mode 100755
index 0000000..724e0bb
--- /dev/null
+++ b/doc/Examples/Functionals.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Functionals</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><strong><img src="functionals0.bmp" alt="[functionals0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Functionals: integration and<br> algebraic equations
</font><font face="Arial" color="#0000FF" size="5"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="3">In the BUGS language logical nodes can be functions of other logical nodes. Sometimes a logical node is needed that depends on another logical node evaluated at arbitrary points. One example is an definite integral and another is an algebraic equation. We call these more general logical nodes "functionals" and introduce a special notation to describe them. A slot in a logical node that has a F(x) parameter is able to as [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"> zero -6.9388939E-17
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">The third functional depends on a stochastic variable limit and so changes it value as limit changes.<br>
</font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model{<br> F(x[1]) <- cos(x[1])<br> int <- integral(F(x[1]), 0, halfPi, 1.0E-6)<br> halfPi <- 3.141592659 / 2<br> <br> sol <- solution(F(x[2]), 0, 1, 1.0E-6)<br> F(x[2]) <- x[2] * x[2] - pow(1 - x[2], 5)<br> &nbs [...]
</font><font face="Arial" color="#0000FF" size="5"><strong>Inits
</strong></font><font face="Arial" color="#000100" size="3"> list(limit = 0.5)
</font><font face="Arial" color="#000100" size="2"><br> <br>
</font><font face="Arial" color="#000100" size="5"><strong><br>
</strong></font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Funshapes.html b/doc/Examples/Funshapes.html
new file mode 100755
index 0000000..477b85f
--- /dev/null
+++ b/doc/Examples/Funshapes.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Funshapes</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#0000FF" size="5"><img src="funshapes0.bmp" alt="[funshapes0]">
</font><font face="Courier New" color="#000100" size="6">Fun shapes: general constraints
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="3">These toy examples illustrate how to implement general inequality constraints. They generate points uniformly over a restricted region of the square with corners at (1, 1) and (-1, -1). A dummy bernoulli variable is introduced and its corresponding proportion set to the step function of the required constraint. The only useful example is the parallelagram where x + y is constrained to be less than or equal to one, this idea can be used to [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Circle<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">x ~ dunif(-1, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">y ~ dunif(-1, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">O <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">O ~ dbern(constraint)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">constraint <- step(x * x + y * y - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Funshapesinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits
</u></font><font face="Arial" color="#000100" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )<br><center><br><br><img src="funshapes1.bmp" alt="[funshapes1]"><br></center><br>
</font><font face="Arial" color="#0000FF" size="5">Square minus circle
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">x ~ dunif(-1, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">y ~ dunif(-1, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">O <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">O ~ dbern(constraint)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">constraint <- step(x * x + y * y - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Funshapesinits2.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits
</u></font><font face="Arial" color="#000100" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )<br><center><br><br><img src="funshapes2.bmp" alt="[funshapes2]"><br></center><br>
</font><font face="Arial" color="#0000FF" size="5">Ring<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> x ~ dunif(-1, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y ~ dunif(-1, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O1 <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O1 ~ dbern(constraint1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> constraint1 <- step(x * x + y * y - 1) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O2 <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O2 ~ dbern(constraint2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> constraint2 <- step( x * x + y * y - 0.25)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Funshapesinits3.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits
</u></font><font face="Arial" color="#000100" size="3"></a> ( click to open )<br><center><br><br><img src="funshapes3.bmp" alt="[funshapes3]"><br></center><br>
</font><font face="Arial" color="#0000FF" size="5">Hollow square
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> x ~ dunif(-1, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y ~ dunif(-1, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O ~ dbern(constraint)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> constraint <- (step(0.5 - abs(x)) * step(0.50 - abs(y)))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Funshapesinits4.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits
</u></font><font face="Arial" color="#000100" size="3"></a> ( click to open )<br><center><br><br><img src="funshapes4.bmp" alt="[funshapes4]"><br></center><br><br>
</font><font face="Arial" color="#0000FF" size="5">Parallelagram
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> x ~ dunif(0, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y ~ dunif(-1, 1.0)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O1 <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O1 ~ dbern(constraint1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> constraint1 <- step(x + y)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O2 <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O2 ~ dbern(constraint2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> constraint2 <- step(x + y - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Funshapesinits5.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits
</u></font><font face="Arial" color="#000100" size="3"></a> ( click to open )<br><center><br><img src="funshapes5.bmp" alt="[funshapes5]"><br></center>
</font>
</p>
</body>
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<html>
<head>
<title>Funshapesinits2</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(x = 0.99, y = 0.99)
</font>
</p>
</body>
</html>
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+list(x = 0.99, y = 0.99)
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Funshapesinits3</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(x = 0.6, y = 0.6)
</font>
</p>
</body>
</html>
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+list(x = 0.6, y = 0.6)
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Funshapesinits4</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(x = 0.75, y = 0.75)
</font>
</p>
</body>
</html>
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new file mode 100755
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@@ -0,0 +1 @@
+list(x = 0.75, y = 0.75)
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new file mode 100755
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Funshapesinits5</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(x = 0.5, y = 0)
</font>
</p>
</body>
</html>
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+list(x = 0.5, y = 0)
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gentians</title>
</head>
<body>
<p>
<font face="Arial" color="#0000FF" size="5"><strong><img src="gentians0.bmp" alt="[gentians0]">
</strong></font><font face="Courier New" color="#000100" size="6"> Gentians: accounting for imperfect<br> detection in site-occupancy models<br> for species distribution<br> <br> [...]
</font><font face="Arial" color="#000100" size="3"><br>Modelling species distributions is important in both basic and applied ecology (e.g., Scott
</font><font face="Arial" color="#000100" size="3"><em>et al.
</em></font><font face="Arial" color="#000100" size="3">, 2002, Island Press). Typically, logistic regression-types of models (GLM) with perhaps added smooth terms (GAMs) are used to model detection/non-detection data by a set of explanatory variables. However, most organisms are not always found at all the sites they actually occur. Hence, virtually always people don't model actual distributions, i.e., probability of occurrence
</font><font face="Arial" color="#000100" size="3"><em>per se
</em></font><font face="Arial" color="#000100" size="3">, but rather the product of the probability of occurrence and the probability of detection, given occurrence. Imperfect detection means that true distribution is underestimated and that factors that affect detection rather than occurrence may end up in predictive models of occurrence.<br><br>To model distributions free from the biasing effects of detection, MacKenzie
</font><font face="Arial" color="#000100" size="3"><em>et al.
</em></font><font face="Arial" color="#000100" size="3"> (Ecology, 2002, 2003; 2006; Academic Press) developed site-occupancy models, a sort of coupled logistic regression models where one submodel describes actual occurrence and the other detection given occurrence. Royle and Kery (Ecology, 2007) presented a hierarchical formulation of these models that may easily be fitted using BUGS. Site-occupancy models may be applied whenever information about the detection process separate from tha [...]
</font><font face="Arial" color="#000100" size="3"><em>et al.
</em></font><font face="Arial" color="#000100" size="3"> 2003, 2006; Royle and Kery 2007).<br><br>The single-season site-occupancy model can be succinctly written as a state-space model in two linked equations:<br><br> z
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli(
</font><font face="Symbol" color="#000100" size="3">y
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) State equation<br> y
</font><font face="Arial" color="#000100" size="1"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli( z
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> * p
</font><font face="Arial" color="#000100" size="1"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">) Observation equation<br><br>The first line describes the true biological process: true occurrence, the latent state z
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, at site
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> is a Bernoulli random variable governed by the parameter
</font><font face="Symbol" color="#000100" size="3">y
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, which is occurrence probability or occupancy. The second line describes the actual observation of the study species y
</font><font face="Arial" color="#000100" size="1"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">, that is, detection or nondetection at site
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> during survey
</font><font face="Arial" color="#000100" size="3"><em>j
</em></font><font face="Arial" color="#000100" size="3">. This is another Bernoulli random variable governed by a parameter that is the product of actual occurrence at that site, z
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, and detection probability p
</font><font face="Arial" color="#000100" size="1"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> at site
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> during survey
</font><font face="Arial" color="#000100" size="3"><em>j
</em></font><font face="Arial" color="#000100" size="3">. Both Bernoulli parameters, occurrence
</font><font face="Symbol" color="#000100" size="3">y
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and detection p
</font><font face="Arial" color="#000100" size="1"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">, can be expressed as linear or other functions of covariates via a logit link. Note that covariates for occurrence will be constant over replicated surveys, while those for detection may be either constant or variable (survey-specific). Technically, the site-occupancy model can be described as a non-standard generalized linear mixed model with a random effect that follows a Bernoulli rather than normal distribution.<br><br>This exa [...]
</font><font face="Arial" color="#000100" size="3"><em>Gentianella germanica
</em></font><font face="Arial" color="#000100" size="3">, was inventoried at 150 grassland sites using three independent surveys at each site. The aim was to estimate prevalence of the gentian and quantify the (positive) relationship between occurrence and site wetness (continuous 0 to 1). Detection probability was assumed to be lower at wetter sites because of greater vegetation height, leading to the absence of an observed occurrence-wetness relationship in a naive analysis using simple [...]
</font><font face="Arial" color="#000100" size="3"><strong>Notes:
</strong></font><font face="Arial" color="#000100" size="3"> A good choice of starting values can be essential for successfully fitting the model. In particular, it ia a good idea to use the observed occupancy state of each site as starting value for the latent state is a good idea. The model can be fitted with missing y values, but there should not be missing values in the explanatory variables (unless they are modelled). For very imbalanced data sets, it is more efficient to fit the mod [...]
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model <br>
</font><font face="Arial" color="#000000" size="3"> {<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> # Priors<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> alpha.occ ~ dunif(-20, 20)<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> beta.occ ~ dunif(-20, 20)<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> alpha.p ~ dunif(-20, 20)<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> beta1.p ~ dunif(-20, 20)<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> beta2.p ~ dunif(-20, 20)<br><br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> # Likelihood<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1:R) {<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> # Model for partially latent state<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> z[i] ~ dbern(psi[i]) # True occupancy z at site i<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> logit(psi[i]) <- alpha.occ + beta.occ * wetness[i]<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> for (j in 1:T) {<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> # Observation model for actual observations<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> y[i, j] ~ dbern(eff.p[i, j]) # Det.-nondet. at i and j<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> eff.p[i, j] <- z[i] * p[i, j]<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> logit(p[i, j]) <- alpha.p + beta1.p * wetness [i] + beta2.p * experience[i, j]<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> # Derived quantity<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"> occ.fs <- sum(z[ ]) # Finite sample number of occupied sites<br> }<br>
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Gentiansdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Gentiansinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="3"> </a>
</font><font face="Arial" color="#0000FF" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Gentiansinits2.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Gentiansinits3.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 3
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="3"><br><br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br><br>
</font><font face="Arial" color="#000100" size="3">Running 3 parallel chains with 11000 iterations each and with the first 1000 updates discarded yields this:<br>
</font><font face="Arial" color="#0000FF" size="3"><strong><center><img src="gentians1.bmp" alt="[gentians1]"><br></center>
</strong></font><font face="Arial" color="#000100" size="3"><br>Compare this with the "known truth" of the data-generating parameters:<br> alpha.occ = -1<br> alpha.p = 1<br> beta.occ = 5<br> beta1.p = -5<br> beta2.p = 5<br><br>In this example, the gentian was discovered at only 65 among the 108 sites where [...]
</font>
</p>
</body>
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diff --git a/doc/Examples/Gentiansdata.html b/doc/Examples/Gentiansdata.html
new file mode 100755
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+++ b/doc/Examples/Gentiansdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gentiansdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(y= structure(.Data= c(0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Gentiansdata.txt b/doc/Examples/Gentiansdata.txt
new file mode 100755
index 0000000..91802de
--- /dev/null
+++ b/doc/Examples/Gentiansdata.txt
@@ -0,0 +1 @@
+list(y= structure(.Data= c(0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, [...]
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diff --git a/doc/Examples/Gentiansinits1.html b/doc/Examples/Gentiansinits1.html
new file mode 100755
index 0000000..ecc213c
--- /dev/null
+++ b/doc/Examples/Gentiansinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gentiansinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(z=c(0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Gentiansinits1.txt b/doc/Examples/Gentiansinits1.txt
new file mode 100755
index 0000000..e4caa79
--- /dev/null
+++ b/doc/Examples/Gentiansinits1.txt
@@ -0,0 +1 @@
+list(z=c(0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 1), alpha.occ=-3.28, beta.occ=-3.55, [...]
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diff --git a/doc/Examples/Gentiansinits2.html b/doc/Examples/Gentiansinits2.html
new file mode 100755
index 0000000..574a5c2
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+++ b/doc/Examples/Gentiansinits2.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gentiansinits2</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(z=c(0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Gentiansinits2.txt b/doc/Examples/Gentiansinits2.txt
new file mode 100755
index 0000000..bf275a0
--- /dev/null
+++ b/doc/Examples/Gentiansinits2.txt
@@ -0,0 +1 @@
+list(z=c(0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 1), alpha.occ=9.82, beta.occ=2.44, a [...]
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diff --git a/doc/Examples/Gentiansinits3.html b/doc/Examples/Gentiansinits3.html
new file mode 100755
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--- /dev/null
+++ b/doc/Examples/Gentiansinits3.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gentiansinits3</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(z=c(0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Gentiansinits3.txt b/doc/Examples/Gentiansinits3.txt
new file mode 100755
index 0000000..fbdae0d
--- /dev/null
+++ b/doc/Examples/Gentiansinits3.txt
@@ -0,0 +1 @@
+list(z=c(0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 1), alpha.occ=3.49, beta.occ=-3.65, [...]
diff --git a/doc/Examples/Gentiansmodel.html b/doc/Examples/Gentiansmodel.html
new file mode 100755
index 0000000..97266da
--- /dev/null
+++ b/doc/Examples/Gentiansmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gentiansmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model <br> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#0000FF" size="3"> # Priors
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha.occ ~ dunif(-20, 20)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta.occ ~ dunif(-20, 20)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha.p ~ dunif(-20, 20)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta1.p ~ dunif(-20, 20)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta2.p ~ dunif(-20, 20)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#0000FF" size="3"> # Likelihood
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1:R) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#0000FF" size="3"> # Model for partially latent state
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> z[i] ~ dbern(psi[i]) # True occupancy z at site i<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> logit(psi[i]) <- alpha.occ + beta.occ * wetness[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1:T) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#0000FF" size="3"> # Observation model for actual observations
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y[i,j] ~ dbern(eff.p[i,j]) # Det.-nondet. at i and j<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> eff.p[i,j] <- z[i] * p[i,j]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> logit(p[i,j]) <- alpha.p + beta1.p * wetness [i] + beta2.p * experience[i,j]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#0000FF" size="3"> # Derived quantity<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> occ.fs <- sum(z[]) # Finite sample number of occupied sites<br> }<br>
</font>
</p>
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diff --git a/doc/Examples/Gentiansmodel.txt b/doc/Examples/Gentiansmodel.txt
new file mode 100755
index 0000000..e070e35
--- /dev/null
+++ b/doc/Examples/Gentiansmodel.txt
@@ -0,0 +1,24 @@
+ model
+ {
+ # Priors
+ alpha.occ ~ dunif(-20, 20)
+ beta.occ ~ dunif(-20, 20)
+ alpha.p ~ dunif(-20, 20)
+ beta1.p ~ dunif(-20, 20)
+ beta2.p ~ dunif(-20, 20)
+
+ # Likelihood
+ for (i in 1:R) {
+ # Model for partially latent state
+ z[i] ~ dbern(psi[i]) # True occupancy z at site i
+ logit(psi[i]) <- alpha.occ + beta.occ * wetness[i]
+ for (j in 1:T) {
+ # Observation model for actual observations
+ y[i,j] ~ dbern(eff.p[i,j]) # Det.-nondet. at i and j
+ eff.p[i,j] <- z[i] * p[i,j]
+ logit(p[i,j]) <- alpha.p + beta1.p * wetness [i] + beta2.p * experience[i,j]
+ }
+ }
+ # Derived quantity
+ occ.fs <- sum(z[]) # Finite sample number of occupied sites
+ }
diff --git a/doc/Examples/Hearts.html b/doc/Examples/Hearts.html
new file mode 100755
index 0000000..4a24426
--- /dev/null
+++ b/doc/Examples/Hearts.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hearts</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="hearts0.bmp" alt="[hearts0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Hearts: a mixture model for count<br> data
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"><br>The table below presents data given by Berry (1987) on the effect of a drug used to treat patients with frequent premature ventricular contractions (PVCs) of the heart.
</font><font face="Arial" color="#000100" size="2"><img src="hearts1.bmp" alt="[hearts1]">
</font><font face="Arial" color="#000100" size="3"><br>Farewell and Sprott (1988) model these data as a mixture distribution of Poisson counts in which some patients are "cured" by the drug, whilst others experience varying levels of response but remain abnormal. A zero count for the post-drug PVC may indicate a "cure", or may represent a sampling zero from a patient with a mildly abnormal PVC count. The following model thus is assumed:<br><br> x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Poisson(
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) for all patients<br> y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Poisson(
</font><font face="Symbol" color="#000100" size="3">bl
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) for all
</font><font face="Arial" color="#000100" size="3"><em>uncured
</em></font><font face="Arial" color="#000100" size="3">patients<br> P(cure) =
</font><font face="Symbol" color="#000100" size="3">q<br> <br>
</font><font face="Arial" color="#000100" size="3">To eliminate nuisance parameters l
</font><font face="Arial" color="#000100" size="2">i
</font><font face="Arial" color="#000100" size="3">, Farewell and Sprott use the conditional distribution of y
</font><font face="Arial" color="#000100" size="2">i
</font><font face="Arial" color="#000100" size="3"> given t
</font><font face="Arial" color="#000100" size="2">i
</font><font face="Arial" color="#000100" size="3"> = x
</font><font face="Arial" color="#000100" size="2">i
</font><font face="Arial" color="#000100" size="3"> + y
</font><font face="Arial" color="#000100" size="2">i
</font><font face="Arial" color="#000100" size="3">. This is equivalent to a binomial likelihood for y
</font><font face="Arial" color="#000100" size="2">i
</font><font face="Arial" color="#000100" size="3"> with denominator t
</font><font face="Arial" color="#000100" size="2">i
</font><font face="Arial" color="#000100" size="3"> and probability p = b /(1+b) (see Cox and Hinkley, 1974 pp. 136-137 for further details of the conditional distribution for Poisson variables). Hence the final mixture model may be expressed as follows:<br><br> P(y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = 0 | t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3"> + (1
</font><font face="Symbol" color="#000100" size="3">- q
</font><font face="Arial" color="#000100" size="3">) (1
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3"> p) t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><br> P(y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> | t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">) = (1
</font><font face="Symbol" color="#000100" size="3">- q
</font><font face="Arial" color="#000100" size="3">) (t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">! / (y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">! (t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)!)) (p
</font><font face="Arial" color="#000100" size="2"><sup>y
</sup></font><font face="Arial" color="#000100" size="2"><sup>i
</sup></font><font face="Arial" color="#000100" size="3"><sup>
</sup></font><font face="Arial" color="#000100" size="3">(1
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">p)
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sup>(t
</sup></font><font face="Arial" color="#000100" size="2"><sup>i
</sup></font><font face="Symbol" color="#000100" size="2"><sup>-
</sup></font><font face="Arial" color="#000100" size="2"><sup> y
</sup></font><font face="Arial" color="#000100" size="2"><sup>i
</sup></font><font face="Arial" color="#000100" size="2"><sup>)
</sup></font><font face="Arial" color="#000100" size="3"> y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = 1,2,...,t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> <br><br>The BUGS code for this model is given below:<br><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"> model <br> {<br> for (i in 1 : N) {<br> y[i] ~ dbin(P[state1[i]], t[i])<br> state[i] ~ dbern(theta)<br> state1[i] <- state[i] + 1 <br> t[i] <- x[i] + y[i] [...]
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Heartsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Heartsinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Heartsinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center><br><br><img src="hearts2.bmp" alt="[hearts2]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Heartsdata.html b/doc/Examples/Heartsdata.html
new file mode 100755
index 0000000..9aa5c62
--- /dev/null
+++ b/doc/Examples/Heartsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Heartsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">list(x = c(6, 9, 17, 22, 7, 5, 5, 14, 9, 7, 9, 51),<br> y = c(5, 2, 0, 0, 2, 1, 0, 0, 0, 0, 13, 0), N = 12)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Heartsdata.txt b/doc/Examples/Heartsdata.txt
new file mode 100755
index 0000000..72878b7
--- /dev/null
+++ b/doc/Examples/Heartsdata.txt
@@ -0,0 +1,2 @@
+list(x = c(6, 9, 17, 22, 7, 5, 5, 14, 9, 7, 9, 51),
+ y = c(5, 2, 0, 0, 2, 1, 0, 0, 0, 0, 13, 0), N = 12)
\ No newline at end of file
diff --git a/doc/Examples/Heartsinits.html b/doc/Examples/Heartsinits.html
new file mode 100755
index 0000000..913ada3
--- /dev/null
+++ b/doc/Examples/Heartsinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Heartsinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">list(delta = 0, alpha = 0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Heartsinits.txt b/doc/Examples/Heartsinits.txt
new file mode 100755
index 0000000..4bba1aa
--- /dev/null
+++ b/doc/Examples/Heartsinits.txt
@@ -0,0 +1 @@
+list(delta = 0, alpha = 0)
\ No newline at end of file
diff --git a/doc/Examples/Heartsinits1.html b/doc/Examples/Heartsinits1.html
new file mode 100755
index 0000000..6caf6e7
--- /dev/null
+++ b/doc/Examples/Heartsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Heartsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">list(delta = 2, alpha = 2)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Heartsinits1.txt b/doc/Examples/Heartsinits1.txt
new file mode 100755
index 0000000..5890d89
--- /dev/null
+++ b/doc/Examples/Heartsinits1.txt
@@ -0,0 +1 @@
+list(delta = 2, alpha = 2)
\ No newline at end of file
diff --git a/doc/Examples/Heartsmodel.html b/doc/Examples/Heartsmodel.html
new file mode 100755
index 0000000..95876fa
--- /dev/null
+++ b/doc/Examples/Heartsmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Heartsmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model <br> {<br> for (i in 1 : N) {<br> y[i] ~ dbin(P[state1[i]], t[i])<br> state[i] ~ dbern(theta)<br> state1[i] <- state[i] + 1 <br> t[i] <- x[i] + y[i] <br>&n [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Heartsmodel.txt b/doc/Examples/Heartsmodel.txt
new file mode 100755
index 0000000..b2cc034
--- /dev/null
+++ b/doc/Examples/Heartsmodel.txt
@@ -0,0 +1,17 @@
+ model
+ {
+ for (i in 1 : N) {
+ y[i] ~ dbin(P[state1[i]], t[i])
+ state[i] ~ dbern(theta)
+ state1[i] <- state[i] + 1
+ t[i] <- x[i] + y[i]
+ prop[i] <- P[state1[i]]
+ }
+ P[1] <- p
+ P[2] <- 0
+ logit(p) <- alpha
+ alpha ~ dnorm(0,1.0E-4)
+ beta <- exp(alpha)
+ logit(theta) <- delta
+ delta ~ dnorm(0, 1.0E-4)
+ }
diff --git a/doc/Examples/Hepatitis.html b/doc/Examples/Hepatitis.html
new file mode 100755
index 0000000..02be8f6
--- /dev/null
+++ b/doc/Examples/Hepatitis.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hepatitis</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#0000FF" size="5"><strong><br><img src="hepatitis0.bmp" alt="[hepatitis0]">
</strong></font><font face="Courier New" color="#000100" size="6">Hepatitis: a normal hierarchical<br> model with measurement error
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><br>This example is taken from Spiegelhalter et al (1996) (chapter in
</font><font face="Arial" color="#000100" size="3"><em>Markov Chain Monte Carlo in Practice
</em></font><font face="Arial" color="#000100" size="3">) and concerns 106 children whose post-vaccination anti Hb titre was measured 2 or 3 times. Both measurements and times have been transformed to a log scale. One covariate y0 = log titre at baseline, is available.<br><br>The model is essentially a random effects linear growth curve<br><br> Y
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">~ Normal(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">(
</font><font face="Arial" color="#000100" size="2">t
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> -t
</font><font face="Arial" color="#000100" size="2"><sub>bar
</sub></font><font face="Arial" color="#000100" size="3">),
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">)<br><br>
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Symbol" color="#000100" size="2"><sub>a
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Symbol" color="#000100" size="2"><sub>b
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>where
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> represents the
</font><font face="Arial" color="#000100" size="3"><em>precision
</em></font><font face="Arial" color="#000100" size="3"> (1/variance) of a normal distribution. We note the absence of a parameter representing correlation between
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> unlike in Gelfand
</font><font face="Arial" color="#000100" size="3"><em>et al
</em></font><font face="Arial" color="#000100" size="3"> 1990. However, see the
</font><font face="Courier" color="#000100" size="3">Birats
</font><font face="Arial" color="#000100" size="3"> example in Volume 2 which does explicitly model the covariance between
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">. <br><br>
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3"> ,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Symbol" color="#000100" size="2"><sub>a
</sub></font><font face="Symbol" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Symbol" color="#000100" size="2"><sub>b
</sub></font><font face="Symbol" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">are given independent ``noninformative'' priors. <br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><center>
</font><font face="Arial" color="#000100" size="3"><em>Graphical model for hep example:
</em></font><font face="Arial" color="#0000FF" size="5"><strong><br><img src="hepatitis1.bmp" alt="[hepatitis1]">
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br><br>BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for hep example:
</em></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"></center>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for( i in 1 : N ) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for( j in 1 : T ) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Y[i , j] ~ dnorm(mu[i , j],tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i , j] <- alpha[i] + beta[i] * (t[i,j] - 6.5) + <br> gamma * (y0[i] - mean(y0[]))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha[i] ~ dnorm(alpha0,tau.alpha)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta[i] ~ dnorm(beta0,tau.beta)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau ~ dgamma(0.001,0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma <- 1 / sqrt(tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha0 ~ dnorm(0.0,1.0E-6) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau.alpha ~ dgamma(0.001,0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta0 ~ dnorm(0.0,1.0E-6)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau.beta ~ dgamma(0.001,0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">gamma ~ dnorm(0.0,1.0E-6)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Note the use of a very flat but conjugate prior for the population effects: a locally uniform prior could also have been used.<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Hepatitisdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Hepatitisinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Hepatitisinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br><center><br><img src="hepatitis2.bmp" alt="[hepatitis2]"><br>
</font><font face="Arial" color="#000100" size="3"><br></center>With measurement error<br><center>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><img src="hepatitis3.bmp" alt="[hepatitis3]"><br>
</font><font face="Arial" color="#000100" size="1"></center>
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br> {<br> tau.alpha ~ dgamma(0.001,0.001)<br> alpha0 ~ dnorm( 0.0,1.0E-6)<br> beta0 ~ dnorm( 0.0,1.0E-6)<br> tau.beta ~ dgamma(0.001,0.001)<br> &nbs [...]
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/HepatitisMEdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/HepatitisMEinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/HepatitisMEinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><br>Results
</font><font face="Arial" color="#000100" size="1"><br><center><br><img src="hepatitis4.bmp" alt="[hepatitis4]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/HepatitisMEdata.html b/doc/Examples/HepatitisMEdata.html
new file mode 100755
index 0000000..9621197
--- /dev/null
+++ b/doc/Examples/HepatitisMEdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>HepatitisMEdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(
</font><font face="Arial" color="#000100" size="2"> N = 106, T = 3,
</font><font face="Arial" color="#000100" size="1"><br>Y = <br>structure(.Data =<br>c(4.997 , 8.028 , NA, <br>6.830 , 4.905 , 6.295,<br> 3.95124371858143, 4.35670882668959, <br> NA, 6.79794041297493, 5.27299955856375, 4.31748811353631, <br> 4.71849887129509, 3.49650756146648, 4.29045944114839, 5.78996017089725, <br> 3.68887945411394, 3.43398720448515, 6.13122648948314, 3.85014760171006, <br> NA, 6.7627295 [...]
</font><font face="Arial" color="#000100" size="2">.Dim = c(106,3)),<br>
</font><font face="Arial" color="#000100" size="1">t = <br> structure(.Data =<br> c(6.541 , 6.963 , 10, <br> 5.8406416573734, 6.52941883826223, 6.98193467715639, 6.60123011872888, <br> 7.02553831463852, 10, 5.8636311755981, 6.51767127291227, <br> 6.96790920180188, 5.91350300563827, 6.5694814204143, 7.00850518208228, <br> 5.91889385427315, 6.5694814204143, 7.00760061395185, 5.8749307308520 [...]
</font><font face="Arial" color="#000100" size="2">.Dim = c(106,3)),
</font><font face="Arial" color="#000100" size="1"><br> y0 = c(8.613 , 7.105 , 6.896 , <br> 5.63835466933375, 6.35088571671474, 5.03043792139244, 5.8664680569333, <br> 5.73979291217923, 7.07834157955767, 8.56655462095396, 6.86171134048073, <br> 6.97354301952014, 7.34213173058472, 8.82629423124132, 6.48768401848461, <br> 6.66440902035041, 7.0343879299155, 4.49980967033027, 6.85118492749374, <br>   [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/HepatitisMEdata.txt b/doc/Examples/HepatitisMEdata.txt
new file mode 100755
index 0000000..f5ae3a2
--- /dev/null
+++ b/doc/Examples/HepatitisMEdata.txt
@@ -0,0 +1,192 @@
+list( N = 106, T = 3,
+Y =
+ structure(.Data =
+ c(4.997 , 8.028 , NA,
+ 6.830 , 4.905 , 6.295,
+ 3.95124371858143, 4.35670882668959,
+ NA, 6.79794041297493, 5.27299955856375, 4.31748811353631,
+ 4.71849887129509, 3.49650756146648, 4.29045944114839, 5.78996017089725,
+ 3.68887945411394, 3.43398720448515, 6.13122648948314, 3.85014760171006,
+ NA, 6.76272950693188, 3.29583686600433, NA, 6.14846829591765,
+ 5.25749537202778, 5.37527840768417, 10.7579879834538, 10.4925789214972,
+ NA, 5.63121178182137, 4.20469261939097, 3.49650756146648,
+ 3.46573590279973, 1.79175946922805, 2.77258872223978, 7.92479591395644,
+ 7.54750168281497, 6.40687998606931, 9.16115012778541, 8.34236350038058,
+ 7.9483852851119, 8.74257423767064, 7.07580886397839, 6.3919171133926,
+ 5.91079664404053, 5.11198778835654, 5.37989735354046, 6.54678541076052,
+ 4.93447393313069, 5.86929691313377, 2.94443897916644, 3.17805383034795,
+ NA, 7.05272104923232, 6.25382881157547, 5.34233425196481, 0,
+ 7.19067603433221, NA, 9.13905916997122, 7.82724090175281, NA,
+ 8.48260174664662, 7.51697722460432, 4.45434729625351, 7.11963563801764,
+ 5.8348107370626, 6.5424719605068, 7.64300363556072, 6.35610766069589,
+ 6.89365635460264, 9.42294862137501, 8.57073395834427, 8.79026911147866,
+ 8.2553088117856, 7.16394668434255, 7.46278915741245, 4.82028156560504,
+ 3.40119738166216, 3.66356164612965, 6.54678541076052, 5.95583736946483,
+ 4.99721227376411, 8.67470962929122, 7.32383056620232, 8.03040956213048,
+ 7.86326672400957, 7.63385355968177, 7.16006920759613, 4.67282883446191,
+ 3.36729582998647, 3.17805383034795, 7.41878088275079, 6.76157276880406,
+ NA, 6.84587987526405, 8.38845031552351, 6.31535800152233,
+ 5.46383180502561, 9.9219166880045, NA, 3.43398720448515,
+ 1.6094379124341, 2.77258872223978, 7.7553388128465, 7.44366368311559,
+ 7.82803803212583, 9.04239498112674, 6.64768837356333, 7.11151211649616,
+ 8.45212119467252, 6.85118492749374, 7.01481435127554, 7.91425227874244,
+ 6.16961073249146, 6.00881318544259, 7.72885582385254, 9.75214127004149,
+ 9.59703032475801, 9.31433996199467, 8.26359043261732, NA,
+ 6.35957386867238, 5.84643877505772, NA, 2.30258509299405, 0,
+ 2.30258509299405, 8.29354951506035, 7.60589000105312, 10.1017644761202,
+ 8.90082160491523, 6.25958146406492, 7.06561336359772, 8.87905466204227,
+ 8.88391747120797, NA, 11.5129154649202, 8.54286093816481,
+ 8.97575663051942, 8.79618763547045, 7.86095636487639, 7.08757370555797,
+ 8.40155784781731, 6.91075078796194, 7.22256601882217, 8.89370997756851,
+ 7.59588991771854, NA, 7.1800698743028, 7.03174125876313,
+ 2.07944154167984, 4.82028156560504, 2.99573227355399, 2.70805020110221,
+ 5.77765232322266, 3.91202300542815, 3.61091791264422, 6.4707995037826,
+ 5.4510384535657, NA, 4.40671924726425, 5.12989871492307,
+ 3.85014760171006, 8.17413934342947, 7.88419993367604, 7.22766249872866,
+ 2.30258509299405, 2.30258509299405, 0, 9.77104128523582,
+ 9.32892308780313, 9.61767040669386, 6.95081476844258, 10.5472081164337,
+ 8.66905554072548, 5.97635090929793, 5.71042701737487, 5.24174701505964,
+ 5.8805329864007, 6.50128967054039, 5.48479693349065, 5.73979291217923,
+ 5.53338948872752, 4.04305126783455, 5.75574221358691, 4.99043258677874,
+ NA, 5.15329159449778, 3.61091791264422, NA, 8.11761074646623,
+ 7.34729970074316, 6.55250788703459, 8.54636356871602, 8.03138533062553,
+ 7.35115822643069, 7.58171964012531, 6.92264389147589, 6.52502965784346,
+ 6.9037472575846, 6.7202201551353, 5.74939298590825, 4.66343909411207,
+ 3.43398720448515, 3.09104245335832, 7.47986413116503, 6.19236248947487,
+ NA, 3.61091791264422, 3.78418963391826, NA, 4.64439089914137,
+ 4.51085950651685, 2.99573227355399, 4.39444915467244, 3.55534806148941,
+ 3.29583686600433, 8.23509549725836, 7.81116338502528, 7.54855597916987,
+ 6.12905021006055, 6.19847871649231, 4.81218435537242, 8.4424696452203,
+ 3.55534806148941, 2.94443897916644, 6.88755257166462, 5.07517381523383,
+ NA, 7.29233717617388, 7.25417784645652, NA, 6.38856140554563,
+ 6.21460809842219, 5.03043792139244, 8.75998249497728, 7.19593722647557,
+ NA, 6.08677472691231, 4.66343909411207, 2.39789527279837,
+ 4.02535169073515, 3.78418963391826, 2.94443897916644, 4.38202663467388,
+ 2.484906649788, NA, 6.85540879860993, 6.08221891037645,
+ 5.45958551414416, 8.17919979842309, 6.04500531403601, NA,
+ 4.24849524204936, 3.52636052461616, 3.58351893845611, 8.98343977178426,
+ 9.69990150043745, 8.74097653801779, 8.4721958254855, 7.76004068088038,
+ NA, 9.480214825778, 7.78113850984502, NA, 6.1463292576689,
+ 6.289715570909, 5.87493073085203, 9.93542217106647, 9.39806397805913,
+ 9.17294998275762, 4.27666611901606, 5.34710753071747, 3.46573590279973,
+ 5.36597601502185, 5.88887795833288, 3.36729582998647, 4.60517018598809,
+ 5.29831736654804, 3.58351893845611, 3.2188758248682, 4.27666611901606,
+ 7.63867982387611, 6.81783057145415, 3.46573590279973, NA,
+ 6.58479139238572, 7.2152399787301, 5.90808293816893, 5.91889385427315,
+ 5.68357976733868, 5.8171111599632, 8.67641669696422, 7.72179177681754,
+ 6.19031540585315, 2.484906649788, 1.38629436111989, 2.56494935746154,
+ 6.73933662735717, 6.73221070646721, 4.51085950651685, 3.91202300542815,
+ 5.4971682252932, 4.39444915467244, 4.56434819146784, 2.83321334405622,
+ NA, 9.15925758174687, 8.58073121222023, NA, 7.07326971745971,
+ 7.12608727329912, 5.01063529409626, 9.08636319215647, 7.9359451033537,
+ NA),
+ .Dim = c(106,3)),
+ t =
+ structure(.Data =
+ c(6.541 , 6.963 , 10,
+ 5.8406416573734, 6.52941883826223, 6.98193467715639, 6.60123011872888,
+ 7.02553831463852, 10, 5.8636311755981, 6.51767127291227,
+ 6.96790920180188, 5.91350300563827, 6.5694814204143, 7.00850518208228,
+ 5.91889385427315, 6.5694814204143, 7.00760061395185, 5.87493073085203,
+ 6.97447891102505, 10, 5.82008293035236, 6.56244409369372, 10,
+ 5.91350300563827, 6.5510803350434, 7.00306545878646, 5.98896141688986,
+ 7.0335064842877, 10, 5.95064255258773, 6.59987049921284,
+ 7.00940893270864, 5.75574221358691, 6.65544035036765, 6.9555926083963,
+ 5.92157841964382, 6.70686233660275, 6.98286275146894, 5.93489419561959,
+ 6.63987583382654, 6.9782137426307, 5.91350300563827, 6.63987583382654,
+ 6.9782137426307, 5.97126183979046, 6.55961523749324, 7.00124562206948,
+ 5.97126183979046, 6.60123011872888, 7.00033446027523, 6.59987049921284,
+ 7.00215595440362, 10, 5.92157841964382, 6.68959926917897,
+ 6.96224346426621, 6.71780469502369, 6.98286275146894, 10,
+ 5.92958914338989, 6.56807791141198, 10, 5.92157841964382,
+ 6.71780469502369, 6.98286275146894, 5.92157841964382, 6.54821910276237,
+ 6.98193467715639, 5.92157841964382, 6.54821910276237, 6.98193467715639,
+ 5.92157841964382, 6.54821910276237, 6.98100574072173, 5.8406416573734,
+ 6.54821910276237, 6.98100574072173, 5.89440283426485, 6.49072353450251,
+ 6.95654544315157, 5.93489419561959, 6.70686233660275, 7.00306545878646,
+ 5.93224518744801, 6.56103066589657, 7.0335064842877, 5.96870755998537,
+ 6.52795791762255, 6.94215670569947, 5.8805329864007, 6.56244409369372,
+ 6.97728134163075, 6.62671774924902, 6.94889722231331, 10,
+ 5.87773578177964, 6.54965074223381, 6.98841318199959, 6.59030104819669,
+ 7.00669522683704, 10, 5.92958914338989, 6.56807791141198,
+ 6.98193467715639, 5.92958914338989, 6.56807791141198, 6.98193467715639,
+ 5.86078622346587, 6.55819780281227, 6.97447891102505, 5.89440283426485,
+ 6.59030104819669, 6.98378996525813, 5.95064255258773, 6.51767127291227,
+ 6.97447891102505, 5.93224518744801, 6.70196036600254, 6.97447891102505,
+ 5.97126183979046, 6.60934924316738, 10, 6.57088296233958,
+ 7.01571242048723, 10, 5.93753620508243, 6.5206211275587,
+ 6.97073007814353, 5.87493073085203, 6.56103066589657, 6.97447891102505,
+ 5.89164421182577, 6.59030104819669, 6.98378996525813, 6.74170069465205,
+ 6.98933526597456, 10, 5.89440283426485, 6.5410299991899,
+ 6.98286275146894, 5.94803498918065, 6.5510803350434, 6.99668148817654,
+ 5.77455154554441, 6.49828214947643, 6.95844839329766, 5.97126183979046,
+ 6.54965074223381, 10, 5.96870755998537, 6.58892647753352,
+ 7.01481435127554, 5.8805329864007, 6.59030104819669, 6.98378996525813,
+ 5.89440283426485, 6.5410299991899, 6.98286275146894, 6.62936325343745,
+ 6.98471632011826, 10, 5.93224518744801, 6.62007320653036,
+ 7.03174125876313, 5.99146454710798, 6.63856778916652, 7.04053639021596,
+ 5.88887795833288, 6.59441345974978, 7.02908756414966, 5.93489419561959,
+ 6.61873898351722, 7.04577657687951, 5.94017125272043, 6.62140565176413,
+ 7.05272104923232, 5.95583736946483, 6.62936325343745, 7.05272104923232,
+ 5.93489419561959, 6.61873898351722, 7.04490511712937, 5.92692602597041,
+ 6.61204103483309, 7.04141166379481, 6.64639051484773, 7.04403289727469,
+ 10, 5.93224518744801, 6.62007320653036, 10, 5.96870755998537,
+ 6.64639051484773, 7.03174125876313, 5.93224518744801, 6.64768837356333,
+ 7.028201432058, 5.93224518744801, 6.62007320653036, 7.03174125876313,
+ 5.93224518744801, 6.62671774924902, 7.02731451403978, 5.94542060860658,
+ 6.62140565176413, 7.05272104923232, 5.86929691313377, 6.5875500148248,
+ 10, 6.65801104587075, 7.05875815251866, 10, 5.89715386763674,
+ 6.59714570188665, 7.03174125876313, 6.00881318544259, 6.62936325343745,
+ 7.03966034986208, 5.97126183979046, 6.66568371778241, 7.03878354138854,
+ 5.97126183979046, 6.66440902035041, 7.04403289727469, 5.97126183979046,
+ 6.66440902035041, 7.04403289727469, 6.00881318544259, 7.05185562295589,
+ 10, 6.64639051484773, 7.04403289727469, 10, 5.88610403145016,
+ 6.59167373200866, 7.028201432058, 5.75257263882563, 6.96129604591017,
+ 10, 5.68017260901707, 6.50876913697168, 6.97541392745595,
+ 5.77144112313002, 6.56244409369372, 6.99759598298193, 5.96100533962327,
+ 6.66695679242921, 10, 5.75257263882563, 6.49828214947643,
+ 6.99025650049388, 5.81413053182507, 7.02108396428914, 10,
+ 5.63478960316925, 6.46769872610435, 6.95081476844258, 5.77455154554441,
+ 6.48768401848461, 6.92067150424868, 5.77765232322266, 6.52209279817015,
+ 10, 5.63121178182137, 6.55535689181067, 10, 5.70711026474888,
+ 6.45833828334479, 6.91473089271856, 5.89164421182577, 6.48920493132532,
+ 6.92165818415113, 5.77455154554441, 6.48920493132532, 6.92165818415113,
+ 6.0591231955818, 6.62671774924902, 7.01391547481053, 5.8171111599632,
+ 6.49223983502047, 6.94119005506837, 5.65248918026865, 6.42162226780652,
+ 6.86380339145295, 5.60947179518496, 6.44413125670044, 10,
+ 5.83773044716594, 6.48616078894409, 6.92165818415113, 5.91350300563827,
+ 6.52649485957079, 6.97447891102505, 5.77455154554441, 6.45047042214418,
+ 6.92755790627832, 5.83773044716594, 6.48463523563525, 6.91869521902047,
+ 5.98645200528444, 6.51025834052315, 6.96413561241824, 5.8171111599632,
+ 6.48463523563525, 6.94793706861497, 6.49526555593701, 6.94215670569947,
+ 10, 5.68697535633982, 6.47850964220857, 10, 5.8171111599632,
+ 6.51174532964473, 6.93634273583405, 5.85793315448346, 6.92264389147589,
+ 10),
+ .Dim = c(106,3)),
+ y0 = c(8.613 , 7.105 , 6.896 ,
+ 5.63835466933375, 6.35088571671474, 5.03043792139244, 5.8664680569333,
+ 5.73979291217923, 7.07834157955767, 8.56655462095396, 6.86171134048073,
+ 6.97354301952014, 7.34213173058472, 8.82629423124132, 6.48768401848461,
+ 6.66440902035041, 7.0343879299155, 4.49980967033027, 6.85118492749374,
+ 3.04452243772342, 8.63905677917308, 1.79175946922805, 7.01660968389422,
+ 7.09090982207998, 7.42356844425917, 8.09620827165004, 5.70711026474888,
+ 7.01031186730723, 7.18311170174328, 8.15219801586179, 5.99645208861902,
+ 7.0825485693553, 5.06890420222023, 7.04228617193974, 4.0943445622221,
+ 7.32052696227274, 7.12689080889881, 7.24136628332232, 6.62007320653036,
+ 7.36897040219479, 8.47720418319987, 7.20340552108309, 2.89037175789616,
+ 7.39141523467536, 6.25190388316589, 8.38160253710989, 11.5129154649202,
+ 6.60258789218934, 7.61283103040736, 7.42476176182321, 6.71174039505618,
+ 5.56068163101553, 6.0282785202307, 7.10085190894405, 7.52671756135271,
+ 7.92948652331429, 1.6094379124341, 6.85856503479136, 8.05006542291597,
+ 5.83188247728352, 7.15851399732932, 7.01481435127554, 7.70120018085745,
+ 7.16239749735572, 5.99893656194668, 5.41610040220442, 8.40782465436087,
+ 7.18462915271731, 3.25809653802148, 8.14380797677148, 5.24702407216049,
+ 5.73979291217923, 4.55387689160054, 7.72444664563354, 7.91425227874244,
+ 7.11476944836646, 8.24064886337491, 8.56044423341055, 6.78558764500793,
+ 10.8861838116069, 2.07944154167984, 5.82894561761021, 4.0943445622221,
+ 7.53208814354172, 5.66988092298052, 3.46573590279973, 10.7229148990064,
+ 8.02910705461974, 9.23092700558457, 6.42971947803914, 11.5129154649202,
+ 7.25700270709207, 6.62007320653036, 9.41995278900604, 5.28826703069454,
+ 8.04654935728308, 7.58984151218266, 6.39024066706535, 6.04025471127741,
+ 2.77258872223978, 7.62948991639399, 7.85476918349913, 7.09007683577609,
+ 5.50125821054473, 6.98100574072173, 5.50533153593236))
\ No newline at end of file
diff --git a/doc/Examples/HepatitisMEinits.html b/doc/Examples/HepatitisMEinits.html
new file mode 100755
index 0000000..e9de335
--- /dev/null
+++ b/doc/Examples/HepatitisMEinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>HepatitisMEinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha0 = 4, beta0 = 0, gamma = 0, tau.alpha = 1, tau.beta = 1, tau = 1, theta = 6, psi = 1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/HepatitisMEinits.txt b/doc/Examples/HepatitisMEinits.txt
new file mode 100755
index 0000000..d8a467a
--- /dev/null
+++ b/doc/Examples/HepatitisMEinits.txt
@@ -0,0 +1 @@
+list(alpha0 = 4, beta0 = 0, gamma = 0, tau.alpha = 1, tau.beta = 1, tau = 1, theta = 6, psi = 1)
\ No newline at end of file
diff --git a/doc/Examples/HepatitisMEinits1.html b/doc/Examples/HepatitisMEinits1.html
new file mode 100755
index 0000000..9604b63
--- /dev/null
+++ b/doc/Examples/HepatitisMEinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>HepatitisMEinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha0 = 1, beta0 = 1, gamma = 0, tau.alpha = 0.1, tau.beta = 0.1, tau = 0.1, theta = 1, psi = 1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/HepatitisMEinits1.txt b/doc/Examples/HepatitisMEinits1.txt
new file mode 100755
index 0000000..8840521
--- /dev/null
+++ b/doc/Examples/HepatitisMEinits1.txt
@@ -0,0 +1 @@
+list(alpha0 = 1, beta0 = 1, gamma = 0, tau.alpha = 0.1, tau.beta = 0.1, tau = 0.1, theta = 1, psi = 1)
\ No newline at end of file
diff --git a/doc/Examples/HepatitisMEmodel.html b/doc/Examples/HepatitisMEmodel.html
new file mode 100755
index 0000000..f6a2dc1
--- /dev/null
+++ b/doc/Examples/HepatitisMEmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>HepatitisMEmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br> {<br> tau.alpha ~ dgamma(0.001,0.001)<br> alpha0 ~ dnorm( 0.0,1.0E-6)<br> beta0 ~ dnorm( 0.0,1.0E-6)<br> tau.beta ~ dgamma(0.001,0.001)<br> &nbs [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/HepatitisMEmodel.txt b/doc/Examples/HepatitisMEmodel.txt
new file mode 100755
index 0000000..3ea5b4a
--- /dev/null
+++ b/doc/Examples/HepatitisMEmodel.txt
@@ -0,0 +1,25 @@
+ model
+ {
+ tau.alpha ~ dgamma(0.001,0.001)
+ alpha0 ~ dnorm( 0.0,1.0E-6)
+ beta0 ~ dnorm( 0.0,1.0E-6)
+ tau.beta ~ dgamma(0.001,0.001)
+ for( i in 1 : N ) {
+ alpha[i] ~ dnorm(alpha0,tau.alpha)
+ beta[i] ~ dnorm(beta0,tau.beta)
+ y0[i] ~ dnorm(mu0[i],tau)
+ mu0[i] ~ dnorm(theta,psi)
+ }
+ for( j in 1 : T ) {
+ for( i in 1 : N ) {
+ Y[i , j] ~ dnorm(mu[i , j],tau)
+ mu[i , j] <- alpha[i] + beta[i] * (t[i , j] - 6.5) +
+ gamma * (mu0[i] - mean(y0[]))
+ }
+ }
+ tau ~ dgamma(0.001,0.001)
+ sigma <- 1 / sqrt(tau)
+ gamma ~ dnorm( 0.0,1.0E-6)
+ theta ~ dnorm( 0.0,1.0E-6)
+ psi ~ dgamma(0.001,0.001)
+ }
diff --git a/doc/Examples/Hepatitisdata.html b/doc/Examples/Hepatitisdata.html
new file mode 100755
index 0000000..b1a1372
--- /dev/null
+++ b/doc/Examples/Hepatitisdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hepatitisdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(
</font><font face="Arial" color="#000100" size="2"> N = 106, T = 3,
</font><font face="Arial" color="#000100" size="1"><br>Y = <br>structure(.Data =<br>c(4.997 , 8.028 , NA, <br>6.830 , 4.905 , 6.295,<br> 3.95124371858143, 4.35670882668959, <br> NA, 6.79794041297493, 5.27299955856375, 4.31748811353631, <br> 4.71849887129509, 3.49650756146648, 4.29045944114839, 5.78996017089725, <br> 3.68887945411394, 3.43398720448515, 6.13122648948314, 3.85014760171006, <br> NA, 6.7627295 [...]
</font><font face="Arial" color="#000100" size="2">.Dim = c(106,3)),<br>
</font><font face="Arial" color="#000100" size="1">t = <br> structure(.Data =<br> c(6.541 , 6.963 , 10, <br> 5.8406416573734, 6.52941883826223, 6.98193467715639, 6.60123011872888, <br> 7.02553831463852, 10, 5.8636311755981, 6.51767127291227, <br> 6.96790920180188, 5.91350300563827, 6.5694814204143, 7.00850518208228, <br> 5.91889385427315, 6.5694814204143, 7.00760061395185, 5.8749307308520 [...]
</font><font face="Arial" color="#000100" size="2">.Dim = c(106,3)),
</font><font face="Arial" color="#000100" size="1"><br> y0 = c(8.613 , 7.105 , 6.896 , <br> 5.63835466933375, 6.35088571671474, 5.03043792139244, 5.8664680569333, <br> 5.73979291217923, 7.07834157955767, 8.56655462095396, 6.86171134048073, <br> 6.97354301952014, 7.34213173058472, 8.82629423124132, 6.48768401848461, <br> 6.66440902035041, 7.0343879299155, 4.49980967033027, 6.85118492749374, <br>   [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Hepatitisdata.txt b/doc/Examples/Hepatitisdata.txt
new file mode 100755
index 0000000..f5ae3a2
--- /dev/null
+++ b/doc/Examples/Hepatitisdata.txt
@@ -0,0 +1,192 @@
+list( N = 106, T = 3,
+Y =
+ structure(.Data =
+ c(4.997 , 8.028 , NA,
+ 6.830 , 4.905 , 6.295,
+ 3.95124371858143, 4.35670882668959,
+ NA, 6.79794041297493, 5.27299955856375, 4.31748811353631,
+ 4.71849887129509, 3.49650756146648, 4.29045944114839, 5.78996017089725,
+ 3.68887945411394, 3.43398720448515, 6.13122648948314, 3.85014760171006,
+ NA, 6.76272950693188, 3.29583686600433, NA, 6.14846829591765,
+ 5.25749537202778, 5.37527840768417, 10.7579879834538, 10.4925789214972,
+ NA, 5.63121178182137, 4.20469261939097, 3.49650756146648,
+ 3.46573590279973, 1.79175946922805, 2.77258872223978, 7.92479591395644,
+ 7.54750168281497, 6.40687998606931, 9.16115012778541, 8.34236350038058,
+ 7.9483852851119, 8.74257423767064, 7.07580886397839, 6.3919171133926,
+ 5.91079664404053, 5.11198778835654, 5.37989735354046, 6.54678541076052,
+ 4.93447393313069, 5.86929691313377, 2.94443897916644, 3.17805383034795,
+ NA, 7.05272104923232, 6.25382881157547, 5.34233425196481, 0,
+ 7.19067603433221, NA, 9.13905916997122, 7.82724090175281, NA,
+ 8.48260174664662, 7.51697722460432, 4.45434729625351, 7.11963563801764,
+ 5.8348107370626, 6.5424719605068, 7.64300363556072, 6.35610766069589,
+ 6.89365635460264, 9.42294862137501, 8.57073395834427, 8.79026911147866,
+ 8.2553088117856, 7.16394668434255, 7.46278915741245, 4.82028156560504,
+ 3.40119738166216, 3.66356164612965, 6.54678541076052, 5.95583736946483,
+ 4.99721227376411, 8.67470962929122, 7.32383056620232, 8.03040956213048,
+ 7.86326672400957, 7.63385355968177, 7.16006920759613, 4.67282883446191,
+ 3.36729582998647, 3.17805383034795, 7.41878088275079, 6.76157276880406,
+ NA, 6.84587987526405, 8.38845031552351, 6.31535800152233,
+ 5.46383180502561, 9.9219166880045, NA, 3.43398720448515,
+ 1.6094379124341, 2.77258872223978, 7.7553388128465, 7.44366368311559,
+ 7.82803803212583, 9.04239498112674, 6.64768837356333, 7.11151211649616,
+ 8.45212119467252, 6.85118492749374, 7.01481435127554, 7.91425227874244,
+ 6.16961073249146, 6.00881318544259, 7.72885582385254, 9.75214127004149,
+ 9.59703032475801, 9.31433996199467, 8.26359043261732, NA,
+ 6.35957386867238, 5.84643877505772, NA, 2.30258509299405, 0,
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+ 8.90082160491523, 6.25958146406492, 7.06561336359772, 8.87905466204227,
+ 8.88391747120797, NA, 11.5129154649202, 8.54286093816481,
+ 8.97575663051942, 8.79618763547045, 7.86095636487639, 7.08757370555797,
+ 8.40155784781731, 6.91075078796194, 7.22256601882217, 8.89370997756851,
+ 7.59588991771854, NA, 7.1800698743028, 7.03174125876313,
+ 2.07944154167984, 4.82028156560504, 2.99573227355399, 2.70805020110221,
+ 5.77765232322266, 3.91202300542815, 3.61091791264422, 6.4707995037826,
+ 5.4510384535657, NA, 4.40671924726425, 5.12989871492307,
+ 3.85014760171006, 8.17413934342947, 7.88419993367604, 7.22766249872866,
+ 2.30258509299405, 2.30258509299405, 0, 9.77104128523582,
+ 9.32892308780313, 9.61767040669386, 6.95081476844258, 10.5472081164337,
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+ 5.53338948872752, 4.04305126783455, 5.75574221358691, 4.99043258677874,
+ NA, 5.15329159449778, 3.61091791264422, NA, 8.11761074646623,
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+ 3.43398720448515, 3.09104245335832, 7.47986413116503, 6.19236248947487,
+ NA, 3.61091791264422, 3.78418963391826, NA, 4.64439089914137,
+ 4.51085950651685, 2.99573227355399, 4.39444915467244, 3.55534806148941,
+ 3.29583686600433, 8.23509549725836, 7.81116338502528, 7.54855597916987,
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+ 3.55534806148941, 2.94443897916644, 6.88755257166462, 5.07517381523383,
+ NA, 7.29233717617388, 7.25417784645652, NA, 6.38856140554563,
+ 6.21460809842219, 5.03043792139244, 8.75998249497728, 7.19593722647557,
+ NA, 6.08677472691231, 4.66343909411207, 2.39789527279837,
+ 4.02535169073515, 3.78418963391826, 2.94443897916644, 4.38202663467388,
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+ 9.69990150043745, 8.74097653801779, 8.4721958254855, 7.76004068088038,
+ NA, 9.480214825778, 7.78113850984502, NA, 6.1463292576689,
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+ 7.63867982387611, 6.81783057145415, 3.46573590279973, NA,
+ 6.58479139238572, 7.2152399787301, 5.90808293816893, 5.91889385427315,
+ 5.68357976733868, 5.8171111599632, 8.67641669696422, 7.72179177681754,
+ 6.19031540585315, 2.484906649788, 1.38629436111989, 2.56494935746154,
+ 6.73933662735717, 6.73221070646721, 4.51085950651685, 3.91202300542815,
+ 5.4971682252932, 4.39444915467244, 4.56434819146784, 2.83321334405622,
+ NA, 9.15925758174687, 8.58073121222023, NA, 7.07326971745971,
+ 7.12608727329912, 5.01063529409626, 9.08636319215647, 7.9359451033537,
+ NA),
+ .Dim = c(106,3)),
+ t =
+ structure(.Data =
+ c(6.541 , 6.963 , 10,
+ 5.8406416573734, 6.52941883826223, 6.98193467715639, 6.60123011872888,
+ 7.02553831463852, 10, 5.8636311755981, 6.51767127291227,
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+ 6.51174532964473, 6.93634273583405, 5.85793315448346, 6.92264389147589,
+ 10),
+ .Dim = c(106,3)),
+ y0 = c(8.613 , 7.105 , 6.896 ,
+ 5.63835466933375, 6.35088571671474, 5.03043792139244, 5.8664680569333,
+ 5.73979291217923, 7.07834157955767, 8.56655462095396, 6.86171134048073,
+ 6.97354301952014, 7.34213173058472, 8.82629423124132, 6.48768401848461,
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+ 7.09090982207998, 7.42356844425917, 8.09620827165004, 5.70711026474888,
+ 7.01031186730723, 7.18311170174328, 8.15219801586179, 5.99645208861902,
+ 7.0825485693553, 5.06890420222023, 7.04228617193974, 4.0943445622221,
+ 7.32052696227274, 7.12689080889881, 7.24136628332232, 6.62007320653036,
+ 7.36897040219479, 8.47720418319987, 7.20340552108309, 2.89037175789616,
+ 7.39141523467536, 6.25190388316589, 8.38160253710989, 11.5129154649202,
+ 6.60258789218934, 7.61283103040736, 7.42476176182321, 6.71174039505618,
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+ 5.83188247728352, 7.15851399732932, 7.01481435127554, 7.70120018085745,
+ 7.16239749735572, 5.99893656194668, 5.41610040220442, 8.40782465436087,
+ 7.18462915271731, 3.25809653802148, 8.14380797677148, 5.24702407216049,
+ 5.73979291217923, 4.55387689160054, 7.72444664563354, 7.91425227874244,
+ 7.11476944836646, 8.24064886337491, 8.56044423341055, 6.78558764500793,
+ 10.8861838116069, 2.07944154167984, 5.82894561761021, 4.0943445622221,
+ 7.53208814354172, 5.66988092298052, 3.46573590279973, 10.7229148990064,
+ 8.02910705461974, 9.23092700558457, 6.42971947803914, 11.5129154649202,
+ 7.25700270709207, 6.62007320653036, 9.41995278900604, 5.28826703069454,
+ 8.04654935728308, 7.58984151218266, 6.39024066706535, 6.04025471127741,
+ 2.77258872223978, 7.62948991639399, 7.85476918349913, 7.09007683577609,
+ 5.50125821054473, 6.98100574072173, 5.50533153593236))
\ No newline at end of file
diff --git a/doc/Examples/Hepatitisinits.html b/doc/Examples/Hepatitisinits.html
new file mode 100755
index 0000000..bd7e8ad
--- /dev/null
+++ b/doc/Examples/Hepatitisinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hepatitisinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha0 = 4, beta0 = 0, gamma = 0, tau.alpha = 1, tau.beta = 1, tau = 1 )
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Hepatitisinits.txt b/doc/Examples/Hepatitisinits.txt
new file mode 100755
index 0000000..3122e60
--- /dev/null
+++ b/doc/Examples/Hepatitisinits.txt
@@ -0,0 +1 @@
+list(alpha0 = 4, beta0 = 0, gamma = 0, tau.alpha = 1, tau.beta = 1, tau = 1 )
\ No newline at end of file
diff --git a/doc/Examples/Hepatitisinits1.html b/doc/Examples/Hepatitisinits1.html
new file mode 100755
index 0000000..d490e90
--- /dev/null
+++ b/doc/Examples/Hepatitisinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hepatitisinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha0 = 1, beta0 = 1, gamma = 1, tau.alpha = 0.1, tau.beta = 1, tau = 0.1 )
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Hepatitisinits1.txt b/doc/Examples/Hepatitisinits1.txt
new file mode 100755
index 0000000..9a02926
--- /dev/null
+++ b/doc/Examples/Hepatitisinits1.txt
@@ -0,0 +1 @@
+list(alpha0 = 1, beta0 = 1, gamma = 1, tau.alpha = 0.1, tau.beta = 1, tau = 0.1 )
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diff --git a/doc/Examples/Hepatitismodel.html b/doc/Examples/Hepatitismodel.html
new file mode 100755
index 0000000..6467a8f
--- /dev/null
+++ b/doc/Examples/Hepatitismodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hepatitismodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for( i in 1 : N ) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for( j in 1 : T ) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Y[i , j] ~ dnorm(mu[i , j],tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i , j] <- alpha[i] + beta[i] * (t[i,j] - 6.5) + <br> gamma * (y0[i] - mean(y0[]))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha[i] ~ dnorm(alpha0,tau.alpha)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta[i] ~ dnorm(beta0,tau.beta)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau ~ dgamma(0.001,0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma <- 1 / sqrt(tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha0 ~ dnorm(0.0,1.0E-6) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau.alpha ~ dgamma(0.001,0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta0 ~ dnorm(0.0,1.0E-6)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau.beta ~ dgamma(0.001,0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">gamma ~ dnorm(0.0,1.0E-6)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Hepatitismodel.txt b/doc/Examples/Hepatitismodel.txt
new file mode 100755
index 0000000..df6d78c
--- /dev/null
+++ b/doc/Examples/Hepatitismodel.txt
@@ -0,0 +1,19 @@
+ model
+ {
+ for( i in 1 : N ) {
+ for( j in 1 : T ) {
+ Y[i , j] ~ dnorm(mu[i , j],tau)
+ mu[i , j] <- alpha[i] + beta[i] * (t[i,j] - 6.5) +
+ gamma * (y0[i] - mean(y0[]))
+ }
+ alpha[i] ~ dnorm(alpha0,tau.alpha)
+ beta[i] ~ dnorm(beta0,tau.beta)
+ }
+ tau ~ dgamma(0.001,0.001)
+ sigma <- 1 / sqrt(tau)
+ alpha0 ~ dnorm(0.0,1.0E-6)
+ tau.alpha ~ dgamma(0.001,0.001)
+ beta0 ~ dnorm(0.0,1.0E-6)
+ tau.beta ~ dgamma(0.001,0.001)
+ gamma ~ dnorm(0.0,1.0E-6)
+ }
diff --git a/doc/Examples/Hips1.html b/doc/Examples/Hips1.html
new file mode 100755
index 0000000..f673eaf
--- /dev/null
+++ b/doc/Examples/Hips1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hips1</title>
</head>
<body>
<p>
<font face="Arial" color="#FF0000" size="3"><strong><img src="hips10.bmp" alt="[hips10]">
</strong></font><font face="Courier New" color="#000100" size="6">Hips model 1: Closed form<br> estimates for each strata -   [...]
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Times New Roman" color="#000100" size="3">Spiegelhalter, D.J. and Best, N.G. “Bayesian approaches to multiple sources of evidence and uncertainty in complex cost-effectiveness modelling”.
</font><font face="Times New Roman" color="#000100" size="3"><u>Statistics in Medicine 22
</u></font><font face="Times New Roman" color="#000100" size="3">, (2003), 3687-3709.<br>
</font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000000" size="2">No updates are required for this model; just load data and compile, then obtain values for C, mean.C, sd.C, BL, mean.BL, sd.BL, BQ, mean.BQ and sd.BQ using the node tool from the Info menu.
</font><font face="Arial" color="#FF0000" size="2"><br>
</font><font face="Arial" color="#FF0000" size="1"><br><br><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">model {<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(k in 1 : K) { # loop over strata<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Cost and benefit equations in closed form:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">####################################<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Costs<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> ct[k, t] <- inprod(pi[k, t, ], c[]) / pow((1 + delta.c), t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">C[k] <- C0 + sum(ct[k, ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Benefits - life expectancy<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> blt[k, t] <- inprod(pi[k, t, ], bl[]) / pow((1 + delta.b), t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">BL[k] <- sum(blt[k, ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Benefits - QALYs<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> bqt[k, t] <- inprod(pi[k,t, ], bq[]) / pow((1 + delta.b), t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">BQ[k] <- sum(bqt[k, ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Markov model probabilities:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">#######################<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Transition matrix<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 2 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 1] <- 1 - gamma[k, t] - lambda[k, t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 2] <- gamma[k, t] * lambda.op<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 3] <- gamma[k, t] * (1 - lambda.op)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 4] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 5] <- lambda[k, t] <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 2] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 3] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 4] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 5] <- 1 <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 2] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 3] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 4] <- 1 - lambda[k, t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 5] <- lambda[k, t]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 2] <- rho * lambda.op<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 3] <- rho * (1 - lambda.op)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 4] <- 1 - rho - lambda[k, t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 5] <- lambda[k,t]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 2] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 3] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 4] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 5] <- 1<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">gamma[k, t] <- h[k] * (t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Marginal probability of being in each state at time 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">pi[k,1,1] <- 1 - lambda.op pi[k,1, 2]<-0 pi[k,1,3] <- 0 <br> pi[k,1, 4] <- 0 pi[k,1, 5] <- lambda.op<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Marginal probability of being in each state at time t>1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 2:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> for(s in 1:S) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> pi[k, t, s] <- inprod(pi[k, t - 1, ], Lambda[k, t, , s])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Mean and sd of costs and benefits over strata<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">#######################################<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">mean.C <- inprod(p.strata[], C[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(k in 1:12) { <br> dev.C[k] <- pow(C[k] - mean.C, 2) <br> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">var.C <- inprod(p.strata[], dev.C[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">sd.C <- sqrt(var.C)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">mean.BL <- inprod(p.strata[], BL[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(k in 1:12) { <br> dev.BL[k] <- pow(BL[k] - mean.BL, 2) <br> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">var.BL <- inprod(p.strata[], dev.BL[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">sd.BL <- sqrt(var.BL)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">mean.BQ <- inprod(p.strata[], BQ[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(k in 1:12) { <br> dev.BQ[k] <- pow(BQ[k] - mean.BQ, 2) <br> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">var.BQ <- inprod(p.strata[], dev.BQ[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">sd.BQ <- sqrt(var.BQ)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br>
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Hipsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><strong><u>Data
</u></strong></font><font face="Arial" color="#0000FF" size="5"><strong></a>
</strong></font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#FF0000" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><strong>Results
</strong></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"><img src="hips11.bmp" alt="[hips11]">
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Hips2.html b/doc/Examples/Hips2.html
new file mode 100755
index 0000000..527b79e
--- /dev/null
+++ b/doc/Examples/Hips2.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hips2</title>
</head>
<body>
<p>
<font face="Arial" color="#FF0000" size="2"><strong><img src="hips20.bmp" alt="[hips20]">
</strong></font><font face="Courier New" color="#000100" size="6">Hips model 2: MC estimates for<br> each strata - give results for<br> "Monte Carlo" columns in Table 2
</font><font face="Arial" color="#000000" size="2"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Times New Roman" color="#000100" size="3"><br>Spiegelhalter, D.J. and Best, N.G. “Bayesian approaches to multiple sources of evidence and uncertainty in complex cost-effectiveness modelling”.
</font><font face="Times New Roman" color="#000100" size="3"><u>Statistics in Medicine 22
</u></font><font face="Times New Roman" color="#000100" size="3">, (2003), 3687-3709.<br>
</font><font face="Arial" color="#000000" size="2"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3">n = 10000 updates (1 per simulated patient) are required for this model; monitor C, mean.C, BL, mean.BL, BQ, mean.BQ.
</font><font face="Arial" color="#FF0000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3"><strong>Sections of the code that have changed from Model 1 are shown in bold
</strong></font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000000" size="1"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">model {<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(k in 1 : K) { # loop over strata<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Cost and benefit equations <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">#######################<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Costs<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> ct[k, t] <- inprod(y[k, t, ], c[]) / pow(1 + delta.c, t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">C[k] <- C0 + sum(ct[k, ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Benefits - life expectancy<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> blt[k, t] <- inprod(y[k, t, ], bl[]) / pow(1 + delta.b, t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">BL[k] <- sum(blt[k, ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Benefits - QALYs<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> bqt[k, t] <- inprod(y[k, t, ], bq[]) / pow(1 + delta.b, t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">BQ[k] <- sum(bqt[k, ])<br><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Markov model probabilities:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">#######################<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Transition matrix<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 1] <- 1 - gamma[k, t] - lambda[k, t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 2] <- gamma[k, t] * lambda.op<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 3] <- gamma[k, t] *(1 - lambda.op)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 4] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 5] <- lambda[k, t] <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 2] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 3] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 4] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 5] <- 1 <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 2] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 3] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 4] <- 1 - lambda[k, t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 5] <- lambda[k, t]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 2] <- rho * lambda.op<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 3] <- rho * (1 - lambda.op)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 4] <- 1 - rho - lambda[k, t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 5] <- lambda[k, t]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 2] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 3] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 4] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 5] <- 1<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">gamma[k, t] <- h[k] * (t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Marginal probability of being in each state at time 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">pi[k, 1, 1] <- 1 - lambda.op pi[k, 1, 2]<-0 pi[k, 1, 3] <- 0 pi[k, 1, 4] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> pi[k, 1, 5] <- lambda.op<br>
</font><font face="Arial" color="#FF00FF" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong># state of each individual in strata k at time t =1 <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>y[k,1,1 : S] ~ dmulti(pi[k,1, ], 1) <br><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong># state of each individual in strata k at time t > 1<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>for(t in 2 : N) {<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>for(s in 1:S) { <br> # sampling probabilities <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong> pi[k, t, s] <- inprod(y[k, t - 1, ], Lambda[k, t, , s]) <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong> }<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong> y[k, t, 1 : S] ~ dmulti(pi[k, t, ], 1) <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>}
</strong></font><font face="Arial" color="#FF00FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Mean of costs and benefits over strata<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">#################################<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">mean.C <- inprod(p.strata[], C[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">mean.BL <- inprod(p.strata[], BL[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">mean.BQ <- inprod(p.strata[], BQ[])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Hipsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><strong><u>Data
</u></strong></font><font face="Arial" color="#0000FF" size="5"><strong></a>
</strong></font><font face="Arial" color="#000000" size="3"> ( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#0000FF" size="2"><strong> <br><center><br><img src="hips21.bmp" alt="[hips21]"><br></center>
</strong></font><font face="Arial" color="#0000FF" size="1"><br>Overall SD for Monte Carlo estimates at bottom of Table 2 is just the weighted SD of the strata-specific Monte Carlo means<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font>
</p>
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<head>
<title>Hips3</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2"><strong><img src="hips30.bmp" alt="[hips30]">
</strong></font><font face="Arial" color="#000000" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Hips model 3: MC estimates for<br> each strata, allowing<br> for parameter uncertainty in<br> [...]
</font><font face="Arial" color="#000000" size="2"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Times New Roman" color="#000100" size="3">Spiegelhalter, D.J. and Best, N.G. “Bayesian approaches to multiple sources of evidence and uncertainty in complex cost-effectiveness modelling”.
</font><font face="Times New Roman" color="#000100" size="3"><u>Statistics in Medicine 22
</u></font><font face="Times New Roman" color="#000100" size="3">, (2003), 3687-3709.<br>
</font><font face="Arial" color="#000000" size="3"><br>n = 10000 updates (1 per simulated set of parameter values) are required for this model; monitor C, BL, BQ to get posterior mean and sd for each subgroup for results in top part of Table 3.<br><br>
</font><font face="Arial" color="#000000" size="3"><strong>For results in bottom part of Table 3:
</strong></font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3"><u>Approach 1: p(s, theta) = p(s | theta) p(theta)
</u></font><font face="Arial" color="#000000" size="3"><br>m_theta and v_theta are the mean and variance across subgroups for a given value of theta<br>=> within BUGS code, calculate mean and variance of C[k], BL[k], BQ[k] across subgroups at each iteration, then take Monte Carlo expectation at end of run<br>=> monitor mean.C, mean.BL, mean.BQ, var.C, var.BL, var.BQ<br><br>
</font><font face="Arial" color="#000000" size="3"><u>Approach 2: p(s, theta) = p(theta | s) p(s)
</u></font><font face="Arial" color="#000000" size="3"><br>overall mean, m = weighted mean of posterior means of C[k], BL[k], BQ[k] => calculate after BUGS run var due to uncertainty, vP2 = weighted mean of posterior variances of C[k], BL[k], BQ[k] => calculate after BUGS run var due to heterogeneity = vH2 = weighted variance of posterior means of C[k], BL[k], BQ[k] => calculate after BUGS run<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><strong>Sections of the code that have changed from Model 1 are shown in bold<br>
</strong></font><font face="Arial" color="#000000" size="1"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">model {<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(k in 1 : K) { # loop over strata<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Cost and benefit equations <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">#######################<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Costs<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> ct[k, t] <- inprod(pi[k, t, ], c[]) / pow(1 + delta.c, t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">C[k] <- C0 + sum(ct[k, ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Benefits - life expectancy<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> blt[k, t] <- inprod(pi[k, t, ], bl[]) / pow(1 + delta.b, t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">BL[k] <- sum(blt[k, ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Benefits - QALYs<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> bqt[k, t] <- inprod(pi[k, t, ], bq[]) / pow(1 + delta.b, t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">BQ[k] <- sum(bqt[k, ])<br><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Markov model probabilities:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">#######################<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Transition matrix<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 2 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 1] <- 1 - gamma[k, t] - lambda[k, t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 2] <- gamma[k, t] * lambda.op<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 3] <- gamma[k, t] *(1 - lambda.op)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 4] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 1, 5] <- lambda[k, t] <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 2] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 3] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 4] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 2, 5] <- 1 <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 2] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k,t,3,3] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 4] <- 1 - lambda[k, t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 3, 5] <- lambda[k, t]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 2] <- rho * lambda.op<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k,t,4,3] <- rho * (1 - lambda.op)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 4] <- 1 - rho - lambda[k, t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 4, 5] <- lambda[k, t]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 2] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 3] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5, 4] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[k, t, 5,5 ] <- 1<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">gamma[k, t] <- h[k] * (t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Marginal probability of being in each state at time 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">pi[k,1,1] <- 1 - lambda.op pi[k,1, 2] <- 0 pi[k,1, 3] <- 0 ; <br> pi[k,1, 4] <- 0 pi[k,1, 5] <- lambda.op<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Marginal probability of being in each state at time t > 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 2 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(s in 1 : S) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> pi[k, t, s] <- inprod(pi[k, t - 1, ], Lambda[k, t, , s])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong># age-sex specific revision hazard<br>
</strong></font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>for(k in 1 : K) { <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>logh[k] ~ dnorm(logh0[k], tau)<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>h[k] <- exp(logh[k]) <br>
</strong></font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>}<br><br>
</strong></font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong># Calculate mean and variance across strata at each iteration <br>
</strong></font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong># (Gives overall mean and variance using approach 1)<br><br>
</strong></font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>mean.C <- inprod(p.strata[], C[])<br>
</strong></font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>mean.BL <- inprod(p.strata[], BL[])<br>
</strong></font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>mean.BQ <- inprod(p.strata[], BQ[])<br><br>
</strong></font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>for(k in 1:12) {<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>C.dev[k] <- pow(C[k]-mean.C , 2)<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>BL.dev[k] <- pow(BL[k]-mean.BL , 2)<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>BQ.dev[k] <- pow(BQ[k]-mean.BQ , 2)<br>
</strong></font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong> }<br>
</strong></font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>var.C <- inprod(p.strata[], C.dev[])<br>
</strong></font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>var.BL <- inprod(p.strata[], BL.dev[])<br>
</strong></font><font face="Arial" color="#000000" size="1"><strong>
</strong></font><font face="Arial" color="#000000" size="2"><strong>var.BQ <- inprod(p.strata[], BQ.dev[])
</strong></font><font face="Arial" color="#FF00FF" size="2"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Hipsdata3.html">
</font><font face="Arial" color="#0000FF" size="5"><strong><u>Data
</u></strong></font><font face="Arial" color="#0000FF" size="5"><strong></a>
</strong></font><font face="Arial" color="#000000" size="3"> ( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#0000FF" size="2"><strong> <br><center><br><img src="hips31.bmp" alt="[hips31]"><br></center>
</strong></font><font face="Arial" color="#FF0000" size="1"><br>
</font><font face="Arial" color="#000000" size="3">Note: results for the bottom panel of Table 3 (approach 1) for costs are given by<br>m = posterior mean of mean.C = 4609<br>vP1 = posterior variance of mean.C = 31.82 * 31.82<br>vH1 = posterior mean of var.C = 174400<br>
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000000" size="3"><strong> 'Model' to calculate overall mean (m), var due to uncertainty (vP2) and var due to heterogeneity (vH2) using approach 2
</strong></font><font face="Arial" color="#000000" size="3"><br> <br> No updates needed - just compile model, load data, and gen inits, then use node tool from info menu to obtain values of mC, mBL, mBQ, vP2.C, vP2.BL, vP2.BQ, vH2.C, vH2.BL, vH2.BQ, TC, TBL, TBQ, pcC, pcBL, pcBQ.<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"> model { <br> <br> # overall mean outcome (m)<br>mC <- inprod(p.strata[], C[])<br>mBL <- inprod(p.strata[], BL[])<br>mBQ <- inprod(p.strata[], BQ[])<br><br># variance due to uncertainty, vP<br>for(k in 1:12) {<br>VC[k] <- sdC[k]*sdC[k]<br>VBL[k] <- sdBL[k]*sdBL[k]<br>VBQ[k] <- sdBQ[k]*sdBQ[k]<br>}<br>vP2.C <- inprod(p.strata[], VC[])<br>vP2.BL <- inprod(p.strata[], [...]
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Hipsdata32.html">
</font><font face="Arial" color="#0000FF" size="5"><strong><u>Data
</u></strong></font><font face="Arial" color="#0000FF" size="5"><strong></a>
</strong></font><font face="Arial" color="#000000" size="3"> ( click to open, posterior means and posterior sd of C, BL and BQ from running model 3)
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><strong>Results
</strong></font><font face="Arial" color="#0000FF" size="2"><strong> <br>
</strong></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">mC 4609.03<br>mBL 8.687390000000001<br>mBQ 8.01488<br>vP2.C 11472.793425<br>vP2.BL 3.3068250474E-6<br>vP2.BQ 7.493649773900001E-4<br>vH2.C 163953.4291<br>vH2.BL 6.713258897899999<br>vH2.BQ 5.464389485600001<br>TC 175426.222525<br>TBL 6.713262204725046<br>TBQ 5.465138850577391<br>pcC 0.9346004647431485<br>pcBL 0.999999507419054<br>pcBQ 0.9998628827193821
</font>
</p>
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</head>
<body>
<p>
<font face="Arial" color="#000000" size="2"><strong><img src="hips40.bmp" alt="[hips40]">
</strong></font><font face="Courier New" color="#000100" size="6">Hips model 4: Comparative<br> analysis of Stanmore &<br> Charnley incorporating evidence
</font><font face="Arial" color="#000000" size="2"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Times New Roman" color="#000100" size="3">Spiegelhalter, D.J. and Best, N.G. “Bayesian approaches to multiple sources of evidence and uncertainty in complex cost-effectiveness modelling”.
</font><font face="Times New Roman" color="#000100" size="3"><u>Statistics in Medicine 22
</u></font><font face="Times New Roman" color="#000100" size="3">, (2003), 3687-3709.<br>
</font><font face="Arial" color="#000000" size="2"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3">n = 10000 updates (1 per simulated set of parameter values) are required for this model; <br>For hazard ratio estimates in bottom of table 4, monitor HR. For results in table 5, monitor C.incr, BQ.incr, ICER.strata, mean.C.incr, mean.BQ.incr, mean.ICER, P.CEA.strata[30,],<br>P.CEA.strata[50,], P.CEA[30] and P.CEA[50]. To produce plots in Fig 2, use coda option to save samples of C.incr, BQ.incr, mean.C.incr, mean.BQ.incr. To prod [...]
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><strong>Sections of the code that have changed from Model 1 are shown in bold<br>
</strong></font><font face="Arial" color="#FF0000" size="1"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">model {<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong># Evidence<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>#########<br><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>for (i in 1 : M){ # loop over studies<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>rC[i] ~ dbin(pC[i], nC[i]) # number of revisions on Charnley<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>rS[i] ~ dbin(pS[i], nS[i]) # number of revisions on Stanmore<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>cloglog(pC[i]) <- base[i] - logHR[i]/2 <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>cloglog(pS[i]) <- base[i] + logHR[i]/2 <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>base[i] ~ dunif(-100,100) <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong># log hazard ratio for ith study<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>logHR[i] ~ dnorm(LHR,tauHR[i]) <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>tauHR[i] <- qualweights[i] * tauh # precision for ith study weighted by quality weights<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>} <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>LHR ~ dunif(-100,100) <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>log(HR) <- LHR <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>tauh <- 1 / (sigmah * sigmah) <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>sigmah ~ dnorm( 0.2, 400)C(0, ) # between-trial sd = 0.05 (prior constrained to be positive)<br><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>for(k in 1 : K) { <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>logh[k] ~ dnorm(logh0[k], tau)<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>h[1, k] <- exp(logh[k]) # revision hazard for Charnley<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>h[2, k] <- HR * h[1, k] # revision hazard for Stanmore<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>}
</strong></font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Cost-effectiveness model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">###################### <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(k in 1 : K) { # loop over strata<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>for(n in 1 : 2) { # loop over protheses<br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Cost and benefit equations in closed form:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">####################################<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Costs<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> ct[n, k, t] <- inprod(pi[n, k, t, ], c[n, ]) / pow(1 + delta.c, t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">C[n,k] <- C0[n] + sum(ct[n, k, ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Benefits - life expectancy<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> blt[n, k, t] <- inprod(pi[n, k, t, ], bl[]) / pow(1 + delta.b, t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">BL[n, k] <- sum(blt[n, k, ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Benefits - QALYs<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> bqt[n, k, t] <- inprod(pi[n, k, t, ], bq[]) / pow(1 + delta.b, t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">BQ[n, k] <- sum(bqt[n, k, ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Markov model probabilities:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">#######################<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Transition matrix<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 2:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 1, 1] <- 1 - gamma[n, k, t] - lambda[k, t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 1, 2] <- gamma[n, k, t] * lambda.op<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 1, 3] <- gamma[n, k, t] *(1 - lambda.op)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 1, 4] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 1, 5] <- lambda[k, t] <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 2, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 2, 2] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 2, 3] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 2, 4] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k ,t, 2, 5] <- 1 <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 3, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 3, 2] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 3, 3] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 3, 4] <- 1 - lambda[k, t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 3, 5] <- lambda[k, t]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 4, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 4, 2] <- rho * lambda.op<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 4, 3] <- rho * (1 - lambda.op)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 4, 4] <- 1 - rho - lambda[k, t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 4, 5] <- lambda[k, t]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 5, 1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 5, 2] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 5, 3] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 5, 4] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">Lambda[n, k, t, 5, 5] <- 1<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">gamma[n, k, t] <- h[n, k] * (t - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Marginal probability of being in each state at time 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">pi[n, k, 1, 1] <- 1 - lambda.op pi[n, k, 1, 2] <- 0 pi[n, k, 1, 3] <- 0 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> pi[n, k, 1, 4] <- 0 pi[n, k, 1, 5] <- lambda.op<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"># Marginal probability of being in each state at time t>1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(t in 2 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">for(s in 1 : S) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"> pi[n, k,t, s] <- inprod(pi[n, k, t - 1, ], Lambda[n, k, t, , s])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong># Incremental costs and benefits<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>##########################<br><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>for(k in 1 : K) {<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>C.incr[k] <- C[2, k] - C[1, k]<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>BQ.incr[k] <-BQ[2, k] - BQ[1, k]<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>ICER.strata[k] <- C.incr[k] / BQ.incr[k]<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>} <br><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong># Probability of cost effectiveness @ KK pounds per QALY<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong># (values of KK considered range from 200 to 20000 in 200 pound increments)<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>for(m in 1 : 100) {<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>for(k in 1 : 12) { <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong> P.CEA.strata[m,k] <- step(KK[m] * BQ.incr[k] - C.incr[k])<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>}<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong> P.CEA[m] <- step(KK[m] * mean.BQ.incr - mean.C.incr)<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>}<br><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong># overall incremental costs and benefit <br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>for(n in 1 : 2) {<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>mean.C[n] <- inprod(p.strata[], C[n, ])<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>mean.BQ[n] <- inprod(p.strata[], BQ[n, ])<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>}<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>mean.C.incr <- mean.C[2] - mean.C[1]<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>mean.BQ.incr <- mean.BQ[2] - mean.BQ[1]<br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><strong>mean.ICER <- mean.C.incr / mean.BQ.incr
</strong></font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">}<br><br>
</font><font face="Arial" color="#000000" size="1"><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Hipsdata4.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Hips4inits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits
</u></font><font face="Arial" color="#0000FF" size="5"><strong><u>for chain 1</a>
</u></strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Hips4inits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits
</u></font><font face="Arial" color="#0000FF" size="5"><strong><u>for chain 2</a>
</u></strong></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="1"><br><br><br>(quality weights c(0.5, 1, 0.2), delta.c = 0.06, delta.b = 0.06)<br><center><img src="hips41.bmp" alt="[hips41]"><br><br><br><img src="hips42.bmp" alt="[hips42]">
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Hips4inits.html b/doc/Examples/Hips4inits.html
new file mode 100755
index 0000000..077a6c0
--- /dev/null
+++ b/doc/Examples/Hips4inits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hips4inits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(base=c(-3.09,-3.25,-2.12),logHR=c(-0.63,0.15,-0.92),LHR=-0.35)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Hips4inits.txt b/doc/Examples/Hips4inits.txt
new file mode 100755
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--- /dev/null
+++ b/doc/Examples/Hips4inits.txt
@@ -0,0 +1 @@
+list(base=c(-3.09,-3.25,-2.12),logHR=c(-0.63,0.15,-0.92),LHR=-0.35)
\ No newline at end of file
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new file mode 100755
index 0000000..de83d9d
--- /dev/null
+++ b/doc/Examples/Hips4inits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hips4inits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(base=c(0,0,0),logHR=c(1,1,1),LHR=1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Hips4inits1.txt b/doc/Examples/Hips4inits1.txt
new file mode 100755
index 0000000..ffabf16
--- /dev/null
+++ b/doc/Examples/Hips4inits1.txt
@@ -0,0 +1 @@
+list(base=c(0,0,0),logHR=c(1,1,1),LHR=1)
\ No newline at end of file
diff --git a/doc/Examples/Hipsdata.html b/doc/Examples/Hipsdata.html
new file mode 100755
index 0000000..3c5736e
--- /dev/null
+++ b/doc/Examples/Hipsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hipsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 60, # Number of cycles<br>K = 12, # Number of age-sex strata<br>S = 5, # Number of states in Markov model<br>rho = 0.04, # re-revision rate<br>lambda.op = 0.01, # post-operative mortality rate<br># age-sex specific revision hazard:<br>h = c(0.0022, 0.0022, 0.0022, 0.0016, 0.0016, 0.0016, 0.0017, 0.0017, 0.0017, 0.0012, 0.0012, 0.0012),<br>C0 = 4052, # set-up costs of primary operation<br>c = c(0, 5290, 5290, 0, 0), # additional costs as [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Hipsdata.txt b/doc/Examples/Hipsdata.txt
new file mode 100755
index 0000000..712b78d
--- /dev/null
+++ b/doc/Examples/Hipsdata.txt
@@ -0,0 +1,97 @@
+list(N = 60, # Number of cycles
+ K = 12, # Number of age-sex strata
+ S = 5, # Number of states in Markov model
+ rho = 0.04, # re-revision rate
+ lambda.op = 0.01, # post-operative mortality rate
+ # age-sex specific revision hazard:
+ h = c(0.0022, 0.0022, 0.0022, 0.0016, 0.0016, 0.0016, 0.0017, 0.0017, 0.0017, 0.0012, 0.0012, 0.0012),
+ C0 = 4052, # set-up costs of primary operation
+ c = c(0, 5290, 5290, 0, 0), # additional costs associated with each state (zero except for revision states 2 and 3)
+ bl = c(1,0,1,1,0), # life-expectancy benefits associated with each state (one except for death states 2 and 5)
+ bq = c(0.938, -0.622, -0.3387, 0.938, 0), # QALYs associated with each state
+ delta.c = 0.06, # cost discount
+ delta.b = 0.06, # health discount
+ # probablilty of hip replacement by age and sex
+ p.strata = c(0.02, 0.03, 0.07, 0.13, 0.10, 0.00, 0.02, 0.04, 0.10, 0.22, 0.26, 0.01),
+ lambda = structure(.Data = c(0.0017, 0.0017, 0.0017, 0.0017, 0.0017, 0.0044, 0.0044,
+ 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0138,
+ 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138,
+ 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379,
+ 0.0379, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912,
+ 0.0912, 0.0912, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.0044,
+ 0.0044, 0.0044, 0.0044, 0.0044, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138,
+ 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0379, 0.0379, 0.0379, 0.0379,
+ 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0912, 0.0912, 0.0912,
+ 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.0138, 0.0138, 0.0138, 0.0138,
+ 0.0138, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379,
+ 0.0379, 0.0379, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912,
+ 0.0912, 0.0912, 0.0912, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0912, 0.0912,
+ 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.0912,
+ 0.0912, 0.0912, 0.0912, 0.0912, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.0011, 0.0011, 0.0011, 0.0011, 0.0011, 0.0028, 0.0028,
+ 0.0028, 0.0028, 0.0028, 0.0028, 0.0028, 0.0028, 0.0028, 0.0028, 0.0081,
+ 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081,
+ 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022,
+ 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.0028, 0.0028,
+ 0.0028, 0.0028, 0.0028, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081,
+ 0.0081, 0.0081, 0.0081, 0.0081, 0.022, 0.022, 0.022, 0.022, 0.022,
+ 0.022, 0.022, 0.022, 0.022, 0.022, 0.0578, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081,
+ 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022,
+ 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.022, 0.022, 0.022, 0.022, 0.022, 0.0578, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.0578, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503
+ ), .Dim=c(12,60))
+)
\ No newline at end of file
diff --git a/doc/Examples/Hipsdata3.html b/doc/Examples/Hipsdata3.html
new file mode 100755
index 0000000..4911929
--- /dev/null
+++ b/doc/Examples/Hipsdata3.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hipsdata3</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 60, # Number of cycles<br>K = 12, # Number of age-sex strata<br>S = 5, # Number of states in Markov model<br>rho = 0.04, # re-revision rate<br>lambda.op = 0.01, # post-operative mortality rate<br># age-sex specific revision hazard:<br>
</font><font face="Arial" color="#FF00FF" size="1">logh0 = c(-6.119, -6.119, -6.119, -6.438, -6.438, -6.438, -6.377, -6.377, -6.377, -6.725, -6.725, -6.725),
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#FF00FF" size="1">tau = 25, # inverse variance reflecting uncertainty about log revision hazard (= 1 / 0.2^2)
</font><font face="Arial" color="#000100" size="1"><br>C0 = 4052, # set-up costs of primary operation<br>c = c(0, 5290, 5290, 0, 0), # additional costs associated with each state (zero except for revision states 2 and 3) <br>bl = c(1,0,1,1,0), # life-expectancy benefits associated with each state (one except for death states 2 and 5)<br>bq = c(0.938, -0.622, -0.3387, 0.938, 0), # QALYs associated with each state<br>delta.c = 0.06, # cost discount<br>delta.b = 0.06, # health discount<br>p. [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Hipsdata3.txt b/doc/Examples/Hipsdata3.txt
new file mode 100755
index 0000000..c31f0ff
--- /dev/null
+++ b/doc/Examples/Hipsdata3.txt
@@ -0,0 +1,97 @@
+list(N = 60, # Number of cycles
+ K = 12, # Number of age-sex strata
+ S = 5, # Number of states in Markov model
+ rho = 0.04, # re-revision rate
+ lambda.op = 0.01, # post-operative mortality rate
+ # age-sex specific revision hazard:
+ logh0 = c(-6.119, -6.119, -6.119, -6.438, -6.438, -6.438, -6.377, -6.377, -6.377, -6.725, -6.725, -6.725),
+ tau = 25, # inverse variance reflecting uncertainty about log revision hazard (= 1 / 0.2^2)
+ C0 = 4052, # set-up costs of primary operation
+ c = c(0, 5290, 5290, 0, 0), # additional costs associated with each state (zero except for revision states 2 and 3)
+ bl = c(1,0,1,1,0), # life-expectancy benefits associated with each state (one except for death states 2 and 5)
+ bq = c(0.938, -0.622, -0.3387, 0.938, 0), # QALYs associated with each state
+ delta.c = 0.06, # cost discount
+ delta.b = 0.06, # health discount
+ p.strata = c(0.02, 0.03, 0.07, 0.13, 0.10, 0.00, 0.02, 0.04, 0.10, 0.22, 0.26, 0.01), # age-sex distribution
+ lambda = structure(.Data = c(0.0017, 0.0017, 0.0017, 0.0017, 0.0017, 0.0044, 0.0044,
+ 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0138,
+ 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138,
+ 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379,
+ 0.0379, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912,
+ 0.0912, 0.0912, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.0044,
+ 0.0044, 0.0044, 0.0044, 0.0044, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138,
+ 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0379, 0.0379, 0.0379, 0.0379,
+ 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0912, 0.0912, 0.0912,
+ 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.0138, 0.0138, 0.0138, 0.0138,
+ 0.0138, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379,
+ 0.0379, 0.0379, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912,
+ 0.0912, 0.0912, 0.0912, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0912, 0.0912,
+ 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.0912,
+ 0.0912, 0.0912, 0.0912, 0.0912, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.0011, 0.0011, 0.0011, 0.0011, 0.0011, 0.0028, 0.0028,
+ 0.0028, 0.0028, 0.0028, 0.0028, 0.0028, 0.0028, 0.0028, 0.0028, 0.0081,
+ 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081,
+ 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022,
+ 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.0028, 0.0028,
+ 0.0028, 0.0028, 0.0028, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081,
+ 0.0081, 0.0081, 0.0081, 0.0081, 0.022, 0.022, 0.022, 0.022, 0.022,
+ 0.022, 0.022, 0.022, 0.022, 0.022, 0.0578, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081,
+ 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022,
+ 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.022, 0.022, 0.022, 0.022, 0.022, 0.0578, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.0578, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503
+ ), .Dim=c(12,60))
+)
\ No newline at end of file
diff --git a/doc/Examples/Hipsdata32.html b/doc/Examples/Hipsdata32.html
new file mode 100755
index 0000000..2b10e73
--- /dev/null
+++ b/doc/Examples/Hipsdata32.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hipsdata32</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"><br>list(<br># posterior means<br>BL=c(14.48, 12.7, 10.34, 7.737, 5.405, 4.101, 15.13, 13.69, 11.65, 9.1, 6.46, 4.988), <br>BQ = c(13.17, 11.59, 9.469, 7.157, 5.019, 3.812, 13.82, 12.53, 10.69, 8.43, 6.004, 4.64),<br>C = c(5787.0, 5425.0, 4997.0, 4472.0, 4266.0, 4196.0, 5636.0, 5359.0, 5010.0, 4493.0, 4285.0, 4215.0),<br>#posterior sd's<br>sdBL = c(0.005166, 0.003677, 0.002138, 0.0007832, 0.0003237, 0.0002136, [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Hipsdata32.txt b/doc/Examples/Hipsdata32.txt
new file mode 100755
index 0000000..16a6a9b
--- /dev/null
+++ b/doc/Examples/Hipsdata32.txt
@@ -0,0 +1,14 @@
+
+list(
+# posterior means
+BL=c(14.48, 12.7, 10.34, 7.737, 5.405, 4.101, 15.13, 13.69, 11.65, 9.1, 6.46, 4.988),
+BQ = c(13.17, 11.59, 9.469, 7.157, 5.019, 3.812, 13.82, 12.53, 10.69, 8.43, 6.004, 4.64),
+C = c(5787.0, 5425.0, 4997.0, 4472.0, 4266.0, 4196.0, 5636.0, 5359.0, 5010.0, 4493.0, 4285.0, 4215.0),
+#posterior sd's
+sdBL = c(0.005166, 0.003677, 0.002138, 0.0007832, 0.0003237, 0.0002136, 0.005161, 0.003836, 0.002427, 0.0009526, 0.0004226, 0.0002918),
+sdBQ = c(0.06027, 0.05198, 0.03841, 0.01873, 0.009921, 0.006748, 0.05718, 0.05006, 0.03914, 0.01989, 0.01083, 0.007627),
+sdC = c(230.8, 202.1, 151.6, 74.94, 40.06, 27.27, 218.0, 193.5, 153.5, 79.14, 43.46, 30.63),
+p.strata = c(0.02, 0.03, 0.07, 0.13, 0.10, 0.00, 0.02, 0.04, 0.10, 0.22, 0.26, 0.01),
+# strata weights (prob of hip replacement by age and sex)
+p.strata = c(0.02, 0.03, 0.07, 0.13, 0.10, 0.00, 0.02, 0.04, 0.10, 0.22, 0.26, 0.01)
+)
diff --git a/doc/Examples/Hipsdata4.html b/doc/Examples/Hipsdata4.html
new file mode 100755
index 0000000..c809bd3
--- /dev/null
+++ b/doc/Examples/Hipsdata4.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hipsdata4</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 60, # Number of cycles<br>K = 12, # Number of age-sex strata<br>S = 5, # Number of states in Markov model<br>
</font><font face="Arial" color="#FF00FF" size="1">M = 3, # Number of studies in evidence synthesis
</font><font face="Arial" color="#000100" size="1"><br>rho = 0.04, # re-revision rate<br>lambda.op = 0.01, # post-operative mortality rate<br># age-sex specific mean revision hazard for Charnley:<br>
</font><font face="Arial" color="#FF00FF" size="1">logh0 = c(-6.119, -6.119, -6.119, -6.438, -6.438, -6.438, -6.377, -6.377, -6.377, -6.725, -6.725, -6.725), <br>tau = 25,
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#FF00FF" size="1">C0 = c(4052, 4402), # set-up costs of primary operation<br>c = structure(.Data = c(0, 5290, 5290, 0, 0, <br>0, 5640, 5640, 0, 0), .Dim=c(2,5)), # additional costs associated with each state and prothesis <br># (zero except for revision states 2 and 3)
</font><font face="Arial" color="#000100" size="1"><br>bl = c(1,0,1,1,0), # life-expectancy benefits associated with each state (one except for death states 2 and 5)<br>bq = c(0.938, -0.622, -0.3387, 0.938, 0), # QALYs associated with each state<br>delta.c = 0.06, # cost discount<br>delta.b = 0.06, # health discount<br>
</font><font face="Arial" color="#FF00FF" size="1"># delta.b = 0.015, # alternative health discount (for sensitivity analysis)
</font><font face="Arial" color="#000100" size="1"><br># probablilty of hip replacement by age and sex<br>p.strata = c(0.02, 0.03, 0.07, 0.13, 0.10, 0.00, 0.02, 0.04, 0.10, 0.22, 0.26, 0.01),<br>lambda = structure(.Data = c(0.0017, 0.0017, 0.0017, 0.0017, 0.0017, 0.0044, 0.0044, <br> 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0138,<br> 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138,<br> 0.037 [...]
</font><font face="Arial" color="#FF00FF" size="1"> # Amount health care provider is willing to pay for each additional QALY <br> KK = c(200, 400, 600, 800, 1000, 1200, 1400, 1600, 1800, 2000, 2200, 2400, 2600, 2800, 3000, 3200, 3400, 3600, 3800, 4000,<br>4200, 4400, 4600, 4800, 5000, 5200, 5400, 5600, 5800, 6000, 6200, 6400, 6600, 6800, 7000, 7200, 7400, 7600, 7800, 8000,<br>8200, 8400, 8600, 8800, 9000, 9200, 9400, 9600, 9800, 10000, 10200, 10400, 10600 [...]
</font><font face="Arial" color="#000100" size="1"><br>)<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Hipsdata4.txt b/doc/Examples/Hipsdata4.txt
new file mode 100755
index 0000000..306fae5
--- /dev/null
+++ b/doc/Examples/Hipsdata4.txt
@@ -0,0 +1,117 @@
+list(N = 60, # Number of cycles
+ K = 12, # Number of age-sex strata
+ S = 5, # Number of states in Markov model
+ M = 3, # Number of studies in evidence synthesis
+ rho = 0.04, # re-revision rate
+ lambda.op = 0.01, # post-operative mortality rate
+ # age-sex specific mean revision hazard for Charnley:
+ logh0 = c(-6.119, -6.119, -6.119, -6.438, -6.438, -6.438, -6.377, -6.377, -6.377, -6.725, -6.725, -6.725),
+ tau = 25,
+ C0 = c(4052, 4402), # set-up costs of primary operation
+ c = structure(.Data = c(0, 5290, 5290, 0, 0,
+ 0, 5640, 5640, 0, 0), .Dim=c(2,5)), # additional costs associated with each state and prothesis
+ # (zero except for revision states 2 and 3)
+ bl = c(1,0,1,1,0), # life-expectancy benefits associated with each state (one except for death states 2 and 5)
+ bq = c(0.938, -0.622, -0.3387, 0.938, 0), # QALYs associated with each state
+ delta.c = 0.06, # cost discount
+ delta.b = 0.06, # health discount
+# delta.b = 0.015, # alternative health discount (for sensitivity analysis)
+ # probablilty of hip replacement by age and sex
+ p.strata = c(0.02, 0.03, 0.07, 0.13, 0.10, 0.00, 0.02, 0.04, 0.10, 0.22, 0.26, 0.01),
+ lambda = structure(.Data = c(0.0017, 0.0017, 0.0017, 0.0017, 0.0017, 0.0044, 0.0044,
+ 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0044, 0.0138,
+ 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138,
+ 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379,
+ 0.0379, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912,
+ 0.0912, 0.0912, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.0044,
+ 0.0044, 0.0044, 0.0044, 0.0044, 0.0138, 0.0138, 0.0138, 0.0138, 0.0138,
+ 0.0138, 0.0138, 0.0138, 0.0138, 0.0138, 0.0379, 0.0379, 0.0379, 0.0379,
+ 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0912, 0.0912, 0.0912,
+ 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.0138, 0.0138, 0.0138, 0.0138,
+ 0.0138, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379,
+ 0.0379, 0.0379, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912,
+ 0.0912, 0.0912, 0.0912, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.0379, 0.0379, 0.0379, 0.0379, 0.0379, 0.0912, 0.0912,
+ 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.0912, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.0912,
+ 0.0912, 0.0912, 0.0912, 0.0912, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958, 0.1958,
+ 0.1958, 0.1958, 0.0011, 0.0011, 0.0011, 0.0011, 0.0011, 0.0028, 0.0028,
+ 0.0028, 0.0028, 0.0028, 0.0028, 0.0028, 0.0028, 0.0028, 0.0028, 0.0081,
+ 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081,
+ 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022,
+ 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.0028, 0.0028,
+ 0.0028, 0.0028, 0.0028, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081,
+ 0.0081, 0.0081, 0.0081, 0.0081, 0.022, 0.022, 0.022, 0.022, 0.022,
+ 0.022, 0.022, 0.022, 0.022, 0.022, 0.0578, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.0081, 0.0081, 0.0081, 0.0081, 0.0081,
+ 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022, 0.022,
+ 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.022, 0.022, 0.022, 0.022, 0.022, 0.0578, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.0578, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.0578, 0.0578, 0.0578,
+ 0.0578, 0.0578, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503,
+ 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503, 0.1503
+ ), .Dim=c(12,60)),
+ # Amount health care provider is willing to pay for each additional QALY
+ KK = c(200, 400, 600, 800, 1000, 1200, 1400, 1600, 1800, 2000, 2200, 2400, 2600, 2800, 3000, 3200, 3400, 3600, 3800, 4000,
+ 4200, 4400, 4600, 4800, 5000, 5200, 5400, 5600, 5800, 6000, 6200, 6400, 6600, 6800, 7000, 7200, 7400, 7600, 7800, 8000,
+ 8200, 8400, 8600, 8800, 9000, 9200, 9400, 9600, 9800, 10000, 10200, 10400, 10600, 10800, 11000,
+ 11200, 11400, 11600, 11800, 12000, 12200, 12400, 12600, 12800, 13000, 13200, 13400, 13600, 13800, 14000,
+ 14200, 14400, 14600, 14800, 15000, 15200, 15400, 15600, 15800, 16000, 16200, 16400, 16600, 16800, 17000,
+ 17200, 17400, 17600, 17800, 18000, 18200, 18400, 18600, 18800, 19000, 19200, 19400, 19600, 19800, 20000),
+ # Evidence
+ rC = c(1683, 7, 33), # number of revisions for each study (Charnley)
+ nC = c(28525, 200, 208), # number of operations for each study (Charnley)
+ rS = c(28, 9, 69), # number of revisions for each study (Stanmore)
+ nS = c(865, 213, 982), # number of operations for each study (Stanmore)
+ # Quality weights for each study
+ qualweights = c(0.5, 1, 0.2)
+ # qualweights = c(0.1, 1, 0.05) # alternative quality weights for sensitivity analysis
+)
diff --git a/doc/Examples/Hipsinits4.html b/doc/Examples/Hipsinits4.html
new file mode 100755
index 0000000..b1faf72
--- /dev/null
+++ b/doc/Examples/Hipsinits4.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Hipsinits4</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(base=c(-3.09,-3.25,-2.12),logHR=c(-.63,.15,-.92),LHR=-0.35)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Hipsinits4.txt b/doc/Examples/Hipsinits4.txt
new file mode 100755
index 0000000..0de8f80
--- /dev/null
+++ b/doc/Examples/Hipsinits4.txt
@@ -0,0 +1 @@
+list(base=c(-3.09,-3.25,-2.12),logHR=c(-.63,.15,-.92),LHR=-0.35)
\ No newline at end of file
diff --git a/doc/Examples/Ice.html b/doc/Examples/Ice.html
new file mode 100755
index 0000000..058f1c4
--- /dev/null
+++ b/doc/Examples/Ice.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ice</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="ice0.bmp" alt="[ice0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Ice: non-parametric smoothing in<br> an age-cohort model
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Breslow and Clayton (1993) analyse breast cancer rates in Iceland by year of birth (K = 11 cohorts from 1840-1849 to 1940-1949) and by age (J =13 groups from 20-24 to 80-84 years). Due to the number of empty cells we consider a single indexing over I = 77 observed number of cases, giving data of the following form.<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="ice1.bmp" alt="[ice1]"></center>
</font><font face="Arial" color="#000100" size="3"><br>In order to pull in the extreme risks associated with small birth cohorts, Breslow and<br>Clayton first consider the exchangeable model<br><br><br> cases
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Poisson(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br> log
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = log person-years
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><sub>age
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"><sub>year
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal( 0,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> )<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>Autoregressive smoothing of relative risks
</strong></font><font face="Arial" color="#000100" size="3"><br><br>They then consider the alternative approach of smoothing the rates for the cohorts by assuming an auto-regressive model on the
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">'s, assuming the second differences are independent normal variates. This is equivalent to a model and prior distribution <br> cases
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Poisson(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br> log
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = log person-years
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><sub>age
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"><sub>year
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal( 0, 0.000001
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> )<br>
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">|
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal( 0, 0.000001
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> )<br>
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">|
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1,...,k-1
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal( 2
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>k-1
</sub></font><font face="Symbol" color="#000100" size="3">- b
</font><font face="Arial" color="#000100" size="2"><sub>k-2
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> ) k > 2<br> <br>We note that
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> are given "non-informative" priors, but retain a
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> term in order to provide the appropriate likelihood for
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">.<br><br>For computational reasons Breslow and Clayton impose constraints on their random effects
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"><sub>k
</sub></font><font face="Arial" color="#000100" size="3">in order that their mean and linear trend are zero, and counter these constraints by introducing a linear term b x year
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and allowing unrestrained estimation of
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">. Since we allow free movement of the
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">'s we dispense with the linear term, and impose a "corner" constraint
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> =0 . <br>
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"> model <br> {<br> for (i in 1:I) {<br> cases[i] ~ dpois(mu[i])<br> log(mu[i]) <- log(pyr[i]) + alpha[age[i]] + beta[year[i]]<br> #cumulative.cases[i] <- cumulative(cases[i], cases[i])<br> &nb [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><u><a href="../Examples/Icedata.html">
</u></font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><u><a href="../Examples/Iceinits.html">
</u></font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#0000FF" size="3"><u><a href="../Examples/Iceinits1.html">
</u></font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 100000 updates gave the parameter estimates<br><center><br><img src="ice2.bmp" alt="[ice2]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Icedata.html b/doc/Examples/Icedata.html
new file mode 100755
index 0000000..4441202
--- /dev/null
+++ b/doc/Examples/Icedata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Icedata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(age = c(1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, <br> 6, 6, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, <br> 11, 11, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13),<br> year = c [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Icedata.txt b/doc/Examples/Icedata.txt
new file mode 100755
index 0000000..32b99cd
--- /dev/null
+++ b/doc/Examples/Icedata.txt
@@ -0,0 +1,16 @@
+list(age = c(1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6,
+ 6, 6, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11,
+ 11, 11, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13),
+ year = c(6, 7, 8, 9, 10, 11, 6, 7, 8, 9, 10, 11, 5, 6, 7, 8, 9, 10, 5, 6, 7, 8, 9, 10, 4, 5, 6, 7, 8, 9, 4, 5, 6, 7,
+ 8, 9, 3, 4, 5, 6, 7, 8, 3, 4, 5, 6, 7, 8, 2, 3, 4, 5, 6, 7, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4,
+ 5, 6, 1, 2, 3, 4, 5, 6, 1, 2, 3, 4, 5),
+ cases = c(2, 0, 1, 1, 1, 2, 0, 2, 1, 1, 5, 5, 1, 1, 3, 7, 12, 10, 6, 11, 9, 14, 20, 14, 7, 14, 22, 25, 29, 37, 21, 11, 29, 33,
+ 57, 24, 15, 8, 22, 27, 38, 52, 10, 15, 22, 26, 47, 31, 8, 11, 17, 23, 31, 38, 8, 10, 24, 30, 53, 26, 5, 3, 10, 18,
+ 22, 30, 1, 7, 11, 26, 32, 17, 5, 8, 17, 32, 31),
+ pyr = c(41380, 43650, 49810, 58105, 57105, 76380, 39615, 42205, 48315, 56785, 55965, 33955, 29150, 38460,
+ 40810, 47490, 55720, 55145, 27950, 37375, 39935, 46895, 54980, 27810, 25055, 27040, 36400, 39355,
+ 46280, 54350, 24040, 26290, 35480, 38725, 45595, 25710, 22890, 23095, 25410, 34420, 37725, 44740,
+ 21415, 21870, 24240, 33175, 36345, 21320, 17450, 19765, 20255, 22760, 31695, 34705, 15350, 17720,
+ 18280, 20850, 29600, 15635, 9965, 12850, 15015, 15725, 18345, 26400, 8175, 11020, 13095, 14050,
+ 16480, 10885, 7425, 10810, 12260, 14780, 13600),
+ I = 77, Nage = 13, K = 11)
\ No newline at end of file
diff --git a/doc/Examples/Iceinits.html b/doc/Examples/Iceinits.html
new file mode 100755
index 0000000..5b4b599
--- /dev/null
+++ b/doc/Examples/Iceinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Iceinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(tau=1,<br>alpha=c(NA,0,0,0,0,0,0,0,0,0,0,0,0),<br>beta =c(0.05,0.1,0,0,0,0,0,0,0,0,0))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Iceinits.txt b/doc/Examples/Iceinits.txt
new file mode 100755
index 0000000..5ae7e1e
--- /dev/null
+++ b/doc/Examples/Iceinits.txt
@@ -0,0 +1,3 @@
+list(tau=1,
+alpha=c(NA,0,0,0,0,0,0,0,0,0,0,0,0),
+beta =c(0.05,0.1,0,0,0,0,0,0,0,0,0))
\ No newline at end of file
diff --git a/doc/Examples/Iceinits1.html b/doc/Examples/Iceinits1.html
new file mode 100755
index 0000000..dedeed0
--- /dev/null
+++ b/doc/Examples/Iceinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Iceinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(tau=1,<br>alpha=c(NA,1,1,1,1,1,1,1,1,1,1,1,1),<br>beta =c(0.5,0.1,1,1,1,1,1,1,1,1,1))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Iceinits1.txt b/doc/Examples/Iceinits1.txt
new file mode 100755
index 0000000..335841f
--- /dev/null
+++ b/doc/Examples/Iceinits1.txt
@@ -0,0 +1,3 @@
+list(tau=1,
+alpha=c(NA,1,1,1,1,1,1,1,1,1,1,1,1),
+beta =c(0.5,0.1,1,1,1,1,1,1,1,1,1))
\ No newline at end of file
diff --git a/doc/Examples/Icemodel.html b/doc/Examples/Icemodel.html
new file mode 100755
index 0000000..6e0d5ca
--- /dev/null
+++ b/doc/Examples/Icemodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Icemodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model <br> {<br> for (i in 1:I) {<br> cases[i] ~ dpois(mu[i])<br> log(mu[i]) <- log(pyr[i]) + alpha[age[i]] + beta[year[i]]<br> }<br> betamean[1] <- 2 * beta[2] - beta[3]<br>   [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Icemodel.txt b/doc/Examples/Icemodel.txt
new file mode 100755
index 0000000..13bb7e3
--- /dev/null
+++ b/doc/Examples/Icemodel.txt
@@ -0,0 +1,35 @@
+ model
+ {
+ for (i in 1:I) {
+ cases[i] ~ dpois(mu[i])
+ log(mu[i]) <- log(pyr[i]) + alpha[age[i]] + beta[year[i]]
+ }
+ betamean[1] <- 2 * beta[2] - beta[3]
+ Nneighs[1] <- 1
+ betamean[2] <- (2 * beta[1] + 4 * beta[3] - beta[4]) / 5
+ Nneighs[2] <- 5
+ for (k in 3 : K - 2) {
+ betamean[k] <- (4 * beta[k - 1] + 4 * beta[k + 1]- beta[k - 2] - beta[k + 2]) / 6
+ Nneighs[k] <- 6
+ }
+ betamean[K - 1] <- (2 * beta[K] + 4 * beta[K - 2] - beta[K - 3]) / 5
+ Nneighs[K - 1] <- 5
+ betamean[K] <- 2 * beta[K - 1] - beta[K - 2]
+ Nneighs[K] <- 1
+ for (k in 1 : K) {
+ betaprec[k] <- Nneighs[k] * tau
+ }
+ for (k in 1 : K) {
+ beta[k] ~ dnorm(betamean[k], betaprec[k])
+ logRR[k] <- beta[k] - beta[5]
+ tau.like[k] <- Nneighs[k] * beta[k] * (beta[k] - betamean[k])
+ }
+ alpha[1] <- 0.0
+ for (j in 2 : Nage) {
+ alpha[j] ~ dnorm(0, 1.0E-6)
+ }
+ d <- 0.0001 + sum(tau.like[]) / 2
+ r <- 0.0001 + K / 2
+ tau ~ dgamma(r, d)
+ sigma <- 1 / sqrt(tau)
+ }
diff --git a/doc/Examples/Impala.html b/doc/Examples/Impala.html
new file mode 100755
index 0000000..5ac35c4
--- /dev/null
+++ b/doc/Examples/Impala.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Impala</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"><br><img src="impala0.bmp" alt="[impala0]">
</font><font face="Arial" color="#0000FF" size="3"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Impala: distance Sampling
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="6"> <br> (contributed by Andy Royle)<br>
</font><font face="Arial" color="#000100" size="3"><br>Distance sampling is a popular method for estimating the density of populations based on observed distances between objects and line or point (see Buckland et al. 2001). It can be viewed as a special type of closed population model for estimating population size, having J=1 replicate sample and with distance from line or point to individual as an "individual covariate". We adopt that view here, and thus analyze the model usi [...]
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> | x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br>where<br><br>p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = g(x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">; theta)<br><br>x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = distance to individual i and g() is the detection probability function. Here we consider the half-normal detection function:<br><br>g(x) = exp-(x / theta)
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"><br><br><br>Data augmentation -- We do not know N in practice. In fact, we only observe the y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">=1 observations. We handle that in the analysis using data augmentation (see Royle and Dorazio (2008, Ch. 7)). We add the "observations" y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">= 0 for i = nind +1, nind + 2,...., M for M sufficiently large. We introduce the latent indicator variables z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> for i=1,2,...., M with<br><br> z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli( psi ) for i = 1, 2, ...., M # note: specified for all M individuals<br><br>(this implies N ~ dunif(0, M) so choose M accordingly). For analysis of the impala data, data augmentation is based on nz=300 y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">=0 observations.<br><br>Distance, x, is only observed for individuals that are detected, and it is regarded as missing data for the augmented individuals. We assume:<br><br>x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ uniform(0, B) for i = 1, 2, ...., M # note: specified for all M individuals<br><br>Where B is chosen to represent the upper-limit of observation (in practice, observations are truncated at some large distance). For the Impala data, B=4 (i.e., 400 meters). The "missing" values of x have to be passed to WinBUGS as missing values, indicated by NA (see below).<br><br>Model summary:<br> y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> | x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> * z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) # observation model<br> p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = g(x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">; theta)<br>g(x) = exp((x / theta
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">))<br>z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli(psi) for i = 1, 2, ...., M # data augmentation<br>x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ unif(0, B) for i = 1, 2, ...., M # distances<br><br>Prior distributions are specified as:<br>psi ~ uniform(0,1)<br>theta ~ uniform(0, U) # U chosen arbitrarily large<br><br>Under data augmentation, population size, N, and density, D are derived parameters: N =
</font><font face="Symbol" color="#000100" size="6">S
</font><font face="Arial" color="#000100" size="3"> z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and, D = N / a, where a = area of the sample unit(s).<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model <br> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Prior distributions<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">theta ~ dunif(0, 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">theta2 <- theta *theta<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">psi ~ dunif(0,1)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(i in 1 : nind+nz){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">z[i] ~ dbern(psi) # latent indicator variables from data augmentation<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">x[i] ~ dunif(0, 4) # distance is a random variable<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logp[i]<- -((x[i] * x[i]) / theta2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">p[i] <- exp(logp[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i] <- z[i] * p[i] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">y[i] ~ dbern(mu[i]) # observation model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">N<-sum(z[1:nind + nz])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">D<- N / 48 # 48 km*km = total area of transects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="5"><br><br>
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Impaladata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Impalainits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="3"> </a>
</font><font face="Arial" color="#0000FF" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Impalainits2.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="3"></a><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">Note that initial values for the missing values of x are not provided. WinBUGS seems to do a good job picking those, but not always (sometimes there is a crash, so try again).
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="3">Results from 2 chains of length 10000 after 1000 burn-in. Estimated density is 3.75 individuals per square kilometer<br><center><br>
</font><font face="Arial" color="#000100" size="1"><br><img src="impala1.bmp" alt="[impala1]"><br>
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Impaladata.html b/doc/Examples/Impaladata.html
new file mode 100755
index 0000000..e616f2c
--- /dev/null
+++ b/doc/Examples/Impaladata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Impaladata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(y=<br>c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, <br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, <br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, <br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, <br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, <br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, <br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Impaladata.txt b/doc/Examples/Impaladata.txt
new file mode 100755
index 0000000..6454245
--- /dev/null
+++ b/doc/Examples/Impaladata.txt
@@ -0,0 +1,48 @@
+list(y=
+c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
+x=c(0.72, 0.26, 0.58, 0.92, 1.64, 0.85, 1.64, 1.57, 0.22, 0.72,
+0.87, 0.51, 0, 0.73, 0, 1.29, 1.64, 0.72, 0.3, 0.71, 1.51, 0.69,
+0.9, 0.65, 1.66, 0.38, 3.78, 0.78, 0.42, 0, 4, 1.75, 0.3, 0.35,
+0.86, 0.32, 2, 2.72, 0.26, 0.77, 0.41, 2, 0.86, 0, 0.94, 0.55,
+0.1, 0.85, 0, 0.78, 0, 0.96, 0, 0.64, 1.88, 0, 1.61, 1.5, 0.64,
+1.93, 1.06, 1.15, 1.43, 1.29, 2.46, 1.23, 1.23, 1.53, 1.43, 0.34,
+0.96, 2.6, 0.09, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
+NA),
+nind=73,
+nz=300)
+
diff --git a/doc/Examples/Impalainits1.html b/doc/Examples/Impalainits1.html
new file mode 100755
index 0000000..9e91602
--- /dev/null
+++ b/doc/Examples/Impalainits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Impalainits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(theta = 3, psi = 0.5, z = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, <br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, <br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, <br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,<br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, <br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, <br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Impalainits1.txt b/doc/Examples/Impalainits1.txt
new file mode 100755
index 0000000..9591cb9
--- /dev/null
+++ b/doc/Examples/Impalainits1.txt
@@ -0,0 +1,19 @@
+list(theta = 3, psi = 0.5, z = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
diff --git a/doc/Examples/Impalainits2.html b/doc/Examples/Impalainits2.html
new file mode 100755
index 0000000..2a2db4f
--- /dev/null
+++ b/doc/Examples/Impalainits2.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Impalainits2</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(theta = 1, psi = 0.8, z = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, <br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, <br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, <br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,<br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, <br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, <br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Impalainits2.txt b/doc/Examples/Impalainits2.txt
new file mode 100755
index 0000000..155d381
--- /dev/null
+++ b/doc/Examples/Impalainits2.txt
@@ -0,0 +1,19 @@
+list(theta = 1, psi = 0.8, z = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
diff --git a/doc/Examples/Impalamodel.html b/doc/Examples/Impalamodel.html
new file mode 100755
index 0000000..dddb2de
--- /dev/null
+++ b/doc/Examples/Impalamodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Impalamodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">model <br> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Prior distributions<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">theta~dunif(0,10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">theta2<-theta*theta<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">psi~dunif(0,1)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(i in 1:(nind+nz)){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">z[i]~dbern(psi) # latent indicator variables from data augmentation<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">x[i]~dunif(0,4) # distance is a random variable<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">logp[i]<- -((x[i]*x[i])/theta2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">p[i]<-exp(logp[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i]<-z[i]*p[i] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">y[i]~dbern(mu[i]) # observation model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">N<-sum(z[1:(nind+nz)])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">D<- N/48 # 48 km*km = total area of transects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Impalamodel.txt b/doc/Examples/Impalamodel.txt
new file mode 100755
index 0000000..ce0865f
--- /dev/null
+++ b/doc/Examples/Impalamodel.txt
@@ -0,0 +1,18 @@
+model
+ {
+ # Prior distributions
+ theta~dunif(0,10)
+ theta2<-theta*theta
+ psi~dunif(0,1)
+
+ for(i in 1:(nind+nz)){
+ z[i]~dbern(psi) # latent indicator variables from data augmentation
+ x[i]~dunif(0,4) # distance is a random variable
+ logp[i]<- -((x[i]*x[i])/theta2)
+ p[i]<-exp(logp[i])
+ mu[i]<-z[i]*p[i]
+ y[i]~dbern(mu[i]) # observation model
+ }
+ N<-sum(z[1:(nind+nz)])
+ D<- N/48 # 48 km*km = total area of transects
+ }
\ No newline at end of file
diff --git a/doc/Examples/Inhalers.html b/doc/Examples/Inhalers.html
new file mode 100755
index 0000000..a0c8dee
--- /dev/null
+++ b/doc/Examples/Inhalers.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Inhalers</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="inhalers0.bmp" alt="[inhalers0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Inhaler: ordered categorical data
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><br>Ezzet and Whitehead (1993) analyse data from a two-treatment, two-period crossover trial to compare 2 inhalation devices for delivering the drug salbutamol in 286 asthma patients. Patients were asked to rate the clarity of leaflet instructions accompanying each device, using a 4-point ordinal scale. In the table below, the first entry in each cell (r,c) gives the number of subjects in Group 1 (who received device A in period [...]
</font><font face="Arial" color="#000100" size="2"><img src="inhalers1.bmp" alt="[inhalers1]"></center>
</font><font face="Arial" color="#000100" size="3"><br>The response R
</font><font face="Arial" color="#000100" size="3"><sub>it
</sub></font><font face="Arial" color="#000100" size="3"> from the
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> th subject (
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> = 1,...,286) in the
</font><font face="Arial" color="#000100" size="3"><em>t
</em></font><font face="Arial" color="#000100" size="3"> th period (
</font><font face="Arial" color="#000100" size="3"><em>t
</em></font><font face="Arial" color="#000100" size="3"> = 1,2) thus assumes integer values between 1 and 4. It may be expressed in terms of a continuous latent variable Y
</font><font face="Arial" color="#000100" size="2"><sub>it
</sub></font><font face="Arial" color="#000100" size="3"> taking values on (-inf, inf) as follows:<br><br> R
</font><font face="Arial" color="#000100" size="2"><sub>it
</sub></font><font face="Arial" color="#000100" size="3"> = j if Y
</font><font face="Arial" color="#000100" size="2"><sub>it
</sub></font><font face="Arial" color="#000100" size="3"> in [a
</font><font face="Arial" color="#000100" size="2"><sub>j - 1
</sub></font><font face="Arial" color="#000100" size="3">, a
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">), j = 1,..,4<br><br>where a
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"> = -inf and a
</font><font face="Arial" color="#000100" size="2"><sub>4
</sub></font><font face="Arial" color="#000100" size="3"> = inf. Assuming a logistic distribution with mean
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>it
</sub></font><font face="Arial" color="#000100" size="3"> for Y
</font><font face="Arial" color="#000100" size="2"><sub>it
</sub></font><font face="Arial" color="#000100" size="3">, then the cumulative probability Q
</font><font face="Arial" color="#000100" size="2"><sub>itj
</sub></font><font face="Arial" color="#000100" size="3"> of subject
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> rating the treatment in period
</font><font face="Arial" color="#000100" size="3"><em>t
</em></font><font face="Arial" color="#000100" size="3"> as worse than category
</font><font face="Arial" color="#000100" size="3"><em>j
</em></font><font face="Arial" color="#000100" size="3">(i.e. Prob( Y
</font><font face="Arial" color="#000100" size="2"><sub>it
</sub></font><font face="Arial" color="#000100" size="3"> >= a
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">) is given by<br> <br> logitQ
</font><font face="Arial" color="#000100" size="2"><sub>itj
</sub></font><font face="Arial" color="#000100" size="3"> = -(a
</font><font face="Arial" color="#000100" size="2">j
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>s
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>t
</sub></font><font face="Arial" color="#000100" size="3">+ b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br>where b
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> represents the random effect for subject
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">. Here,
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="3"><sub>s
</sub></font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>t
</sub></font><font face="Arial" color="#000100" size="3">depends only on the period
</font><font face="Arial" color="#000100" size="3"><em>t
</em></font><font face="Arial" color="#000100" size="3"> and the
</font><font face="Arial" color="#000100" size="3"><em>sequence
</em></font><font face="Arial" color="#000100" size="3"> s
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = 1,2 to which patient
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> belongs. It is defined as<br> <br>
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>11
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">/ 2 +
</font><font face="Symbol" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="3">/ 2<br> <br>
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>12
</sub></font><font face="Arial" color="#000100" size="3"> = -
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> / 2 -
</font><font face="Symbol" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="3"> / 2 -
</font><font face="Symbol" color="#000100" size="3">k
</font><font face="Arial" color="#000100" size="3"><br> <br>
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>21
</sub></font><font face="Arial" color="#000100" size="3"> = -
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> / 2 +
</font><font face="Symbol" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="3"> / 2<br> <br>
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>22
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> / 2 -
</font><font face="Symbol" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="3"> / 2 +
</font><font face="Symbol" color="#000100" size="3">k
</font><font face="Arial" color="#000100" size="3"><br> <br>where
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> represents the treatment effect,
</font><font face="Symbol" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="3"> represents the period effect and
</font><font face="Symbol" color="#000100" size="3">k
</font><font face="Arial" color="#000100" size="3"> represents the carryover effect. The probability of subject
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">giving response
</font><font face="Arial" color="#000100" size="3"><em> j
</em></font><font face="Arial" color="#000100" size="3">in period
</font><font face="Arial" color="#000100" size="3"><em>t
</em></font><font face="Arial" color="#000100" size="3"> is thus given by p
</font><font face="Arial" color="#000100" size="2"><sub>itj
</sub></font><font face="Arial" color="#000100" size="3"> = Q
</font><font face="Arial" color="#000100" size="2"><sub>itj - 1
</sub></font><font face="Arial" color="#000100" size="3"> - Q
</font><font face="Arial" color="#000100" size="2"><sub>itj
</sub></font><font face="Arial" color="#000100" size="3">, where Q
</font><font face="Arial" color="#000100" size="2"><sub>it0
</sub></font><font face="Arial" color="#000100" size="3"> = 1 and Q
</font><font face="Arial" color="#000100" size="2"><sub>it4
</sub></font><font face="Arial" color="#000100" size="3"> = 0 (see also the Bones example). <br><br>The
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language for this model is shown below. We assume the b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">'s to be normally distributed with zero mean and common precision
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">. The fixed effects
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">k
</font><font face="Arial" color="#000100" size="3"> are given vague normal priors, as are the unknown cut points a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">, a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> and a
</font><font face="Arial" color="#000100" size="2"><sub>3
</sub></font><font face="Arial" color="#000100" size="3">. We also impose order constraints on the latter using the T(,) notation in
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3">, to ensure that a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> < a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> < a
</font><font face="Arial" color="#000100" size="2"><sub>3
</sub></font><font face="Arial" color="#000100" size="3">. <br>
</font><font face="Arial" color="#000100" size="3"><br> model <br> {<br> #<br> # Construct individual response data from contingency table<br> #<br> for (i in 1 : Ncum[1, 1]) { <br> group[i] <- 1<br> for (t in 1 : T) { response[i, t] <- pattern[1, t] }<br>  [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Note that the data is read into
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> in the original contigency table format to economize on space and effort. The indivdual responses for each of the 286 patients are then constructed within
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3">. <br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Inhalersdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Inhalersinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Inhalersinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center><br><img src="inhalers2.bmp" alt="[inhalers2]">
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br></center>The estimates can be compared with those of Ezzet and Whitehead, who used the Newton-Raphson method and numerical integration to obtain maximum-likelihood estimates of the parameters. They reported
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000000" size="3"> = 1.17 +/- 0.75,
</font><font face="Symbol" color="#000100" size="3">p
</font><font face="Arial" color="#000000" size="3"> = -0.23 +/- 0.20,
</font><font face="Symbol" color="#000100" size="3">k
</font><font face="Arial" color="#000000" size="3"> = 0.21 +/- 0.49, log
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000000" size="3"> = 0.17 +/- 0.23, a1 = 0.68, a2 = 3.85, a3 = 5.10
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Inhalersdata.html b/doc/Examples/Inhalersdata.html
new file mode 100755
index 0000000..d4a700d
--- /dev/null
+++ b/doc/Examples/Inhalersdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Inhalersdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 286, T = 2, G = 2, Npattern = 16, Ncut = 3,<br> pattern = structure(.Data = <br> c(1, 1, <br>1, 2, <br>1, 3, <br>1, 4,<br>2, 1,<br>2, 2,<br>2, 3,<br>2, 4,<br>3, 1,<br>3, 2,<br>3, 3,<br>3, 4,<br>4, 1,<br>4, 2,<br>4, 3,<br>4, 4), .Dim = c(16, 2)),<br>Ncum = structure(.Data = <br> c( 59, 122,<br>157, 170,<br>173, 173,< [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Inhalersdata.txt b/doc/Examples/Inhalersdata.txt
new file mode 100755
index 0000000..be1f850
--- /dev/null
+++ b/doc/Examples/Inhalersdata.txt
@@ -0,0 +1,45 @@
+list(N = 286, T = 2, G = 2, Npattern = 16, Ncut = 3,
+ pattern = structure(.Data =
+ c(1, 1,
+ 1, 2,
+ 1, 3,
+ 1, 4,
+ 2, 1,
+ 2, 2,
+ 2, 3,
+ 2, 4,
+ 3, 1,
+ 3, 2,
+ 3, 3,
+ 3, 4,
+ 4, 1,
+ 4, 2,
+ 4, 3,
+ 4, 4), .Dim = c(16, 2)),
+ Ncum = structure(.Data =
+ c( 59, 122,
+ 157, 170,
+ 173, 173,
+ 175, 175,
+ 186, 226,
+ 253, 268,
+ 270, 270,
+ 271, 271,
+ 271, 278,
+ 278, 280,
+ 280, 281,
+ 281, 281,
+ 282, 284,
+ 285, 285,
+ 285, 286,
+ 286, 286), .Dim = c(16, 2)),
+ treat = structure(.Data =
+ c( 1, -1,
+ -1, 1), .Dim = c(2, 2)),
+ period = structure(.Data =
+ c( 1, -1,
+ 1, -1), .Dim = c(2, 2)),
+ carry = structure(.Data =
+ c( 0, -1,
+ 0, 1), .Dim = c(2, 2))
+)
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diff --git a/doc/Examples/Inhalersinits.html b/doc/Examples/Inhalersinits.html
new file mode 100755
index 0000000..47a5654
--- /dev/null
+++ b/doc/Examples/Inhalersinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Inhalersinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(beta = 0, pi = 0, kappa = 0, a = c(2, 3, 4), tau = 1)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Inhalersinits.txt b/doc/Examples/Inhalersinits.txt
new file mode 100755
index 0000000..a86b2d2
--- /dev/null
+++ b/doc/Examples/Inhalersinits.txt
@@ -0,0 +1 @@
+list(beta = 0, pi = 0, kappa = 0, a = c(2, 3, 4), tau = 1)
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diff --git a/doc/Examples/Inhalersinits1.html b/doc/Examples/Inhalersinits1.html
new file mode 100755
index 0000000..0e26c7c
--- /dev/null
+++ b/doc/Examples/Inhalersinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Inhalersinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(beta = 1, pi = 1, kappa = 0, a = c(3, 4, 5), tau = 0.1)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Inhalersinits1.txt b/doc/Examples/Inhalersinits1.txt
new file mode 100755
index 0000000..2ee8fcf
--- /dev/null
+++ b/doc/Examples/Inhalersinits1.txt
@@ -0,0 +1 @@
+list(beta = 1, pi = 1, kappa = 0, a = c(3, 4, 5), tau = 0.1)
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diff --git a/doc/Examples/Inhalersmodel.html b/doc/Examples/Inhalersmodel.html
new file mode 100755
index 0000000..94c7767
--- /dev/null
+++ b/doc/Examples/Inhalersmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Inhalersmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model <br> {<br> #<br> # Construct individual response data from contingency table<br> #<br> for (i in 1 : Ncum[1, 1]) { <br> group[i] <- 1<br> for (t in 1 : T) { response[i, t] <- pattern[1, t] }<br> &nbs [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Inhalersmodel.txt b/doc/Examples/Inhalersmodel.txt
new file mode 100755
index 0000000..14e7127
--- /dev/null
+++ b/doc/Examples/Inhalersmodel.txt
@@ -0,0 +1,70 @@
+ model
+ {
+ #
+ # Construct individual response data from contingency table
+ #
+ for (i in 1 : Ncum[1, 1]) {
+ group[i] <- 1
+ for (t in 1 : T) { response[i, t] <- pattern[1, t] }
+ }
+ for (i in (Ncum[1,1] + 1) : Ncum[1, 2]) {
+ group[i] <- 2 for (t in 1 : T) { response[i, t] <- pattern[1, t] }
+ }
+
+ for (k in 2 : Npattern) {
+ for(i in (Ncum[k - 1, 2] + 1) : Ncum[k, 1]) {
+ group[i] <- 1 for (t in 1 : T) { response[i, t] <- pattern[k, t] }
+ }
+ for(i in (Ncum[k, 1] + 1) : Ncum[k, 2]) {
+ group[i] <- 2 for (t in 1 : T) { response[i, t] <- pattern[k, t] }
+ }
+ }
+ #
+ # Model
+ #
+ for (i in 1 : N) {
+ for (t in 1 : T) {
+ for (j in 1 : Ncut) {
+ #
+ # Cumulative probability of worse response than j
+ #
+ logit(Q[i, t, j]) <- -(a[j] + mu[group[i], t] + b[i])
+ }
+ #
+ # Probability of response = j
+ #
+ p[i, t, 1] <- 1 - Q[i, t, 1]
+ for (j in 2 : Ncut) { p[i, t, j] <- Q[i, t, j - 1] - Q[i, t, j] }
+ p[i, t, (Ncut+1)] <- Q[i, t, Ncut]
+
+ response[i, t] ~ dcat(p[i, t, ])
+ }
+ #
+ # Subject (random) effects
+ #
+ b[i] ~ dnorm(0.0, tau)
+ }
+
+ #
+ # Fixed effects
+ #
+ for (g in 1 : G) {
+ for(t in 1 : T) {
+ # logistic mean for group i in period t
+ mu[g, t] <- beta * treat[g, t] / 2 + pi * period[g, t] / 2 + kappa * carry[g, t]
+ }
+ }
+ beta ~ dnorm(0, 1.0E-06)
+ pi ~ dnorm(0, 1.0E-06)
+ kappa ~ dnorm(0, 1.0E-06)
+
+ # ordered cut points for underlying continuous latent variable
+ a[1] ~ dflat()T(-1000, a[2])
+ a[2] ~ dflat()T(a[1], a[3])
+ a[3] ~ dflat()T(a[2], 1000)
+
+ tau ~ dgamma(0.001, 0.001)
+ sigma <- sqrt(1 / tau)
+ log.sigma <- log(sigma)
+
+ }
diff --git a/doc/Examples/Jama.html b/doc/Examples/Jama.html
new file mode 100755
index 0000000..e5e0c5c
--- /dev/null
+++ b/doc/Examples/Jama.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Jama</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><img src="jama0.bmp" alt="[jama0]">
</font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Jama River Valley Ecuador - <br> Radiocarbon calibration with<br> phase information
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">This example is from the book Buck CE, Cavanagh WG, & Litton CD (1996)
</font><font face="Arial" color="#000100" size="3"><em>Bayesian approach to interpreting archaeological data
</em></font><font face="Arial" color="#000100" size="3">. Wiley: Chichester. p226-232 See also Zeidler,JA, Buck CE & Litton CD (1998) The integration of archaeological phase information and radiocarbon results from the Jama River Valley, Ecuador: a Bayesian approach.
</font><font face="Arial" color="#000100" size="3"><em>Latin American Antiquity
</em></font><font face="Arial" color="#000100" size="3"><strong>9
</strong></font><font face="Arial" color="#000100" size="3"> 160-179 .The model was set up by Andrew Millard. <br><br>© Andrew Millard 2001 <br>
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#000100" size="3"> model{ <br> for (i in 1 : nDate){<br> theta[i] ~ dunif(beta[phase[i]], alpha[phase[i]] )<br> X[i] ~ dnorm(mu[i], tau[i])<br> tau[i] <- 1 / pow(sigma[i], 2)<br> mu[i] <- in [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Jamadata1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Examples/Jamadata2.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data2
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Examples/RCdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Radio Carbon Calibration Curve
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Jamainits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Jamainits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br><center>
</font><font face="Arial" color="#000100" size="1"><br><img src="jama1.bmp" alt="[jama1]"><img src="jama2.bmp" alt="[jama2]"><br><img src="jama3.bmp" alt="[jama3]"><br><img src="jama4.bmp" alt="[jama4]"><img src="jama5.bmp" alt="[jama5]"><img src="jama6.bmp" alt="[jama6]"><img src="jama7.bmp" alt="[jama7]"><img src="jama8.bmp" alt="[jama8]"><img src="jama9.bmp" alt="[jama9]"><img src="jama10.bmp" alt="[jama10]"><img src="jama11.bmp" alt="[jama11]"><img src="jama12.bmp" alt="[jama12]"><img [...]
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Jamadata1.html b/doc/Examples/Jamadata1.html
new file mode 100755
index 0000000..f6ed14e
--- /dev/null
+++ b/doc/Examples/Jamadata1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Jamadata1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(nDate = 37, theta.max = 10000, theta.min = 0)<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Jamadata1.txt b/doc/Examples/Jamadata1.txt
new file mode 100755
index 0000000..61968d2
--- /dev/null
+++ b/doc/Examples/Jamadata1.txt
@@ -0,0 +1 @@
+list(nDate = 37, theta.max = 10000, theta.min = 0)
diff --git a/doc/Examples/Jamadata2.html b/doc/Examples/Jamadata2.html
new file mode 100755
index 0000000..5b4e936
--- /dev/null
+++ b/doc/Examples/Jamadata2.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Jamadata2</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">X[] sigma[] phase[]<br> 3630 70 1<br> 3620 70 1<br> 3560 70 1<br> 3545 135 1<br> 3500 70 1<br> 3030 80 2<br>& [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Jamadata2.txt b/doc/Examples/Jamadata2.txt
new file mode 100755
index 0000000..3256e25
--- /dev/null
+++ b/doc/Examples/Jamadata2.txt
@@ -0,0 +1,39 @@
+X[] sigma[] phase[]
+ 3630 70 1
+ 3620 70 1
+ 3560 70 1
+ 3545 135 1
+ 3500 70 1
+ 3030 80 2
+ 2845 95 2
+ 2800 115 2
+ 2500 160 2
+ 2430 170 3
+ 2170 40 3
+ 2125 300 3
+ 1990 100 3
+ 1980 70 3
+ 1960 90 3
+ 1950 70 3
+ 1610 70 4
+ 1590 80 4
+ 1540 70 4
+ 1520 80 4
+ 1480 75 4
+ 1330 70 4
+ 1260 30 4
+ 1240 40 4
+ 1195 85 5
+ 1170 340 5
+ 1120 30 5
+ 1120 90 5
+ 1030 90 5
+ 960 35 5
+ 880 70 5
+ 870 45 5
+ 820 70 5
+ 800 40 5
+ 630 30 6
+ 515 40 6
+ 305 35 7
+ END
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diff --git a/doc/Examples/Jamainits.html b/doc/Examples/Jamainits.html
new file mode 100755
index 0000000..5f7a10c
--- /dev/null
+++ b/doc/Examples/Jamainits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Jamainits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha=c(3640, 3040, 2440, 1620,1200, 640, NA), <br> beta=c(3490, 2490, 1940, 1230, 790, 500, 200),<br>theta = c(3630, 3620, 3560, 3545, 3500, 3030, 2845, 2800, 2500, 2430, 2170, 2125, 1990, <br> 1980, 1960, 1950, 1610, 1590, 1540, 1520, 1480, 1330, 1260, 1240, 1195, 1170,<br> 1120, 1120, 1030, 960, 880, 870, 820, 800, 630, 515, 305))
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Jamainits.txt b/doc/Examples/Jamainits.txt
new file mode 100755
index 0000000..d6e55ce
--- /dev/null
+++ b/doc/Examples/Jamainits.txt
@@ -0,0 +1,5 @@
+list(alpha=c(3640, 3040, 2440, 1620,1200, 640, NA),
+ beta=c(3490, 2490, 1940, 1230, 790, 500, 200),
+theta = c(3630, 3620, 3560, 3545, 3500, 3030, 2845, 2800, 2500, 2430, 2170, 2125, 1990,
+ 1980, 1960, 1950, 1610, 1590, 1540, 1520, 1480, 1330, 1260, 1240, 1195, 1170,
+ 1120, 1120, 1030, 960, 880, 870, 820, 800, 630, 515, 305))
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diff --git a/doc/Examples/Jamainits1.html b/doc/Examples/Jamainits1.html
new file mode 100755
index 0000000..0d890a1
--- /dev/null
+++ b/doc/Examples/Jamainits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Jamainits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha=c(3690, 3090, 2490, 1670,1250, 690, NA), <br> beta=c(3540, 2540, 1990, 1280, 940, 550, 250),<br>theta = c(3680, 3670, 3610, 3595, 3550, 3080, 2895, 2850, 2550, 2480, 2220, 2175, 2040, <br> 2030, 2010, 2000, 1660, 1640, 1590, 1570, 1530, 1380, 1310, 1290, 1245, 1220,<br> 1170, 1170, 1080, 1010, 1000, 1000, 1000, 1000, 680, 565, 355))
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Jamainits1.txt b/doc/Examples/Jamainits1.txt
new file mode 100755
index 0000000..e805ac0
--- /dev/null
+++ b/doc/Examples/Jamainits1.txt
@@ -0,0 +1,5 @@
+list(alpha=c(3690, 3090, 2490, 1670,1250, 690, NA),
+ beta=c(3540, 2540, 1990, 1280, 940, 550, 250),
+theta = c(3680, 3670, 3610, 3595, 3550, 3080, 2895, 2850, 2550, 2480, 2220, 2175, 2040,
+ 2030, 2010, 2000, 1660, 1640, 1590, 1570, 1530, 1380, 1310, 1290, 1245, 1220,
+ 1170, 1170, 1080, 1010, 1000, 1000, 1000, 1000, 680, 565, 355))
\ No newline at end of file
diff --git a/doc/Examples/Jamamodel.html b/doc/Examples/Jamamodel.html
new file mode 100755
index 0000000..8aa06dd
--- /dev/null
+++ b/doc/Examples/Jamamodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Jamamodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model{ <br> for (i in 1 : nDate){<br> theta[i] ~ dunif(beta[phase[i]], alpha[phase[i]] )<br> X[i] ~ dnorm(mu[i], tau[i])<br> tau[i] <- 1 / pow(sigma[i], 2)<br> mu[i] <- interp.li [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Jamamodel.txt b/doc/Examples/Jamamodel.txt
new file mode 100755
index 0000000..3cd4d0b
--- /dev/null
+++ b/doc/Examples/Jamamodel.txt
@@ -0,0 +1,32 @@
+ model{
+ for (i in 1 : nDate){
+ theta[i] ~ dunif(beta[phase[i]], alpha[phase[i]] )
+ X[i] ~ dnorm(mu[i], tau[i])
+ tau[i] <- 1 / pow(sigma[i], 2)
+ mu[i] <- interp.lin(theta[i], calBP[], C14BP[])
+ }
+ # priors on phase ordering
+ alpha[1] ~ dunif(beta[1], theta.max)
+ beta[1] ~ dunif(alpha[2], alpha[1])
+ alpha[2] ~ dunif(beta[2], beta[1])
+ beta[2] ~ dunif(alpha[3], alpha[2])
+ alpha[3] ~ dunif(beta[3], beta[2])
+ beta[3] ~ dunif(alpha[4], alpha[3])
+ alpha[4] ~ dunif(alpha4min, beta[3])
+ alpha4min <- max(beta[4], alpha[5])
+ beta[4] ~ dunif(beta[5], alpha[4])
+ alpha[5] ~ dunif(alpha5min, alpha[4])
+ alpha5min <- max(beta[5], alpha[6])
+ beta[5] ~ dunif(beta[6], beta5max)
+ beta5max <- min(beta[4], alpha[5])
+ alpha[6] ~ dunif(beta[6], alpha[5])
+ beta[6] ~ dunif(beta[7], beta6max)
+ beta6max <- min(alpha[6], beta[5])
+ alpha[7] <- beta[6]
+ beta[7] ~ dunif(theta.min,alpha[7])
+
+ for (i in 1 : 7) {
+ alpha.desc[i] <- 10 * round(alpha[i] / 10)
+ beta.desc[i] <- 10 * round(beta[i] / 10)
+ }
+ }
diff --git a/doc/Examples/Jaws.html b/doc/Examples/Jaws.html
new file mode 100755
index 0000000..c0c33e6
--- /dev/null
+++ b/doc/Examples/Jaws.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Jaws</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="jaws0.bmp" alt="[jaws0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Jaws: repeated measures analysis<br> of variance
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3">Elston and Grizzle (1962) present repeated measurements of ramus (jaw) bone height on a <br>cohort of 20 boys over an 18 month period: <br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="jaws1.bmp" alt="[jaws1]"></center><br>
</font><font face="Arial" color="#000100" size="3">Interest focuses on describing the average growth curve of the ramus bone. The 4 <br>measurements
</font><font face="Arial" color="#000100" size="3"><strong>Y
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = {Y
</font><font face="Arial" color="#000100" size="2"><sub>i1
</sub></font><font face="Arial" color="#000100" size="3">, Y
</font><font face="Arial" color="#000100" size="2"><sub>i2
</sub></font><font face="Arial" color="#000100" size="3">, Y
</font><font face="Arial" color="#000100" size="2"><sub>i3
</sub></font><font face="Arial" color="#000100" size="3">, Y
</font><font face="Arial" color="#000100" size="2"><sub>i4
</sub></font><font face="Arial" color="#000100" size="3">} for each child i are assumed to be correlated and follow a multivariate normal (MVN) distribution with unknown population mean vector
</font><font face="Symbol" color="#000100" size="3"><strong>m
</strong></font><font face="Arial" color="#000100" size="3"> and precision matrix
</font><font face="Symbol" color="#000100" size="3"><strong>W
</strong></font><font face="Arial" color="#000100" size="3">. That is
</font><font face="Arial" color="#000100" size="3"><strong>Y
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ MVN(
</font><font face="Symbol" color="#000100" size="3"><strong>m
</strong></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3"><strong> W
</strong></font><font face="Arial" color="#000100" size="3">)<br><br>The following location models for the population mean
</font><font face="Symbol" color="#000100" size="3"><strong>m
</strong></font><font face="Arial" color="#000100" size="3"> were fitted in turn:<br> E(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"> Constant height<br> E(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">+
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> Linear growth curve<br> E(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">+
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> Quadratic growth curve <br><br>where x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> = age at jth measurement. Non-informative independent normal priors were specified for the regression coefficients
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">, and
</font><font face="Symbol" color="#000100" size="3"> b
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">. The population precision matrix
</font><font face="Symbol" color="#000100" size="3"><strong>W
</strong></font><font face="Arial" color="#000100" size="3"> was assumed to follow a Wishart(R,
</font><font face="Symbol" color="#000100" size="3">r
</font><font face="Arial" color="#000100" size="3">) distribution. To represent vague prior knowledge, we chose the the degrees of freedom
</font><font face="Symbol" color="#000100" size="3">r
</font><font face="Arial" color="#000100" size="3"> for this distribution to be as small as possible (i.e. 4, the rank of
</font><font face="Symbol" color="#000100" size="3"><strong>W
</strong></font><font face="Arial" color="#000100" size="3">). The scale matrix R was specified as a 4x4 diag(1) matrix which represents an assessment of the order of magnitude of the covariance matrix
</font><font face="Symbol" color="#000100" size="3"><strong>W
</strong></font><font face="Arial" color="#000100" size="2"><sup>-1
</sup></font><font face="Arial" color="#000100" size="3"> for
</font><font face="Arial" color="#000100" size="3"><strong>Y
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> (see subsection on the use of the Wishart distribution in the "Multivariate normal nodes'' section of the Classic BUGS manual (version 0.50). Note that except for cases with very few individuals, the choice of R has little effect on the posterior estimate of
</font><font face="Symbol" color="#000100" size="3"><strong>W
</strong></font><font face="Arial" color="#000100" size="2"><sup>-1
</sup></font><font face="Arial" color="#000100" size="3"> (Lindley, 1970).<br>
</font><font face="Arial" color="#000100" size="2"><br><center><br>
</font><font face="Arial" color="#000100" size="3"><em>BUGS language for the Jaws example
</em></font><font face="Arial" color="#000100" size="2"><strong><u><br>
</u></strong></font><font face="Arial" color="#000100" size="2"><br></center><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta0 ~ dnorm(0.0, 0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta1 ~ dnorm(0.0, 0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y[i, 1:M] ~ dmnorm(mu[], Omega[ , ]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(j in 1:M) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[j] <- beta0 + beta1* age[j]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Omega[1 : M , 1 : M] ~ dwish(R[ , ], 4)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Sigma[1 : M , 1 : M] <- inverse(Omega[ , ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Jawsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Jawsinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Jawsinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates
</font><font face="Arial" color="#000100" size="3"> <br><br><center><br><img src="jaws2.bmp" alt="[jaws2]">
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Jawsdata.html b/doc/Examples/Jawsdata.html
new file mode 100755
index 0000000..cfda406
--- /dev/null
+++ b/doc/Examples/Jawsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Jawsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"> list(M = 4, N = 20, Y = structure(<br> .Data = c(47.8, 48.8, 49.0, 49.7,<br> 46.4, 47.3, 47.7, 48.4,<br> 46.3, 46.8, 47.8, 48.5,<br> &n [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Jawsdata.txt b/doc/Examples/Jawsdata.txt
new file mode 100755
index 0000000..ff37ff5
--- /dev/null
+++ b/doc/Examples/Jawsdata.txt
@@ -0,0 +1,29 @@
+ list(M = 4, N = 20, Y = structure(
+ .Data = c(47.8, 48.8, 49.0, 49.7,
+ 46.4, 47.3, 47.7, 48.4,
+ 46.3, 46.8, 47.8, 48.5,
+ 45.1, 45.3, 46.1, 47.2,
+ 47.6, 48.5, 48.9, 49.3,
+ 52.5, 53.2, 53.3, 53.7,
+ 51.2, 53.0, 54.3, 54.5,
+ 49.8, 50.0, 50.3, 52.7,
+ 48.1, 50.8, 52.3, 54.4,
+ 45.0, 47.0, 47.3, 48.3,
+ 51.2, 51.4, 51.6, 51.9,
+ 48.5, 49.2, 53.0, 55.5,
+ 52.1, 52.8, 53.7, 55.0,
+ 48.2, 48.9, 49.3, 49.8,
+ 49.6, 50.4, 51.2, 51.8,
+ 50.7, 51.7, 52.7, 53.3,
+ 47.2, 47.7, 48.4, 49.5,
+ 53.3, 54.6, 55.1, 55.3,
+ 46.2, 47.5, 48.1, 48.4,
+ 46.3, 47.6, 51.3, 51.8),
+ .Dim = c(20, 4)),
+ age = c(8.0, 8.5, 9.0, 9.5),
+ R = structure(
+ .Data = c(1, 0, 0, 0,
+ 0, 1, 0, 0,
+ 0, 0, 1, 0,
+ 0, 0, 0, 1), .
+ Dim = c(4, 4)))
\ No newline at end of file
diff --git a/doc/Examples/Jawsinits.html b/doc/Examples/Jawsinits.html
new file mode 100755
index 0000000..dee69aa
--- /dev/null
+++ b/doc/Examples/Jawsinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Jawsinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(beta0 = 40, beta1 = 1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Jawsinits.txt b/doc/Examples/Jawsinits.txt
new file mode 100755
index 0000000..bdffa55
--- /dev/null
+++ b/doc/Examples/Jawsinits.txt
@@ -0,0 +1 @@
+list(beta0 = 40, beta1 = 1)
\ No newline at end of file
diff --git a/doc/Examples/Jawsinits1.html b/doc/Examples/Jawsinits1.html
new file mode 100755
index 0000000..a8ea88d
--- /dev/null
+++ b/doc/Examples/Jawsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Jawsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(beta0 = 10, beta1 = 10)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Jawsinits1.txt b/doc/Examples/Jawsinits1.txt
new file mode 100755
index 0000000..e793628
--- /dev/null
+++ b/doc/Examples/Jawsinits1.txt
@@ -0,0 +1 @@
+list(beta0 = 10, beta1 = 10)
\ No newline at end of file
diff --git a/doc/Examples/Jawsmodel.html b/doc/Examples/Jawsmodel.html
new file mode 100755
index 0000000..68a2412
--- /dev/null
+++ b/doc/Examples/Jawsmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Jawsmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta0 ~ dnorm(0.0, 0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta1 ~ dnorm(0.0, 0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y[i, 1:M] ~ dmnorm(mu[], Omega[ , ]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(j in 1:M) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[j] <- beta0 + beta1* age[j]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Omega[1 : M , 1 : M] ~ dwish(R[ , ], 4)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Sigma[1 : M , 1 : M] <- inverse(Omega[ , ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Jawsmodel.txt b/doc/Examples/Jawsmodel.txt
new file mode 100755
index 0000000..07d2890
--- /dev/null
+++ b/doc/Examples/Jawsmodel.txt
@@ -0,0 +1,14 @@
+ model
+ {
+ beta0 ~ dnorm(0.0, 0.001)
+ beta1 ~ dnorm(0.0, 0.001)
+ for (i in 1:N) {
+ Y[i, 1:M] ~ dmnorm(mu[], Omega[ , ])
+ }
+ for(j in 1:M) {
+ mu[j] <- beta0 + beta1* age[j]
+ }
+ Omega[1 : M , 1 : M] ~ dwish(R[ , ], 4)
+ Sigma[1 : M , 1 : M] <- inverse(Omega[ , ])
+
+ }
diff --git a/doc/Examples/Kidney.html b/doc/Examples/Kidney.html
new file mode 100755
index 0000000..c69b5ef
--- /dev/null
+++ b/doc/Examples/Kidney.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Kidney</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="kidney0.bmp" alt="[kidney0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Kidney: Weibull regression with<br> random efects
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">McGilchrist and Aisbett (1991) analyse time to first and second recurrence of infection in kidney patients on dialysis using a Cox model with a multiplicative frailty parameter for each individual. The risk variables considered are age, sex and underlying disease (coded other, GN, AN and PKD). A portion of the data are shown below.<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="kidney1.bmp" alt="[kidney1]">
</font><font face="Arial" color="#000100" size="3"><br></center>
</font><font face="Arial" color="#000100" size="3"><br>We have analysed the same data assuming a parametric Weibull distribution for the survivor function, and including an additive random effect b
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> for each patient in the exponent of the hazard model as follows<br><br> t
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Weibull(r,
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">) i = 1,...,38; j = 1,2<br> <br> log
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>age
</sub></font><font face="Arial" color="#000100" size="3">AGE
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>sex
</sub></font><font face="Arial" color="#000100" size="3">SEX
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>disease1
</sub></font><font face="Arial" color="#000100" size="3">DISEASE
</font><font face="Arial" color="#000100" size="2"><sub>i1
</sub></font><font face="Arial" color="#000100" size="3"> +<br>
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>disease2
</sub></font><font face="Arial" color="#000100" size="3">DISEASE
</font><font face="Arial" color="#000100" size="2"><sub>i2
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>disease3
</sub></font><font face="Arial" color="#000100" size="3">DISEASE
</font><font face="Arial" color="#000100" size="2"><sub>i3
</sub></font><font face="Arial" color="#000100" size="3"> + b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><br> <br> b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(0,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">)<br> <br>where AGE
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> is a continuous covariate, SEX
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is a 2-level factor and DISEASE
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"> (k = 1,2,3) are dummy variables representing the 4-level factor for underlying disease. Note that the the survival distribution is a truncated Weibull for censored observations as discussed in the mice example. The regression coefficients and the precision of the random effects
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> are given independent ``non-informative'' priors, namely <br><br> b
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(0, 0.0001)<br> <br>
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> ~ Gamma(0.0001, 0.0001)<br> <br>The shape parameter of the survival distribution r is given a Gamma(1, 0.0001) prior which is slowly decreasing on the positive real line.<br><br>The graphical model and
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language are given below. <br>
</font><font face="Arial" color="#000100" size="2"><br><center><br>
</font><font face="Arial" color="#000100" size="3"><em>Graphical model for kidney example:
</em></font><font face="Arial" color="#000100" size="3"> <img src="kidney2.bmp" alt="[kidney2]">
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3">BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for kidney example
</em></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"></center> model<br> {<br> for (i in 1 : N) {<br> for (j in 1 : M) {<br> # Survival times bounded below by censoring times:<br> t[i,j] ~ dweib(r, mu[i,j])C(t.cen[i, j], );<br> &nbs [...]
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Kidneydata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Kidneyinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Kidneyinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center><br><img src="kidney3.bmp" alt="[kidney3]">
</font><font face="Arial" color="#0000FF" size="5"><br><br>
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Kidneydata.html b/doc/Examples/Kidneydata.html
new file mode 100755
index 0000000..7c3f3f1
--- /dev/null
+++ b/doc/Examples/Kidneydata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Kidneydata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 38, M = 2,<br> t = structure(<br> .Data = c( 8, 16,<br> 23, NA,<br> 22, 28,<br> 447, 318,<br>30, 12,<br>24, 245,<br>7, 9,<br>511, 30,<br>53, 196,<br>15, 154,<br>7, 333,<br>141, NA,<br>96, 38,<br>NA, NA,<br>536, NA,<br>17, NA,<br>185, 177,<br>292, 114,<br>NA, NA,<br>15, NA,<br>152, 562,<br>402, NA,<br>13, 66,<br>39, NA,<br>12, 40,<br>NA, 201,<br>132, 156 [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Kidneydata.txt b/doc/Examples/Kidneydata.txt
new file mode 100755
index 0000000..1d63e57
--- /dev/null
+++ b/doc/Examples/Kidneydata.txt
@@ -0,0 +1,123 @@
+list(N = 38, M = 2,
+ t = structure(
+ .Data = c( 8, 16,
+ 23, NA,
+ 22, 28,
+ 447, 318,
+ 30, 12,
+ 24, 245,
+ 7, 9,
+ 511, 30,
+ 53, 196,
+ 15, 154,
+ 7, 333,
+ 141, NA,
+ 96, 38,
+ NA, NA,
+ 536, NA,
+ 17, NA,
+ 185, 177,
+ 292, 114,
+ NA, NA,
+ 15, NA,
+ 152, 562,
+ 402, NA,
+ 13, 66,
+ 39, NA,
+ 12, 40,
+ NA, 201,
+ 132, 156,
+ 34, 30,
+ 2, 25,
+ 130, 26,
+ 27, 58,
+ NA, 43,
+ 152, 30,
+ 190, NA,
+ 119, 8,
+ NA, NA,
+ NA, 78,
+ 63, NA), .Dim = c(38, 2)),
+ t.cen = structure(
+ .Data = c( 0, 0,
+ 0, 13,
+ 0, 0,
+ 0, 0,
+ 0, 0,
+ 0, 0,
+ 0, 0,
+ 0, 0,
+ 0, 0,
+ 0, 0,
+ 0, 0,
+ 0, 8,
+ 0, 0,
+ 149, 70,
+ 0, 25,
+ 0, 4,
+ 0, 0,
+ 0, 0,
+ 22, 159,
+ 0, 108,
+ 0, 0,
+ 0, 24,
+ 0, 0,
+ 0, 46,
+ 0, 0,
+ 113, 0,
+ 0, 0,
+ 0, 0,
+ 0, 0,
+ 0, 0,
+ 0, 0,
+ 5, 0,
+ 0, 0,
+ 0, 5,
+ 0, 0,
+ 54, 16,
+ 6, 0,
+ 0, 8), .Dim = c(38, 2)),
+ age = structure(
+ .Data = c(28, 28,
+ 48, 48,
+ 32, 32,
+ 31, 32,
+ 10, 10,
+ 16, 17,
+ 51, 51,
+ 55, 56,
+ 69, 69,
+ 51, 52,
+ 44, 44,
+ 34, 34,
+ 35, 35,
+ 42, 42,
+ 17, 17,
+ 60, 60,
+ 60, 60,
+ 43, 44,
+ 53, 53,
+ 44, 44,
+ 46, 47,
+ 30, 30,
+ 62, 63,
+ 42, 43,
+ 43, 43,
+ 57, 58,
+ 10, 10,
+ 52, 52,
+ 53, 53,
+ 54, 54,
+ 56, 56,
+ 50, 51,
+ 57, 57,
+ 44, 45,
+ 22, 22,
+ 42, 42,
+ 52, 52,
+ 60, 60), .Dim = c(38, 2)),
+ beta.dis = c(0, NA, NA, NA),
+ sex = c(0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1,
+ 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0),
+ disease = c(1, 2, 1, 1, 1, 1, 2, 2, 3, 2, 3, 1, 3, 3, 1, 3, 1, 1,2, 1, 4, 1, 3, 3,
+ 3, 3, 2, 3, 2, 2, 3, 3, 4, 2, 1, 1, 4, 4))
\ No newline at end of file
diff --git a/doc/Examples/Kidneyinits.html b/doc/Examples/Kidneyinits.html
new file mode 100755
index 0000000..14ef769
--- /dev/null
+++ b/doc/Examples/Kidneyinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Kidneyinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">list(beta.age = 0, beta.sex = 0, beta.dis=c(NA,0,0,0), <br>alpha = 0, r=1, tau=0.3)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Kidneyinits.txt b/doc/Examples/Kidneyinits.txt
new file mode 100755
index 0000000..c611598
--- /dev/null
+++ b/doc/Examples/Kidneyinits.txt
@@ -0,0 +1,2 @@
+list(beta.age = 0, beta.sex = 0, beta.dis=c(NA,0,0,0),
+ alpha = 0, r=1, tau=0.3)
\ No newline at end of file
diff --git a/doc/Examples/Kidneyinits1.html b/doc/Examples/Kidneyinits1.html
new file mode 100755
index 0000000..c334ea8
--- /dev/null
+++ b/doc/Examples/Kidneyinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Kidneyinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">list(beta.age = -1, beta.sex = 1, beta.dis=c(NA,1,1,1), <br>alpha = 1, r=1.5, tau=1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Kidneyinits1.txt b/doc/Examples/Kidneyinits1.txt
new file mode 100755
index 0000000..41cb8df
--- /dev/null
+++ b/doc/Examples/Kidneyinits1.txt
@@ -0,0 +1,2 @@
+list(beta.age = -1, beta.sex = 1, beta.dis=c(NA,1,1,1),
+ alpha = 1, r=1.5, tau=1)
\ No newline at end of file
diff --git a/doc/Examples/Kidneymodel.html b/doc/Examples/Kidneymodel.html
new file mode 100755
index 0000000..742ba2f
--- /dev/null
+++ b/doc/Examples/Kidneymodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Kidneymodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for (i in 1 : N) {<br> for (j in 1 : M) {<br> # Survival times bounded below by censoring times:<br> t[i,j] ~ dweib(r, mu[i,j])C(t.cen[i, j], );<br> lo [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Kidneymodel.txt b/doc/Examples/Kidneymodel.txt
new file mode 100755
index 0000000..71a1a92
--- /dev/null
+++ b/doc/Examples/Kidneymodel.txt
@@ -0,0 +1,25 @@
+ model
+ {
+ for (i in 1 : N) {
+ for (j in 1 : M) {
+ # Survival times bounded below by censoring times:
+ t[i,j] ~ dweib(r, mu[i,j])C(t.cen[i, j], );
+ log(mu[i,j ]) <- alpha + beta.age * age[i, j]
+ + beta.sex *sex[i]
+ + beta.dis[disease[i]] + b[i];
+ }
+ # Random effects:
+ b[i] ~ dnorm(0.0, tau)
+ }
+ # Priors:
+ alpha ~ dnorm(0.0, 0.0001);
+ beta.age ~ dnorm(0.0, 0.0001);
+ beta.sex ~ dnorm(0.0, 0.0001);
+ # beta.dis[1] <- 0; # corner-point constraint
+ for(k in 2 : 4) {
+ beta.dis[k] ~ dnorm(0.0, 0.0001);
+ }
+ tau ~ dgamma(1.0E-3, 1.0E-3);
+ r ~ dgamma(1.0, 1.0E-3);
+ sigma <- 1 / sqrt(tau); # s.d. of random effects
+ }
diff --git a/doc/Examples/Leuk.html b/doc/Examples/Leuk.html
new file mode 100755
index 0000000..09a4339
--- /dev/null
+++ b/doc/Examples/Leuk.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Leuk</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="leuk0.bmp" alt="[leuk0]">
</strong></font><font face="Courier New" color="#000100" size="6">Leuk: Cox regression
</font><font face="Arial" color="#000000" size="5"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="3">Several authors have discussed Bayesian inference for censored survival data where the integrated baseline hazard function is to be estimated non-parametrically Kalbfleisch (1978) ,Kalbfleisch and Prentice (1980), Clayton (1991), Clayton (1994).Clayton (1994) formulates the Cox model using the counting process notation introduced by Andersen and Gill (1982) and discusses estimation of the baseline hazard and regression parameters [...]
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3">.<br><br>For subjects
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> = 1,...,n, we observe processes N
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t) which count the number of failures which have occurred up to time t. The corresponding intensity process I
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t) is given by<br><br> I
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t)dt = E(dN
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t) | F
</font><font face="Arial" color="#000100" size="3"><sub>t-
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br>where dN
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t) is the increment of N
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> over the small time interval [t, t+dt), and F
</font><font face="Arial" color="#000100" size="3"><sub>t-
</sub></font><font face="Arial" color="#000100" size="3"> represents the available data just before time t. If subject
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> is observed to fail during this time interval, dN
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t) will take the value 1; otherwise dN
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t) = 0. Hence E(dN
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t) | F
</font><font face="Arial" color="#000100" size="3"><sub>t-
</sub></font><font face="Arial" color="#000100" size="3">) corresponds to the probability of subject
</font><font face="Arial" color="#000100" size="3"><em> i
</em></font><font face="Arial" color="#000100" size="3"> failing in the interval [t, t+dt). As dt -> 0 (assuming time to be continuous) then this probability becomes the instantaneous hazard at time t for subject
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">. This is assumed to have the proportional hazards form <br><br> I
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t) = Y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t)
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t)exp(
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3"><strong>z
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br>where Y
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t) is an observed process taking the value 1 or 0 according to whether or not subject
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> is observed at time t and
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t)exp(
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3"><strong>z
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) is the familiar Cox regression model. Thus we have observed data D = N
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t), Y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t),
</font><font face="Arial" color="#000100" size="3"><strong>z
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">; i = 1,..n and unknown parameters
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t) = Integral(
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(u), u, t, 0), the latter to be estimated non-parametrically. <br><br>The joint posterior distribution for the above model is defined by<br><br> P(
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">() | D) ~ P(D |
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">()) P(
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3">) P(
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">())<br> <br>For
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3">, we need to specify the form of the likelihood P(D |
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">()) and prior distributions for
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(). Under non-informative censoring, the likelihood of the data is proportional to <br><br>
</font><font face="Arial" color="#000100" size="2">n
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Symbol" color="#000100" size="5">P
</font><font face="Arial" color="#000100" size="5">[
</font><font face="Symbol" color="#000100" size="5">P
</font><font face="Arial" color="#000100" size="5">
</font><font face="Symbol" color="#000100" size="3">I
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t)
</font><font face="Arial" color="#000100" size="3"><sup>dN
</sup></font><font face="Arial" color="#000100" size="3"><sup>i
</sup></font><font face="Arial" color="#000100" size="3"><sup>(t)
</sup></font><font face="Arial" color="#000100" size="5">]
</font><font face="Arial" color="#000100" size="3">exp(- I
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t)dt)<br>
</font><font face="Arial" color="#000100" size="2">i = 1 t >= 0
</font><font face="Arial" color="#000100" size="3"><br> <br> <br>This is essentially as if the counting process increments dN
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t) in the time interval [t, t+dt) are independent Poisson random variables with means I
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t)dt: <br><br> dN
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t) ~ Poisson(I
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t)dt)<br> <br>We may write <br><br> I
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t)dt = Y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(t)exp(
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3"><strong>z
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)d
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t)<br> <br>where d
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t) =
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t)dt is the increment or jump in the integrated baseline hazard function occurring during the time interval [t, t+dt). Since the conjugate prior for the Poisson mean is the gamma distribution, it would be convenient if
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">() were a process in which the increments d
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="3"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t) are distributed according to gamma distributions. We assume the conjugate independent increments prior suggested by Kalbfleisch (1978), namely <br><br> d
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t) ~ Gamma(cd
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Symbol" color="#000100" size="3"><sup>*
</sup></font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t), c)<br> <br>Here, d
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Symbol" color="#000100" size="3"><sup>*
</sup></font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t) can be thought of as a prior guess at the unknown hazard function, with c representing the degree of confidence in this guess. Small values of c correspond to weak prior beliefs. In the example below, we set d
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Symbol" color="#000100" size="3"><sup>*
</sup></font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t) = r dt where r is a guess at the failure rate per unit time, and dt is the size of the time interval. <br> <br>The above formulation is appropriate when genuine prior information exists concerning the underlying hazard function. Alternatively, if we wish to reproduce a Cox analysis but with, say, additional hierarchical structure, we may use the multinomial-Poisson trick described in the
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> manual. This is equivalent to assuming independent increments in the cumulative `non-informative' priors. This formulation is also shown below.<br><br>The fixed effect regression coefficients
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3"> are assigned a vague prior<br><br>
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> ~ Normal(0.0, 0.000001)<br> <br>
</font><font face="Arial" color="#000100" size="2"> <center>
</font><font face="Arial" color="#000100" size="3">BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for the Leuk example:
</em></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br></center> model<br> {<br> # Set up data<br> for(i in 1:N) {<br> for(j in 1:T) {<br> # risk set = 1 if obs.t >= t<br> Y[i,j] <- step(obs.t[i] - t[j] + eps)<br> # counting process jump = 1 i [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Leukdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Leukinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Leukinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center><br><img src="leuk1.bmp" alt="[leuk1]">
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Leukdata.html b/doc/Examples/Leukdata.html
new file mode 100755
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--- /dev/null
+++ b/doc/Examples/Leukdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Leukdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 42, T = 17, eps = 1.0E-10,<br> obs.t = c(1, 1, 2, 2, 3, 4, 4, 5, 5, 8, 8, 8, 8, 11, 11, 12, 12, 15, 17, 22, 23, 6, <br> 6, 6, 6, 7, 9, 10, 10, 11, 13, 16, 17, 19, 20, 22, 23, 25, 32, 32, 34, 35),<br> fail = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0), [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Leukdata.txt b/doc/Examples/Leukdata.txt
new file mode 100755
index 0000000..1e4934b
--- /dev/null
+++ b/doc/Examples/Leukdata.txt
@@ -0,0 +1,7 @@
+list(N = 42, T = 17, eps = 1.0E-10,
+ obs.t = c(1, 1, 2, 2, 3, 4, 4, 5, 5, 8, 8, 8, 8, 11, 11, 12, 12, 15, 17, 22, 23, 6,
+ 6, 6, 6, 7, 9, 10, 10, 11, 13, 16, 17, 19, 20, 22, 23, 25, 32, 32, 34, 35),
+ fail = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0),
+ Z = c(0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
+ -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5),
+ t = c(1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 15, 16, 17, 22, 23, 35))
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diff --git a/doc/Examples/Leukfr.html b/doc/Examples/Leukfr.html
new file mode 100755
index 0000000..5a71187
--- /dev/null
+++ b/doc/Examples/Leukfr.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Leukfr</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="leukfr0.bmp" alt="[leukfr0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">LeukFr: Cox regression with<br> random effects
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="2"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">Freireich et al (1963)'s data presented in the
</font><font face="Courier" color="#000100" size="3">Leuk
</font><font face="Arial" color="#000100" size="3"> example actually arise via a
</font><font face="Arial" color="#000100" size="3"><em>paired
</em></font><font face="Arial" color="#000100" size="3"> design. Patients were matched according to their remission status (partial or complete). One patient from each pair received the drug 6-MP whilst the other received the placebo. We may introduce an additional vector (called
</font><font face="Courier" color="#000100" size="3">pair
</font><font face="Arial" color="#000100" size="3">) in the BUGS data file to indicate each of the 21 pairs of patients.<br><br>We model the potential 'clustering' of failure times within pairs of patients by introducing a group-specific random effect or frailty term into the proportional hazards model. Using the counting process notation introduced in the
</font><font face="Courier" color="#000100" size="3">Leuk
</font><font face="Arial" color="#000100" size="3"> example, this gives<br><br><br> I
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">(t) dt = Y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">(t) exp(
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">' z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> + b
</font><font face="Arial" color="#000100" size="2"><sub>pair
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ) d
</font><font face="Symbol" color="#000100" size="3">L
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t) i = 1,...,42;
</font><font face="Arial" color="#000100" size="2">pair
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">= 1,...,21<br> b
</font><font face="Arial" color="#000100" size="2"><sub>pair
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">Normal(0,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">) <br><br>A non-informative Gamma prior is assumed for
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">, the precision of the frailty parameters. Note that the above 'additive' formualtion of the frailty model is equivalent to assuming multiplicative frailties with a log-Normal population distibution. Clayton (1991) discusses the Cox proportional hazards model with multiplicative frailties, but assumes a Gamma population distribution. <br><br>The modified BUGS code needed to include a fraility term in the
</font><font face="Courier" color="#000100" size="3">Leuk
</font><font face="Arial" color="#000100" size="3"> example is shown below<br>
</font><font face="Arial" color="#000100" size="3"><br> model<br> {<br> # Set up data<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(j in 1 : T) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># risk set = 1 if obs.t >= t<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y[i, j] <- step(obs.t[i] - t[j] + eps) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># counting process jump = 1 if obs.t in [ t[j], t[j+1] )<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># i.e. if t[j] <= obs.t < t[j+1]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> dN[i, j] <- Y[i, j ] *step(t[j+1] - obs.t[i] - eps)*fail[i] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br> }<br> # Model <br> for(j in 1 : T) {<br> for(i in 1 : N) {<br> dN[i, j] ~ dpois(Idt[i, j]) <br> Idt[i, j] <- Y[i, j [...]
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Leukfrdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Leukfrinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Leukfrinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center><br><img src="leukfr1.bmp" alt="[leukfr1]">
</font><font face="Arial" color="#000100" size="1"><br><br>
</font>
</center>
</p>
</body>
</html>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Leukfrdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 42, T = 17, eps = 0.00001, Npairs = 21,<br> t = c(1,2,3,4,5,6,7,8,10,11,12,13,15,16,17,22,23,35),<br>obs.t = c(1,1,2,2,3,4,4,5,5,8,8,8,8,11,11,12,12,15,17,22,23,<br>6,6,6,6,7,9,10,10,11,13,16,17,19,20,22,23,25,32,32,34,35),<br>pair = c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,<br>19,18,8,1,20,6,2,10,3,14,4,11,7,9,12,16,17,5,13,15,21),<br>fail = c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,<br>1,1,1,0,1,0,1,0 [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Leukfrdata.txt b/doc/Examples/Leukfrdata.txt
new file mode 100755
index 0000000..236bceb
--- /dev/null
+++ b/doc/Examples/Leukfrdata.txt
@@ -0,0 +1,14 @@
+list(N = 42, T = 17, eps = 0.00001, Npairs = 21,
+ t = c(1,2,3,4,5,6,7,8,10,11,12,13,15,16,17,22,23,35),
+ obs.t = c(1,1,2,2,3,4,4,5,5,8,8,8,8,11,11,12,12,15,17,22,23,
+ 6,6,6,6,7,9,10,10,11,13,16,17,19,20,22,23,25,32,32,34,35),
+ pair = c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,
+ 19,18,8,1,20,6,2,10,3,14,4,11,7,9,12,16,17,5,13,15,21),
+ fail = c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
+ 1,1,1,0,1,0,1,0,0,1,1,0,0,0,1,1,0,0,0,0,0),
+ Z = c(0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
+ 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
+ 0.5, 0.5, 0.5, -0.5, -0.5, -0.5, -0.5, -0.5,
+ -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5,
+ -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5)
+)
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diff --git a/doc/Examples/Leukfrinits.html b/doc/Examples/Leukfrinits.html
new file mode 100755
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+++ b/doc/Examples/Leukfrinits.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Leukfrinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list( beta = 0.0, <br>dL0 = c(1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,<br>1.0,1.0,1.0,1.0,1.0,1.0, 1.0,1.0),<br>tau=1 <br>)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Leukfrinits.txt b/doc/Examples/Leukfrinits.txt
new file mode 100755
index 0000000..4a4769b
--- /dev/null
+++ b/doc/Examples/Leukfrinits.txt
@@ -0,0 +1,5 @@
+list( beta = 0.0,
+ dL0 = c(1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
+ 1.0,1.0,1.0,1.0,1.0,1.0, 1.0,1.0),
+ tau=1
+)
\ No newline at end of file
diff --git a/doc/Examples/Leukfrinits1.html b/doc/Examples/Leukfrinits1.html
new file mode 100755
index 0000000..7aff1b7
--- /dev/null
+++ b/doc/Examples/Leukfrinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Leukfrinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">list( beta = 1.0, <br>dL0 = c(2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,<br>2.0,2.0,2.0,2.0,2.0,2.0, 2.0,2.0),<br>tau = 0.1)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Leukfrinits1.txt b/doc/Examples/Leukfrinits1.txt
new file mode 100755
index 0000000..61a2d1a
--- /dev/null
+++ b/doc/Examples/Leukfrinits1.txt
@@ -0,0 +1,4 @@
+list( beta = 1.0,
+ dL0 = c(2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,
+ 2.0,2.0,2.0,2.0,2.0,2.0, 2.0,2.0),
+tau = 0.1)
\ No newline at end of file
diff --git a/doc/Examples/Leukfrmodel.html b/doc/Examples/Leukfrmodel.html
new file mode 100755
index 0000000..628217f
--- /dev/null
+++ b/doc/Examples/Leukfrmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Leukfrmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> # Set up data<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(j in 1 : T) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># risk set = 1 if obs.t >= t<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y[i, j] <- step(obs.t[i] - t[j] + eps) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># counting process jump = 1 if obs.t in [ t[j], t[j+1] )<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># i.e. if t[j] <= obs.t < t[j+1]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> dN[i, j] <- Y[i, j ] *step(t[j+1] - obs.t[i] - eps)*fail[i] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br> }<br> # Model <br> for(j in 1 : T) {<br> for(i in 1 : N) {<br> dN[i, j] ~ dpois(Idt[i, j]) <br> Idt[i, j] <- Y[i, j [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Leukfrmodel.txt b/doc/Examples/Leukfrmodel.txt
new file mode 100755
index 0000000..9923eb3
--- /dev/null
+++ b/doc/Examples/Leukfrmodel.txt
@@ -0,0 +1,35 @@
+ model
+ {
+ # Set up data
+ for(i in 1 : N) {
+ for(j in 1 : T) {
+ # risk set = 1 if obs.t >= t
+ Y[i, j] <- step(obs.t[i] - t[j] + eps)
+ # counting process jump = 1 if obs.t in [ t[j], t[j+1] )
+ # i.e. if t[j] <= obs.t < t[j+1]
+ dN[i, j] <- Y[i, j ] *step(t[j+1] - obs.t[i] - eps)*fail[i]
+ }
+ }
+ # Model
+ for(j in 1 : T) {
+ for(i in 1 : N) {
+ dN[i, j] ~ dpois(Idt[i, j])
+ Idt[i, j] <- Y[i, j] * exp(beta * Z[i]+b[pair[i]]) * dL0[j]
+ }
+ dL0[j] ~ dgamma(mu[j], c)
+ mu[j] <- dL0.star[j] * c # prior mean hazard
+ # Survivor function = exp(-Integral{l0(u)du})^exp(beta * z)
+ S.treat[j] <- pow(exp(-sum(dL0[1 : j])), exp(beta * -0.5))
+ S.placebo[j] <- pow(exp(-sum(dL0[1 : j])), exp(beta * 0.5))
+ }
+ for(k in 1 : Npairs) {
+ b[k] ~ dnorm(0.0, tau);
+ }
+ tau ~ dgamma(0.001, 0.001)
+ sigma <- sqrt(1 / tau)
+ c <- 0.001 r <- 0.1
+ for (j in 1 : T) {
+ dL0.star[j] <- r * (t[j+1]-t[j])
+ }
+ beta ~ dnorm(0.0,0.000001)
+ }
diff --git a/doc/Examples/Leukinits.html b/doc/Examples/Leukinits.html
new file mode 100755
index 0000000..45c5178
--- /dev/null
+++ b/doc/Examples/Leukinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Leukinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">list( beta = 0.0, <br>dL0 = c(1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,<br>1.0,1.0,1.0,1.0,1.0,1.0, 1.0,1.0))
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Leukinits.txt b/doc/Examples/Leukinits.txt
new file mode 100755
index 0000000..90114be
--- /dev/null
+++ b/doc/Examples/Leukinits.txt
@@ -0,0 +1,3 @@
+list( beta = 0.0,
+ dL0 = c(1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
+ 1.0,1.0,1.0,1.0,1.0,1.0, 1.0,1.0))
\ No newline at end of file
diff --git a/doc/Examples/Leukinits1.html b/doc/Examples/Leukinits1.html
new file mode 100755
index 0000000..1755582
--- /dev/null
+++ b/doc/Examples/Leukinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Leukinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">list( beta = 1.0, <br>dL0 = c(2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,<br>2.0,2.0,2.0,2.0,2.0,2.0, 2.0,2.0))
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Leukinits1.txt b/doc/Examples/Leukinits1.txt
new file mode 100755
index 0000000..e977334
--- /dev/null
+++ b/doc/Examples/Leukinits1.txt
@@ -0,0 +1,3 @@
+list( beta = 1.0,
+ dL0 = c(2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,
+ 2.0,2.0,2.0,2.0,2.0,2.0, 2.0,2.0))
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diff --git a/doc/Examples/Leukmodel.html b/doc/Examples/Leukmodel.html
new file mode 100755
index 0000000..161fd17
--- /dev/null
+++ b/doc/Examples/Leukmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Leukmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> # Set up data<br> for(i in 1:N) {<br> for(j in 1:T) {<br> # risk set = 1 if obs.t >= t<br> Y[i,j] <- step(obs.t[i] - t[j] + eps)<br> # counting process jump = 1 if obs.t in [ t[j], t [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Leukmodel.txt b/doc/Examples/Leukmodel.txt
new file mode 100755
index 0000000..c9f2e60
--- /dev/null
+++ b/doc/Examples/Leukmodel.txt
@@ -0,0 +1,32 @@
+ model
+ {
+ # Set up data
+ for(i in 1:N) {
+ for(j in 1:T) {
+ # risk set = 1 if obs.t >= t
+ Y[i,j] <- step(obs.t[i] - t[j] + eps)
+ # counting process jump = 1 if obs.t in [ t[j], t[j+1] )
+ # i.e. if t[j] <= obs.t < t[j+1]
+ dN[i, j] <- Y[i, j] * step(t[j + 1] - obs.t[i] - eps) * fail[i]
+ }
+ }
+ # Model
+ for(j in 1:T) {
+ for(i in 1:N) {
+ dN[i, j] ~ dpois(Idt[i, j]) # Likelihood
+ Idt[i, j] <- Y[i, j] * exp(beta * Z[i]) * dL0[j] # Intensity
+ }
+ dL0[j] ~ dgamma(mu[j], c)
+ mu[j] <- dL0.star[j] * c # prior mean hazard
+
+ # Survivor function = exp(-Integral{l0(u)du})^exp(beta*z)
+ S.treat[j] <- pow(exp(-sum(dL0[1 : j])), exp(beta * -0.5));
+ S.placebo[j] <- pow(exp(-sum(dL0[1 : j])), exp(beta * 0.5));
+ }
+ c <- 0.001
+ r <- 0.1
+ for (j in 1 : T) {
+ dL0.star[j] <- r * (t[j + 1] - t[j])
+ }
+ beta ~ dnorm(0.0,0.000001)
+ }
diff --git a/doc/Examples/Line.html b/doc/Examples/Line.html
new file mode 100755
index 0000000..bc98c7b
--- /dev/null
+++ b/doc/Examples/Line.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Line</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="line0.bmp" alt="[line0]">
</strong></font><font face="Courier New" color="#000100" size="6">Line: Linear Regression
</font><font face="Arial" color="#0000FF" size="5"><strong><br><center><br><img src="line1.bmp" alt="[line1]">
</strong></font><font face="Arial" color="#000100" size="5"><strong><br></center><br>
</strong></font><font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : N ) {<br> Y[i] ~ dnorm(mu[i],tau)<br> mu[i] <- alpha + beta * (x[i] - xbar)<br> }<br> tau ~ dgamma(0.001, 0.001) sigma <- 1 / sqrt(tau)<br> [...]
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Linedata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Lineinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Lineinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3">A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center>
</font><font face="Arial" color="#000100" size="3"><br><img src="line2.bmp" alt="[line2]">
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Linedata.html b/doc/Examples/Linedata.html
new file mode 100755
index 0000000..b90c336
--- /dev/null
+++ b/doc/Examples/Linedata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Linedata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(x = c(1, 2, 3, 4, 5), Y= c(1, 3, 3, 3, 5), xbar = 3, N = 5)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Linedata.txt b/doc/Examples/Linedata.txt
new file mode 100755
index 0000000..bcd55ae
--- /dev/null
+++ b/doc/Examples/Linedata.txt
@@ -0,0 +1 @@
+list(x = c(1, 2, 3, 4, 5), Y= c(1, 3, 3, 3, 5), xbar = 3, N = 5)
\ No newline at end of file
diff --git a/doc/Examples/Lineinits.html b/doc/Examples/Lineinits.html
new file mode 100755
index 0000000..cb3074b
--- /dev/null
+++ b/doc/Examples/Lineinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Lineinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = 0, beta = 0, tau = 1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Lineinits.txt b/doc/Examples/Lineinits.txt
new file mode 100755
index 0000000..aba953b
--- /dev/null
+++ b/doc/Examples/Lineinits.txt
@@ -0,0 +1 @@
+list(alpha = 0, beta = 0, tau = 1)
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diff --git a/doc/Examples/Lineinits1.html b/doc/Examples/Lineinits1.html
new file mode 100755
index 0000000..ab71a37
--- /dev/null
+++ b/doc/Examples/Lineinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Lineinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = 10, beta = 10, tau = 0.1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Lineinits1.txt b/doc/Examples/Lineinits1.txt
new file mode 100755
index 0000000..e4f6b68
--- /dev/null
+++ b/doc/Examples/Lineinits1.txt
@@ -0,0 +1 @@
+list(alpha = 10, beta = 10, tau = 0.1)
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diff --git a/doc/Examples/Linemodel.html b/doc/Examples/Linemodel.html
new file mode 100755
index 0000000..2d5fe67
--- /dev/null
+++ b/doc/Examples/Linemodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Linemodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : N ) {<br> Y[i] ~ dnorm(mu[i],tau)<br> mu[i] <- alpha + beta * (x[i] - xbar)<br> }<br> tau ~ dgamma(0.001,0.001) sigma <- 1 / sqrt(tau)<br>   [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Linemodel.txt b/doc/Examples/Linemodel.txt
new file mode 100755
index 0000000..8fd1376
--- /dev/null
+++ b/doc/Examples/Linemodel.txt
@@ -0,0 +1,10 @@
+ model
+ {
+ for( i in 1 : N ) {
+ Y[i] ~ dnorm(mu[i],tau)
+ mu[i] <- alpha + beta * (x[i] - xbar)
+ }
+ tau ~ dgamma(0.001,0.001) sigma <- 1 / sqrt(tau)
+ alpha ~ dnorm(0.0,1.0E-6)
+ beta ~ dnorm(0.0,1.0E-6)
+ }
diff --git a/doc/Examples/Lizards.html b/doc/Examples/Lizards.html
new file mode 100755
index 0000000..d7bb115
--- /dev/null
+++ b/doc/Examples/Lizards.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Lizards</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="lizards0.bmp" alt="[lizards0]">
</font><font face="Courier New" color="#000100" size="6"> Lizards: Binomial mixture model<br> for modelling and estimation of<br> abundance in the presence of<br> imperfect detection
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="6"> <br> (contributed by Marc Kery)<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Abundance, or population size, is the central quantity in much of ecology (e.g., Krebs,
</font><font face="Arial" color="#000100" size="3"><em>Addison Wesley
</em></font><font face="Arial" color="#000100" size="3">, 2001). Abundance is assessed by counting individuals, and patterns in abundance are typically modelled by assuming some sort of a Poisson GLM for these counts. This approach neglects the important fact that almost universally some individuals are overlooked; i.e., individual detection probability is arguably always less than 1 in the field. This means that counts usually underestimate true abundance. Worse yet, covariates that affe [...]
</font><font face="Arial" color="#000100" size="3"><em>et al.
</em></font><font face="Arial" color="#000100" size="3">, 2001, 2004) and capture-recapture (Williams et al.,
</font><font face="Arial" color="#000100" size="3"><em>Academic Press
</em></font><font face="Arial" color="#000100" size="3">, 2002). A third, "cheaper" method (in terms of field protocol) is the binomial mixture or N - mixture model (Royle,
</font><font face="Arial" color="#000100" size="3"><em>Biometrics
</em></font><font face="Arial" color="#000100" size="3">, 2004). Based on counts that are replicated both over multiple sites and multiple surveys within a time period of geographic and demographic closure, abundance and detection probability can be estimated separately along with their relationships with measured covariates. Here, we present a hierarchical, or state-space, implementation of the model that explicitly contains parameters for the latent state N
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, that is, abundance at site i.<br><br>This model is structurally similar to the site-occupancy model (see Gentians example), the main difference being that as a model for the latent state the Poisson is chosen rather than the Bernoulli. Like the site-occupancy model (see there), the binomial mixture model can be fitted in WinBUGS in a "square data format", where rows denote sites and columns repeated surveys. However, for [...]
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> at site
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> by two linked equations:<br><br> N
</font><font face="Arial" color="#000100" size="3"><sub>site
</sub></font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">~ Poisson(lambda
</font><font face="Arial" color="#000100" size="3"><sub>site
</sub></font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br><br> y
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(p
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, N
</font><font face="Arial" color="#000100" size="3"><sub>site
</sub></font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) <br><br>Again, like in the case of the site-occupancy model, the first line describes the true biological process: true abundance, the latent state N
</font><font face="Arial" color="#000100" size="3"><sub>site
</sub></font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, i.e., local population size N at population
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">. The simplest distributional assumption is that of a Poisson distribution, but other distributions like the negative binomial are also possible or one could model a normal random effect into log(lambda). Given the particular realisation of the Poisson random process, i.e., a particular N
</font><font face="Arial" color="#000100" size="3"><sub>site
</sub></font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, the observed data, count y
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, follows a binomial distribution indexed by local population size and "success probability" = detection probability p
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">. Covariate effects can be modelled into the Poisson and the Binomial mean in a simple GLM fashion.<br><br>This binomial mixture model example, though inspired by nature (Kéry
</font><font face="Arial" color="#000100" size="3"><em>et al.
</em></font><font face="Arial" color="#000100" size="3">, in press) is based on simulated data of replicated counts of sand lizards (Lacerta agilis) in The Netherlands. Lizards were counted at 200 survey sites three times during a time period when the population was assumed closed. True abundance was assumed to be positively related to vegetation density (scaled -1 to 1) but detection probability was assumed to be lower in higher than in lower vegetation, and in addition, positively affec [...]
</font><font face="Arial" color="#000100" size="3"><strong>Hints:
</strong></font><font face="Arial" color="#000100" size="3"> Good starting values can be essential for fitting the model successfully. One plus the max observed at each site is a good choice. Scaling of covariates is also important.<br>
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model <br> { # Binomial mixture model for 'vertical' data format<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Priors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">alpha.lam ~ dunif(-10, 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">beta.lam ~ dunif(-10, 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">alpha.p ~ dunif(-10, 10) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">beta1.p ~ dunif(-10, 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">beta2.p ~ dunif(-10, 10)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Likelihood<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Biological model for true abundance<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for (i in 1:R) {# Loop over R sites<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">N[i] ~ dpois(lambda[i])C(,50)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">log(lambda[i]) <- alpha.lam + beta.lam * vege.lam[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Observation model for replicated counts<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for (i in 1:n) {# Loop over all n observations<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">C[i] ~ dbin(p[i], N[site[i]])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">lin.pred[i] <- alpha.p + beta1.p * vege.p[i] + beta2.p * temperature[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">p[i] <- exp(lin.pred[i]) / (1 + exp(lin.pred[i]))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Derived quantities<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> totalN <- sum(N[ ]) # Estimate total population size across all sites<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br><br>
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Lizardsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Lizardsinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="3"> </a>
</font><font face="Arial" color="#0000FF" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Lizardsinits2.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Lizardsinits3.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 3
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#0000FF" size="3"><strong> <br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Running 3 chains for 11k iterations, with 1k discarded as a burnin, yields these results <br><center><br><img src="lizards1.bmp" alt="[lizards1]"><br></center><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Note that although convergence is somewhat iffy, these stimates compare very well with the data-generating parameters (alpha's and beta's, same order as above): 2, -1, 1, -3 and 2. Also, they are almost identical to the MLE's obtained by maximising the likelihood numerically in R (see Kéry
</font><font face="Arial" color="#000100" size="3"><em>et al.
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><em>Ecol. Appl.
</em></font><font face="Arial" color="#000100" size="3">, 2005): 2.142415, -1.258583, 1.113543, -3.169582, and 2.014300.<br> In addition, the estimate of totalN should be compared to known total population size across all 200 sites of 1700, with a sum of site maxima of only 692 observed lizards. In contrast, a naïve Poisson regression on observed max counts for each site is totally unable to pick up the positive effect of vegetation on abundance and vastly underestim [...]
</font>
</p>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Lizardsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(C=c(0, 3, 3, 1, 1, 0, 3, 3, 2, 5, 3, 1, 1, 2, 0, 4, 4, 2, 7, 7, 3, 0, 3, 3, 4, 1, 0, 3, 3, 0, 2, 0, 0, 2, 3, 0, 0, 0, 0, 5, 3, 1, 1, 3, 2, 2, 1, 1, 4, 2, 1, 0, 0, 7, 4, 6, 0, 1, 7, 6, 1, 1, 0, 2, 0, 0, 1, 4, 1, 0, 1, 0, 6, 2, 4, 3, 0, 0, 2, 3, 3, 3, 7, 3, 4, 1, 2, 1, 4, 4, 5, 1, 2, 1, 3, 1, 2, 2, 2, 1, 2, 2, 6, 0, 0, 1, 2, 2, 5, 0, 2, 5, 0, 3, 2, 6, 7, 0, 1, 3, 0, 0, 1, 1, 1, 2, 0, 3, 1, 3, 6, 4, 2, 1, 1, 4, 0, 3, 0, 1, 0, 3, 4, 7, 6, 6, 0, [...]
</font>
</p>
</body>
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diff --git a/doc/Examples/Lizardsdata.txt b/doc/Examples/Lizardsdata.txt
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@@ -0,0 +1,2 @@
+list(C=c(0, 3, 3, 1, 1, 0, 3, 3, 2, 5, 3, 1, 1, 2, 0, 4, 4, 2, 7, 7, 3, 0, 3, 3, 4, 1, 0, 3, 3, 0, 2, 0, 0, 2, 3, 0, 0, 0, 0, 5, 3, 1, 1, 3, 2, 2, 1, 1, 4, 2, 1, 0, 0, 7, 4, 6, 0, 1, 7, 6, 1, 1, 0, 2, 0, 0, 1, 4, 1, 0, 1, 0, 6, 2, 4, 3, 0, 0, 2, 3, 3, 3, 7, 3, 4, 1, 2, 1, 4, 4, 5, 1, 2, 1, 3, 1, 2, 2, 2, 1, 2, 2, 6, 0, 0, 1, 2, 2, 5, 0, 2, 5, 0, 3, 2, 6, 7, 0, 1, 3, 0, 0, 1, 1, 1, 2, 0, 3, 1, 3, 6, 4, 2, 1, 1, 4, 0, 3, 0, 1, 0, 3, 4, 7, 6, 6, 0, 1, 0, 0, 0, 5, 1, 0, 2, 4, 6, 3, 3, 1, 1, [...]
+
diff --git a/doc/Examples/Lizardsinits1.html b/doc/Examples/Lizardsinits1.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Lizardsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><br>list(N=c(2, 4, 6, 2, 5, 5, 5, 4, 3, 6, 4, 4, 2, 7, 8, 6, 6, 3, 8, 8, 4, 2, 8, 7, 8, 3, 4, 4, 4, 3, 3, 3, 2, 4, 4, 2, 1, 2, 1, 6, 4, 5, 4, 4, 3, 3, 2, 5, 5, 6, 2, 5, 9, 8, 5, 7, 1, 2, 8, 7, 2, 11, 1, 3, 5, 7, 7, 5, 2, 2, 6, 3, 9, 3, 5, 6, 5, 4, 3, 6, 5, 5, 8, 5, 6, 2, 5, 2, 5, 5, 6, 2, 6, 2, 4, 2, 4, 6, 3, 6, 3, 4, 7, 2, 1, 2, 3, 4, 6, 3, 3, 6, 1, 4, 5, 7, 8, 2, 5, 4, 7, 2, 3, 4, 2, 3, 3, 4, 3, 6, 7, 5, 5, 4, 6, 6, 1, 5, 2, 4, 2, 4, 5, 8, 7, [...]
</font>
</p>
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@@ -0,0 +1,2 @@
+
+list(N=c(2, 4, 6, 2, 5, 5, 5, 4, 3, 6, 4, 4, 2, 7, 8, 6, 6, 3, 8, 8, 4, 2, 8, 7, 8, 3, 4, 4, 4, 3, 3, 3, 2, 4, 4, 2, 1, 2, 1, 6, 4, 5, 4, 4, 3, 3, 2, 5, 5, 6, 2, 5, 9, 8, 5, 7, 1, 2, 8, 7, 2, 11, 1, 3, 5, 7, 7, 5, 2, 2, 6, 3, 9, 3, 5, 6, 5, 4, 3, 6, 5, 5, 8, 5, 6, 2, 5, 2, 5, 5, 6, 2, 6, 2, 4, 2, 4, 6, 3, 6, 3, 4, 7, 2, 1, 2, 3, 4, 6, 3, 3, 6, 1, 4, 5, 7, 8, 2, 5, 4, 7, 2, 3, 4, 2, 3, 3, 4, 3, 6, 7, 5, 5, 4, 6, 6, 1, 5, 2, 4, 2, 4, 5, 8, 7, 7, 6, 2, 9, 3, 1, 6, 4, 6, 3, 5, 7, 4, 4, 3, 7, [...]
diff --git a/doc/Examples/Lizardsinits2.html b/doc/Examples/Lizardsinits2.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Lizardsinits2</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(N=c(2, 4, 6, 2, 5, 5, 5, 4, 3, 6, 4, 4, 2, 7, 8, 6, 6, 3, 8, 8, 4, 2, 8, 7, 8, 3, 4, 4, 4, 3, 3, 3, 2, 4, 4, 2, 1, 2, 1, 6, 4, 5, 4, 4, 3, 3, 2, 5, 5, 6, 2, 5, 9, 8, 5, 7, 1, 2, 8, 7, 2, 11, 1, 3, 5, 7, 7, 5, 2, 2, 6, 3, 9, 3, 5, 6, 5, 4, 3, 6, 5, 5, 8, 5, 6, 2, 5, 2, 5, 5, 6, 2, 6, 2, 4, 2, 4, 6, 3, 6, 3, 4, 7, 2, 1, 2, 3, 4, 6, 3, 3, 6, 1, 4, 5, 7, 8, 2, 5, 4, 7, 2, 3, 4, 2, 3, 3, 4, 3, 6, 7, 5, 5, 4, 6, 6, 1, 5, 2, 4, 2, 4, 5, 8, 7, 7, 6 [...]
</font>
</p>
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diff --git a/doc/Examples/Lizardsinits2.txt b/doc/Examples/Lizardsinits2.txt
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@@ -0,0 +1 @@
+list(N=c(2, 4, 6, 2, 5, 5, 5, 4, 3, 6, 4, 4, 2, 7, 8, 6, 6, 3, 8, 8, 4, 2, 8, 7, 8, 3, 4, 4, 4, 3, 3, 3, 2, 4, 4, 2, 1, 2, 1, 6, 4, 5, 4, 4, 3, 3, 2, 5, 5, 6, 2, 5, 9, 8, 5, 7, 1, 2, 8, 7, 2, 11, 1, 3, 5, 7, 7, 5, 2, 2, 6, 3, 9, 3, 5, 6, 5, 4, 3, 6, 5, 5, 8, 5, 6, 2, 5, 2, 5, 5, 6, 2, 6, 2, 4, 2, 4, 6, 3, 6, 3, 4, 7, 2, 1, 2, 3, 4, 6, 3, 3, 6, 1, 4, 5, 7, 8, 2, 5, 4, 7, 2, 3, 4, 2, 3, 3, 4, 3, 6, 7, 5, 5, 4, 6, 6, 1, 5, 2, 4, 2, 4, 5, 8, 7, 7, 6, 2, 9, 3, 1, 6, 4, 6, 3, 5, 7, 4, 4, 3, 7, [...]
diff --git a/doc/Examples/Lizardsinits3.html b/doc/Examples/Lizardsinits3.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Lizardsinits3</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(N=c(2, 4, 6, 2, 5, 5, 5, 4, 3, 6, 4, 4, 2, 7, 8, 6, 6, 3, 8, 8, 4, 2, 8, 7, 8, 3, 4, 4, 4, 3, 3, 3, 2, 4, 4, 2, 1, 2, 1, 6, 4, 5, 4, 4, 3, 3, 2, 5, 5, 6, 2, 5, 9, 8, 5, 7, 1, 2, 8, 7, 2, 11, 1, 3, 5, 7, 7, 5, 2, 2, 6, 3, 9, 3, 5, 6, 5, 4, 3, 6, 5, 5, 8, 5, 6, 2, 5, 2, 5, 5, 6, 2, 6, 2, 4, 2, 4, 6, 3, 6, 3, 4, 7, 2, 1, 2, 3, 4, 6, 3, 3, 6, 1, 4, 5, 7, 8, 2, 5, 4, 7, 2, 3, 4, 2, 3, 3, 4, 3, 6, 7, 5, 5, 4, 6, 6, 1, 5, 2, 4, 2, 4, 5, 8, 7, 7, 6 [...]
</font>
</p>
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diff --git a/doc/Examples/Lizardsinits3.txt b/doc/Examples/Lizardsinits3.txt
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+++ b/doc/Examples/Lizardsinits3.txt
@@ -0,0 +1 @@
+list(N=c(2, 4, 6, 2, 5, 5, 5, 4, 3, 6, 4, 4, 2, 7, 8, 6, 6, 3, 8, 8, 4, 2, 8, 7, 8, 3, 4, 4, 4, 3, 3, 3, 2, 4, 4, 2, 1, 2, 1, 6, 4, 5, 4, 4, 3, 3, 2, 5, 5, 6, 2, 5, 9, 8, 5, 7, 1, 2, 8, 7, 2, 11, 1, 3, 5, 7, 7, 5, 2, 2, 6, 3, 9, 3, 5, 6, 5, 4, 3, 6, 5, 5, 8, 5, 6, 2, 5, 2, 5, 5, 6, 2, 6, 2, 4, 2, 4, 6, 3, 6, 3, 4, 7, 2, 1, 2, 3, 4, 6, 3, 3, 6, 1, 4, 5, 7, 8, 2, 5, 4, 7, 2, 3, 4, 2, 3, 3, 4, 3, 6, 7, 5, 5, 4, 6, 6, 1, 5, 2, 4, 2, 4, 5, 8, 7, 7, 6, 2, 9, 3, 1, 6, 4, 6, 3, 5, 7, 4, 4, 3, 7, [...]
diff --git a/doc/Examples/Lsat.html b/doc/Examples/Lsat.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Lsat</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="lsat0.bmp" alt="[lsat0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">LSAT: item response
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Section 6 of the Law School Aptitude Test (LSAT) is a 5-item multiple choice test; students score 1 on each item for the correct answer and 0 otherwise, giving R = 32 possible response patterns.Boch and Lieberman (1970) present data on LSAT for N = 1000 students, part of which is shown below.<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="lsat1.bmp" alt="[lsat1]"><br></center><br>
</font><font face="Arial" color="#000100" size="3">The above data may be analysed using the one-parameter Rasch model (see Andersen (1980), pp.253-254; Boch and Aitkin (1981)). The probability p
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3"> that student
</font><font face="Arial" color="#000100" size="3"><em>j
</em></font><font face="Arial" color="#000100" size="3"> responds correctly to item
</font><font face="Arial" color="#000100" size="3"><em>k
</em></font><font face="Arial" color="#000100" size="3"> is assumed to follow a logistic function parameterized by an `item difficulty' or threshold parameter
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> and a latent variable
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> representing the student's underlying ability. The ability parameters are assumed to have a Normal distribution in the population of students. That is:<br><br> logit(p
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub> -
</sub></font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"><sub>, j = 1,...,1000; k = 1,...,5<br> <br>
</sub></font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Normal(0,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">)<br><br>The above model is equivalent to the following random effects logistic regression:<br> <br> logit(p
</font><font face="Arial" color="#000100" size="2"><sub>jk
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">bq
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub> -
</sub></font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"><sub>, j = 1,...,1000; k = 1,...,5<br> <br>
</sub></font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Normal(0, 1)<br> <br>where
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> corresponds to the scale parameter (
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">t)
</font><font face="Arial" color="#000100" size="3"> of the latent ability distribution. We assume a half-normal distribution with small precision for
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"><sub>;
</sub></font><font face="Arial" color="#000100" size="3"> this represents vague prior information but constrains
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> to be positive. Standard vague normal priors are assumed for the
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3">'s. Note that the location of the
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3">'s depend upon the mean of the prior distribution for
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">which we have arbitrarily fixed to be zero. Alternatively, Boch and Aitkin ensure identifiability by imposing a sum-to-zero constraint on the
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3">'s. Hence we calculate a
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> -
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>bar
</sub></font><font face="Arial" color="#000100" size="3"> to enable comparision of the
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> posterior parameter estimates with the Boch and Aitkin marginal maximum likelihood estimates.<br><center>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for LSAT model
</em></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3"></center> model<br> {<br> # Calculate individual (binary) responses to each test from multinomial data<br> for (j in 1 : culm[1]) {<br> for (k in 1 : T) { <br> r[j, k] <- response[1, k] <br> &nb [...]
</font><font face="Arial" color="#000100" size="3"><br>Note that the data are read into
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> in the original multinomial format to economize on space and effort. The 5 times 1000 individual binary responses for each item and student are then created within
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> using the index variable culm (read in from the data file), where culm[i] = cumulative number of students recording response patterns 1, 2, ..., i; i <= R.<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Lsatdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Lsatinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Lsatinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br> <br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center>
</font><font face="Arial" color="#000100" size="3"><br><img src="lsat2.bmp" alt="[lsat2]">
</font><font face="Arial" color="#000100" size="1"><br>
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Lsatdata.html b/doc/Examples/Lsatdata.html
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+++ b/doc/Examples/Lsatdata.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Lsatdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 1000, R = 32, T = 5,
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1"> culm = c(3, 9, 11, 22, 23, 24, 27, 31, 32, 40, 40, 56, 56, 59, 61, 76, 86, 115, 129, 210, 213, 241, 256, 336, 352, 408,<br> 429, 602, 613, 674, 702, 1000),<br> response = structure(.Data = c( <br> &nb [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Lsatdata.txt b/doc/Examples/Lsatdata.txt
new file mode 100755
index 0000000..a8f6cea
--- /dev/null
+++ b/doc/Examples/Lsatdata.txt
@@ -0,0 +1,37 @@
+list(N = 1000, R = 32, T = 5,
+ culm = c(3, 9, 11, 22, 23, 24, 27, 31, 32, 40, 40, 56, 56, 59, 61, 76, 86, 115, 129, 210, 213, 241, 256, 336, 352, 408,
+ 429, 602, 613, 674, 702, 1000),
+ response = structure(.Data = c(
+ 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 1,
+ 0, 0, 0, 1, 0,
+ 0, 0, 0, 1, 1,
+ 0, 0, 1, 0, 0,
+ 0, 0, 1, 0, 1,
+ 0, 0, 1, 1, 0,
+ 0, 0, 1, 1, 1,
+ 0, 1, 0, 0, 0,
+ 0, 1, 0, 0, 1,
+ 0, 1, 0, 1, 0,
+ 0, 1, 0, 1, 1,
+ 0, 1, 1, 0, 0,
+ 0, 1, 1, 0, 1,
+ 0, 1, 1, 1, 0,
+ 0, 1, 1, 1, 1,
+ 1, 0, 0, 0, 0,
+ 1, 0, 0, 0, 1,
+ 1, 0, 0, 1, 0,
+ 1, 0, 0, 1, 1,
+ 1, 0, 1, 0, 0,
+ 1, 0, 1, 0, 1,
+ 1, 0, 1, 1, 0,
+ 1, 0, 1, 1, 1,
+ 1, 1, 0, 0, 0,
+ 1, 1, 0, 0, 1,
+ 1, 1, 0, 1, 0,
+ 1, 1, 0, 1, 1,
+ 1, 1, 1, 0, 0,
+ 1, 1, 1, 0, 1,
+ 1, 1, 1, 1, 0,
+ 1, 1, 1, 1, 1), .Dim = c(32, 5))
+)
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diff --git a/doc/Examples/Lsatinits.html b/doc/Examples/Lsatinits.html
new file mode 100755
index 0000000..5e7135c
--- /dev/null
+++ b/doc/Examples/Lsatinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Lsatinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = c(0,0,0,0,0), beta = 1)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Lsatinits.txt b/doc/Examples/Lsatinits.txt
new file mode 100755
index 0000000..73af76c
--- /dev/null
+++ b/doc/Examples/Lsatinits.txt
@@ -0,0 +1 @@
+list(alpha = c(0,0,0,0,0), beta = 1)
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diff --git a/doc/Examples/Lsatinits1.html b/doc/Examples/Lsatinits1.html
new file mode 100755
index 0000000..e876be7
--- /dev/null
+++ b/doc/Examples/Lsatinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Lsatinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = c(1.0,1.0,1.0, 1.0, 1.0), beta = 2)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Lsatinits1.txt b/doc/Examples/Lsatinits1.txt
new file mode 100755
index 0000000..4d8d802
--- /dev/null
+++ b/doc/Examples/Lsatinits1.txt
@@ -0,0 +1 @@
+list(alpha = c(1.0,1.0,1.0, 1.0, 1.0), beta = 2)
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diff --git a/doc/Examples/Lsatmodel.html b/doc/Examples/Lsatmodel.html
new file mode 100755
index 0000000..7226aa5
--- /dev/null
+++ b/doc/Examples/Lsatmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Lsatmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> # Calculate individual (binary) responses to each test from multinomial data<br> for (j in 1 : culm[1]) {<br> for (k in 1 : T) { <br> r[j, k] <- response[1, k] <br> } [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Lsatmodel.txt b/doc/Examples/Lsatmodel.txt
new file mode 100755
index 0000000..23bccbf
--- /dev/null
+++ b/doc/Examples/Lsatmodel.txt
@@ -0,0 +1,30 @@
+ model
+ {
+ # Calculate individual (binary) responses to each test from multinomial data
+ for (j in 1 : culm[1]) {
+ for (k in 1 : T) {
+ r[j, k] <- response[1, k]
+ }
+ }
+ for (i in 2 : R) {
+ for (j in culm[i - 1] + 1 : culm[i]) {
+ for (k in 1 : T) {
+ r[j, k] <- response[i, k]
+ }
+ }
+ }
+ # Rasch model
+ for (j in 1 : N) {
+ for (k in 1 : T) {
+ logit(p[j, k]) <- beta * theta[j] - alpha[k]
+ r[j, k] ~ dbern(p[j, k])
+ }
+ theta[j] ~ dnorm(0, 1)
+ }
+ # Priors
+ for (k in 1 : T) {
+ alpha[k] ~ dnorm(0, 0.0001)
+ a[k] <- alpha[k] - mean(alpha[])
+ }
+ beta ~ dflat()T(0, )
+ }
diff --git a/doc/Examples/Magnesium.html b/doc/Examples/Magnesium.html
new file mode 100755
index 0000000..bf86d22
--- /dev/null
+++ b/doc/Examples/Magnesium.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Magnesium</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="5"><strong><img src="magnesium0.bmp" alt="[magnesium0]">
</strong></font><font face="Courier New" color="#000100" size="6">Sensitivity to prior distributions:<br> application to Magnesium <br> meta-analysis
</font><font face="Arial" color="#000000" size="5"><strong><br>
</strong></font><font face="Arial" color="#000000" size="2"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"> model <br> {<br>
</font><font face="Arial" color="#000000" size="3"> # j indexes alternative prior distributions<br> for (j in 1:6) {<br> mu[j] ~ dunif(-10, 10)<br> OR[j] <- exp(mu[j])<br> <br> # k indexes study number<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (k in 1:8) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> theta[j, k] ~ dnorm(mu[j], inv.tau.sqrd[j])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> rtx[j, k] ~ dbin(pt[j, k], nt[k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> rtx[j, k] <- rt[k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> rcx[j, k] ~ dbin(pc[j, k], nc[k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> rcx[j, k] <- rc[k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> logit(pt[j, k]) <- theta[j, k] + phi[j, k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> phi[j, k] <- logit(pc[j, k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> pc[j, k] ~ dunif(0, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br> <br> # k again indexes study number<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (k in 1:8) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> # log-odds ratios:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> y[k] <- log(((rt[k] + 0.5) / (nt[k] - rt[k] + 0.5)) / ((rc[k] + 0.5) / (nc[k] - rc[k] + 0.5)))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># variances & precisions:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> sigma.sqrd[k] <- 1 / (rt[k] + 0.5) + 1 / (nt[k] - rt[k] + 0.5) + 1 / (rc[k] + 0.5) + <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> 1 / (nc[k] - rc[k] + 0.5)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> prec.sqrd[k] <- 1 / sigma.sqrd[k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> s0.sqrd <- 1 / mean(prec.sqrd[1:8])<br>
</font><font face="Arial" color="#000000" size="3"><em><br>
</em></font><font face="Arial" color="#000000" size="3"> # Prior 1: Gamma(0.001, 0.001) on inv.tau.sqrd<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> inv.tau.sqrd[1] ~ dgamma(0.001, 0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau.sqrd[1] <- 1 / inv.tau.sqrd[1]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau[1] <- sqrt(tau.sqrd[1])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Prior 2: Uniform(0, 50) on tau.sqrd<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau.sqrd[2] ~ dunif(0, 50)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau[2] <- sqrt(tau.sqrd[2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> inv.tau.sqrd[2] <- 1 / tau.sqrd[2]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Prior 3: Uniform(0, 50) on tau<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau[3] ~ dunif(0, 50)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau.sqrd[3] <- tau[3] * tau[3]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> inv.tau.sqrd[3] <- 1 / tau.sqrd[3]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Prior 4: Uniform shrinkage on tau.sqrd<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> B0 ~ dunif(0, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau.sqrd[4] <- s0.sqrd * (1 - B0) / B0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau[4] <- sqrt(tau.sqrd[4])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> inv.tau.sqrd[4] <- 1 / tau.sqrd[4]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Prior 5: Dumouchel on tau<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"><em>
</em></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> D0 ~ dunif(0, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau[5] <- sqrt(s0.sqrd) * (1 - D0) / D0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau.sqrd[5] <- tau[5] * tau[5]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> inv.tau.sqrd[5] <- 1 / tau.sqrd[5]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Prior 6: Half-Normal on tau.sqrd<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> p0 <- phi(0.75) / s0.sqrd<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau.sqrd[6] ~ dnorm(0, p0)C(0, )<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau[6] <- sqrt(tau.sqrd[6])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> inv.tau.sqrd[6] <- 1 / tau.sqrd[6]<br><br> }<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Magnesiumdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Magnesiuminits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Magnesiuminits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br> <br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><strong>Results for 6 different prior distributions on the random-effects variance:<br>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><center><br><img src="magnesium1.bmp" alt="[magnesium1]"><br><br></center> <br>
</font><font face="Arial" color="#000000" size="3">Note: Uniform prior on variance increases uncertainty about the mean treatment effect.<br>
</font><font face="Arial" color="#000100" size="3"><br><center><br><img src="magnesium2.bmp" alt="[magnesium2]"><br><br><img src="magnesium3.bmp" alt="[magnesium3]">
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Magnesiumdata.html b/doc/Examples/Magnesiumdata.html
new file mode 100755
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@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Magnesiumdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(rt = c(1, 9, 2, 1, 10, 1, 1, 90), nt = c(40, 135, 200, 48, 150, 59, 25, 1159),<br>rc = c(2, 23, 7, 1, 8, 9, 3, 118), nc = c(36, 135, 200, 46, 148, 56, 23, 1157))<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Magnesiumdata.txt b/doc/Examples/Magnesiumdata.txt
new file mode 100755
index 0000000..91c5c75
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+++ b/doc/Examples/Magnesiumdata.txt
@@ -0,0 +1,2 @@
+list(rt = c(1, 9, 2, 1, 10, 1, 1, 90), nt = c(40, 135, 200, 48, 150, 59, 25, 1159),
+rc = c(2, 23, 7, 1, 8, 9, 3, 118), nc = c(36, 135, 200, 46, 148, 56, 23, 1157))
diff --git a/doc/Examples/Magnesiuminits.html b/doc/Examples/Magnesiuminits.html
new file mode 100755
index 0000000..22b5540
--- /dev/null
+++ b/doc/Examples/Magnesiuminits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Magnesiuminits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(mu = c(-0.5, -0.5, -0.5, -0.5, -0.5, -0.5), tau = c(NA, NA, 1, NA, NA, NA),<br>tau.sqrd = c(NA, 1, NA, NA, NA, 1), inv.tau.sqrd = c(1, NA, NA, NA, NA, NA))<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Magnesiuminits.txt b/doc/Examples/Magnesiuminits.txt
new file mode 100755
index 0000000..171a551
--- /dev/null
+++ b/doc/Examples/Magnesiuminits.txt
@@ -0,0 +1,2 @@
+list(mu = c(-0.5, -0.5, -0.5, -0.5, -0.5, -0.5), tau = c(NA, NA, 1, NA, NA, NA),
+tau.sqrd = c(NA, 1, NA, NA, NA, 1), inv.tau.sqrd = c(1, NA, NA, NA, NA, NA))
diff --git a/doc/Examples/Magnesiuminits1.html b/doc/Examples/Magnesiuminits1.html
new file mode 100755
index 0000000..f70b721
--- /dev/null
+++ b/doc/Examples/Magnesiuminits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Magnesiuminits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(mu = c(0.5, 0.5, 0.5, 0.5, 0.5, 0.5), tau = c(NA, NA, 0.1, NA, NA, NA),<br>tau.sqrd = c(NA, 0.1, NA, NA, NA, 0.1), inv.tau.sqrd = c(0.1, NA, NA, NA, NA, NA))<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Magnesiuminits1.txt b/doc/Examples/Magnesiuminits1.txt
new file mode 100755
index 0000000..db65e94
--- /dev/null
+++ b/doc/Examples/Magnesiuminits1.txt
@@ -0,0 +1,2 @@
+list(mu = c(0.5, 0.5, 0.5, 0.5, 0.5, 0.5), tau = c(NA, NA, 0.1, NA, NA, NA),
+tau.sqrd = c(NA, 0.1, NA, NA, NA, 0.1), inv.tau.sqrd = c(0.1, NA, NA, NA, NA, NA))
diff --git a/doc/Examples/Magnesiummodel.html b/doc/Examples/Magnesiummodel.html
new file mode 100755
index 0000000..1592fa9
--- /dev/null
+++ b/doc/Examples/Magnesiummodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Magnesiummodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model <br> {<br>
</font><font face="Arial" color="#000000" size="3"> # j indexes alternative prior distributions<br> for (j in 1:6) {<br> mu[j] ~ dunif(-10, 10)<br> OR[j] <- exp(mu[j])<br> <br> # k indexes study number<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (k in 1:8) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> theta[j, k] ~ dnorm(mu[j], inv.tau.sqrd[j])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> rtx[j, k] ~ dbin(pt[j, k], nt[k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> rtx[j, k] <- rt[k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> rcx[j, k] ~ dbin(pc[j, k], nc[k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> rcx[j, k] <- rc[k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> logit(pt[j, k]) <- theta[j, k] + phi[j, k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> phi[j, k] <- logit(pc[j, k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> pc[j, k] ~ dunif(0, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br> <br> # k again indexes study number<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (k in 1:8) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> # log-odds ratios:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> y[k] <- log(((rt[k] + 0.5) / (nt[k] - rt[k] + 0.5)) / ((rc[k] + 0.5) / (nc[k] - rc[k] + 0.5)))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># variances & precisions:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> sigma.sqrd[k] <- 1 / (rt[k] + 0.5) + 1 / (nt[k] - rt[k] + 0.5) + 1 / (rc[k] + 0.5) + <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> 1 / (nc[k] - rc[k] + 0.5)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> prec.sqrd[k] <- 1 / sigma.sqrd[k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> s0.sqrd <- 1 / mean(prec.sqrd[1:8])<br>
</font><font face="Arial" color="#000000" size="3"><em><br>
</em></font><font face="Arial" color="#000000" size="3"> # Prior 1: Gamma(0.001, 0.001) on inv.tau.sqrd<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> inv.tau.sqrd[1] ~ dgamma(0.001, 0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau.sqrd[1] <- 1 / inv.tau.sqrd[1]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau[1] <- sqrt(tau.sqrd[1])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Prior 2: Uniform(0, 50) on tau.sqrd<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau.sqrd[2] ~ dunif(0, 50)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau[2] <- sqrt(tau.sqrd[2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> inv.tau.sqrd[2] <- 1 / tau.sqrd[2]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Prior 3: Uniform(0, 50) on tau<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau[3] ~ dunif(0, 50)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau.sqrd[3] <- tau[3] * tau[3]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> inv.tau.sqrd[3] <- 1 / tau.sqrd[3]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Prior 4: Uniform shrinkage on tau.sqrd<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> B0 ~ dunif(0, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau.sqrd[4] <- s0.sqrd * (1 - B0) / B0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau[4] <- sqrt(tau.sqrd[4])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> inv.tau.sqrd[4] <- 1 / tau.sqrd[4]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Prior 5: Dumouchel on tau<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"><em>
</em></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> D0 ~ dunif(0, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau[5] <- sqrt(s0.sqrd) * (1 - D0) / D0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau.sqrd[5] <- tau[5] * tau[5]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> inv.tau.sqrd[5] <- 1 / tau.sqrd[5]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Prior 6: Half-Normal on tau.sqrd<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> p0 <- phi(0.75) / s0.sqrd<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau.sqrd[6] ~ dnorm(0, p0)T(0, )<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau[6] <- sqrt(tau.sqrd[6])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> inv.tau.sqrd[6] <- 1 / tau.sqrd[6]<br><br> }<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Magnesiummodel.txt b/doc/Examples/Magnesiummodel.txt
new file mode 100755
index 0000000..54b7ccf
--- /dev/null
+++ b/doc/Examples/Magnesiummodel.txt
@@ -0,0 +1,71 @@
+ model
+ {
+ # j indexes alternative prior distributions
+ for (j in 1:6) {
+ mu[j] ~ dunif(-10, 10)
+ OR[j] <- exp(mu[j])
+
+ # k indexes study number
+ for (k in 1:8) {
+ theta[j, k] ~ dnorm(mu[j], inv.tau.sqrd[j])
+ rtx[j, k] ~ dbin(pt[j, k], nt[k])
+ rtx[j, k] <- rt[k]
+ rcx[j, k] ~ dbin(pc[j, k], nc[k])
+ rcx[j, k] <- rc[k]
+ logit(pt[j, k]) <- theta[j, k] + phi[j, k]
+ phi[j, k] <- logit(pc[j, k])
+ pc[j, k] ~ dunif(0, 1)
+ }
+ }
+
+ # k again indexes study number
+ for (k in 1:8) {
+ # log-odds ratios:
+ y[k] <- log(((rt[k] + 0.5) / (nt[k] - rt[k] + 0.5)) / ((rc[k] + 0.5) / (nc[k] - rc[k] + 0.5)))
+ # variances & precisions:
+ sigma.sqrd[k] <- 1 / (rt[k] + 0.5) + 1 / (nt[k] - rt[k] + 0.5) + 1 / (rc[k] + 0.5) +
+ 1 / (nc[k] - rc[k] + 0.5)
+ prec.sqrd[k] <- 1 / sigma.sqrd[k]
+ }
+ s0.sqrd <- 1 / mean(prec.sqrd[1:8])
+
+ # Prior 1: Gamma(0.001, 0.001) on inv.tau.sqrd
+
+ inv.tau.sqrd[1] ~ dgamma(0.001, 0.001)
+ tau.sqrd[1] <- 1 / inv.tau.sqrd[1]
+ tau[1] <- sqrt(tau.sqrd[1])
+
+ # Prior 2: Uniform(0, 50) on tau.sqrd
+
+ tau.sqrd[2] ~ dunif(0, 50)
+ tau[2] <- sqrt(tau.sqrd[2])
+ inv.tau.sqrd[2] <- 1 / tau.sqrd[2]
+
+ # Prior 3: Uniform(0, 50) on tau
+
+ tau[3] ~ dunif(0, 50)
+ tau.sqrd[3] <- tau[3] * tau[3]
+ inv.tau.sqrd[3] <- 1 / tau.sqrd[3]
+
+ # Prior 4: Uniform shrinkage on tau.sqrd
+
+ B0 ~ dunif(0, 1)
+ tau.sqrd[4] <- s0.sqrd * (1 - B0) / B0
+ tau[4] <- sqrt(tau.sqrd[4])
+ inv.tau.sqrd[4] <- 1 / tau.sqrd[4]
+
+ # Prior 5: Dumouchel on tau
+
+ D0 ~ dunif(0, 1)
+ tau[5] <- sqrt(s0.sqrd) * (1 - D0) / D0
+ tau.sqrd[5] <- tau[5] * tau[5]
+ inv.tau.sqrd[5] <- 1 / tau.sqrd[5]
+
+ # Prior 6: Half-Normal on tau.sqrd
+
+ p0 <- phi(0.75) / s0.sqrd
+ tau.sqrd[6] ~ dnorm(0, p0)T(0, )
+ tau[6] <- sqrt(tau.sqrd[6])
+ inv.tau.sqrd[6] <- 1 / tau.sqrd[6]
+
+ }
diff --git a/doc/Examples/Mice.html b/doc/Examples/Mice.html
new file mode 100755
index 0000000..24c8667
--- /dev/null
+++ b/doc/Examples/Mice.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Mice</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="mice0.bmp" alt="[mice0]">
</strong></font><font face="Courier New" color="#000100" size="6">Mice: Weibull regression
</font><font face="Arial" color="#000000" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><br>Dellaportas and Smith (1993) analyse data from Grieve (1987) on photocarcinogenicity in four groups, each containing 20 mice, who have recorded a survival time and whether they died or were censored at that time. A portion of the data, giving survival times in weeks, are shown below. A
</font><font face="Arial" color="#000100" size="3"><em>*
</em></font><font face="Arial" color="#000100" size="3">indicates censoring.<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="mice1.bmp" alt="[mice1]"></center>
</font><font face="Arial" color="#000100" size="3"><br>The survival distribution is assumed to be Weibull. That is<br><br>
</font><font face="Times New Roman" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3">(t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><strong>z
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) = re
</font><font face="Symbol" color="#000100" size="3"><strong><sup>b
</sup></strong></font><font face="Arial" color="#000100" size="3"><strong><sup>z
</sup></strong></font><font face="Arial" color="#000100" size="2"><sup>i
</sup></font><font face="Arial" color="#000100" size="3"> t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="2"><sup>r - 1
</sup></font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">exp(-e
</font><font face="Symbol" color="#000100" size="3"><strong><sup>b
</sup></strong></font><font face="Arial" color="#000100" size="3"><strong><sup>z
</sup></strong></font><font face="Arial" color="#000100" size="2"><sup>i
</sup></font><font face="Arial" color="#000100" size="3"><sup>t
</sup></font><font face="Arial" color="#000100" size="2"><sup>i
</sup></font><font face="Arial" color="#000100" size="2"><sup>r
</sup></font><font face="Arial" color="#000100" size="3">)<br> <br>where t
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is the failure time of an individual with covariate vector
</font><font face="Arial" color="#000100" size="3"><strong>z
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">and
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3">is a vector of unknown regression coefficients. This leads to a baseline hazard function of the form <br><br>
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">(t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) = rt
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="2"><sup>r - 1
</sup></font><font face="Arial" color="#000100" size="3"><br><br><br>Setting
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = e
</font><font face="Symbol" color="#000100" size="3"><strong><sup>b
</sup></strong></font><font face="Arial" color="#000100" size="3"><strong><sup>z
</sup></strong></font><font face="Arial" color="#000100" size="2"><sup>i
</sup></font><font face="Arial" color="#000100" size="3"> gives the parameterisation<br><br> t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Weibull(
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>For censored observations, the survival distribution is a truncated Weibull, with lower bound corresponding to the censoring time. The regression
</font><font face="Symbol" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3">coefficients were assumed a priori to follow independent Normal distributions with zero mean and ``vague'' precision 0.0001. The shape parameter r for the survival distribution was given a Gamma(1, 0.0001) prior, which is slowly decreasing on the positive real line. <br><br>Median survival for individuals with covariate vector
</font><font face="Arial" color="#000100" size="3"><strong>z
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">is given by m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = (log2e
</font><font face="Symbol" color="#000100" size="3"><sup>-
</sup></font><font face="Symbol" color="#000100" size="3"><strong><sup>b
</sup></strong></font><font face="Arial" color="#000100" size="3"><strong><sup>z
</sup></strong></font><font face="Arial" color="#000100" size="2"><sup>i
</sup></font><font face="Arial" color="#000100" size="3">)
</font><font face="Arial" color="#000100" size="2"><sup>1/r
</sup></font><font face="Arial" color="#000100" size="3"><sup><br>
</sup></font><font face="Arial" color="#000100" size="3"><br>The appropriate graph and BUGS language are below, using an undirected dashed line to represent a logical range constraint. <br>
</font><font face="Arial" color="#000100" size="2"><br><center>
</font><font face="Arial" color="#000100" size="2"><img src="mice2.bmp" alt="[mice2]">
</font><font face="Arial" color="#000100" size="2"> <br><br>
</font><font face="Arial" color="#000100" size="3"></center> model<br> { <br> for(i in 1 : M) {<br> for(j in 1 : N) { <br> t[i, j] ~ dweib(r, mu[i])C(t.cen[i, j],)<br> cumulative.t[i, j] <- cumulative(t[i, j], [...]
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>We note a number of tricks in setting up this model. First, individuals who are censored are given a missing value in the vector of failure times t, whilst individuals who fail are given a zero in the censoring time vector t.cen (see data file listing below). The truncated Weibull is modelled using C(t.cen[i],) to set a lower bound. Second, we set a parameter beta[j] for each treatment group
</font><font face="Arial" color="#000100" size="3"><em>j
</em></font><font face="Arial" color="#000100" size="3">.
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">The contrasts beta[j] with group 1 (the irradiated control) are calculated at the end. Alternatively, we could have included a grand mean term in the relative risk model and constrained beta[1] to be zero.<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Micedata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Miceinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Miceinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>A burn in of 1000 updates followed by a further 10000 updates gave the parameter estimates
</font><font face="Arial" color="#000100" size="3"><br><center><br><img src="mice3.bmp" alt="[mice3]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Micedata.html b/doc/Examples/Micedata.html
new file mode 100755
index 0000000..c0a64a2
--- /dev/null
+++ b/doc/Examples/Micedata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Micedata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(t = structure(.Data = <br> c(12, 1, 21, 25, 11, 26, 27, 30, 13, 12, 21, 20, 23, 25, 23, 29, 35, NA, 31, 36, <br> 32, 27, 23, 12, 18, NA, NA, 38, 29, 30, NA, 32, NA, NA, NA, NA, 25, 30, 37, 27, <br> 22, 26, NA, 28, 19, 15, 12, 35, 35, 10, 22, 18, NA, 12, NA, NA, 31, 24, 37, 29, <br> &nb [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Micedata.txt b/doc/Examples/Micedata.txt
new file mode 100755
index 0000000..8a60cae
--- /dev/null
+++ b/doc/Examples/Micedata.txt
@@ -0,0 +1,13 @@
+list(t = structure(.Data =
+ c(12, 1, 21, 25, 11, 26, 27, 30, 13, 12, 21, 20, 23, 25, 23, 29, 35, NA, 31, 36,
+ 32, 27, 23, 12, 18, NA, NA, 38, 29, 30, NA, 32, NA, NA, NA, NA, 25, 30, 37, 27,
+ 22, 26, NA, 28, 19, 15, 12, 35, 35, 10, 22, 18, NA, 12, NA, NA, 31, 24, 37, 29,
+ 27, 18, 22, 13, 18, 29, 28, NA, 16, 22, 26, 19, NA, NA, 17, 28, 26, 12, 17, 26),
+ .Dim = c(4, 20)),
+ t.cen = structure(.Data =
+ c( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 40, 0, 0,
+ 0, 0, 0, 0, 0, 40, 40, 0, 0, 0, 40, 0, 40, 40, 40, 40, 0, 0, 0, 0,
+ 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 24, 0, 40, 40, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 20, 0, 0, 0, 0, 29, 10, 0, 0, 0, 0, 0, 0),
+ .Dim = c(4, 20)),
+ M = 4, N = 20)
\ No newline at end of file
diff --git a/doc/Examples/Miceinits.html b/doc/Examples/Miceinits.html
new file mode 100755
index 0000000..e69ee18
--- /dev/null
+++ b/doc/Examples/Miceinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Miceinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(beta = c(-1, -1, -1, -1), r = 1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Miceinits.txt b/doc/Examples/Miceinits.txt
new file mode 100755
index 0000000..80bf4c0
--- /dev/null
+++ b/doc/Examples/Miceinits.txt
@@ -0,0 +1 @@
+list(beta = c(-1, -1, -1, -1), r = 1)
\ No newline at end of file
diff --git a/doc/Examples/Miceinits1.html b/doc/Examples/Miceinits1.html
new file mode 100755
index 0000000..1adca1b
--- /dev/null
+++ b/doc/Examples/Miceinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Miceinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(beta = c(0.0, 0.0, 0.0, 0.0), r = 2)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Miceinits1.txt b/doc/Examples/Miceinits1.txt
new file mode 100755
index 0000000..5784b43
--- /dev/null
+++ b/doc/Examples/Miceinits1.txt
@@ -0,0 +1 @@
+list(beta = c(0.0, 0.0, 0.0, 0.0), r = 2)
\ No newline at end of file
diff --git a/doc/Examples/Micemodel.html b/doc/Examples/Micemodel.html
new file mode 100755
index 0000000..ac801a2
--- /dev/null
+++ b/doc/Examples/Micemodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Micemodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> { <br> for(i in 1 : M) {<br> for(j in 1 : N) { <br> t[i, j] ~ dweib(r, mu[i])C(t.cen[i, j],)<br> }<br> mu[i] <- exp(bet [...]
</font><font face="Arial" color="#000100" size="3"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Micemodel.txt b/doc/Examples/Micemodel.txt
new file mode 100755
index 0000000..524e49d
--- /dev/null
+++ b/doc/Examples/Micemodel.txt
@@ -0,0 +1,15 @@
+ model
+ {
+ for(i in 1 : M) {
+ for(j in 1 : N) {
+ t[i, j] ~ dweib(r, mu[i])C(t.cen[i, j],)
+ }
+ mu[i] <- exp(beta[i])
+ beta[i] ~ dnorm(0.0, 0.001)
+ median[i] <- pow(log(2) * exp(-beta[i]), 1/r)
+ }
+ r ~ dexp(0.001)
+ veh.control <- beta[2] - beta[1]
+ test.sub <- beta[3] - beta[1]
+ pos.control <- beta[4] - beta[1]
+ }
diff --git a/doc/Examples/Otrees.html b/doc/Examples/Otrees.html
new file mode 100755
index 0000000..c5adfad
--- /dev/null
+++ b/doc/Examples/Otrees.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Otrees</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="otrees0.bmp" alt="[otrees0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Orange Trees: Non-linear growth<br> curve
</font><font face="Arial" color="#000000" size="5"><br><br>
</font><font face="Arial" color="#000000" size="3">This dataset was originally presented by Draper and Smith (1981) and reanalysed by Lindstrom and Bates (1990). The data Y
</font><font face="Arial" color="#000000" size="3"><sub>ij
</sub></font><font face="Arial" color="#000000" size="3"> consist of trunk circumference measurements recorded at time x
</font><font face="Arial" color="#000000" size="2"><sub>j
</sub></font><font face="Arial" color="#000000" size="3">, j=1,...,7 for each of i = 1,..., 5 orange trees. We consider a logistic growth curve as follows:<br><br> Y
</font><font face="Arial" color="#000000" size="2"><sub>ij
</sub></font><font face="Arial" color="#000000" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">h
</font><font face="Arial" color="#000000" size="2"><sub>ij
</sub></font><font face="Arial" color="#000000" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000000" size="3"><sub>c
</sub></font><font face="Arial" color="#000000" size="3">)<br> <br>
</font><font face="Symbol" color="#000100" size="3">h
</font><font face="Arial" color="#000000" size="2"><sub>ij
</sub></font><font face="Arial" color="#000000" size="3"><sub>
</sub></font><font face="Arial" color="#000000" size="3">=
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="2"><sub>i1
</sub></font><font face="Arial" color="#000000" size="3"><br> _______________<br> 1 +
</font><font face="Symbol" color="#000100" size="3"> f
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="2"><sub>i2
</sub></font><font face="Arial" color="#000000" size="3"> exp(
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="2"><sub>i3
</sub></font><font face="Arial" color="#000000" size="3"> x
</font><font face="Arial" color="#000000" size="2"><sub>j
</sub></font><font face="Arial" color="#000000" size="3"><sub>
</sub></font><font face="Arial" color="#000000" size="3">)<br> <br>
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000000" size="2"><sub>i1
</sub></font><font face="Arial" color="#000000" size="3"><sub>
</sub></font><font face="Arial" color="#000000" size="3">= log(
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="2"><sub>i1
</sub></font><font face="Arial" color="#000000" size="3">)
</font><font face="Arial" color="#000000" size="3"><sub> <br>
</sub></font><font face="Symbol" color="#000100" size="3">q
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="2"><sub>i2
</sub></font><font face="Arial" color="#000000" size="3"><sub>
</sub></font><font face="Arial" color="#000000" size="3">= log(
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="2"><sub>i2
</sub></font><font face="Arial" color="#000000" size="3"><sub>
</sub></font><font face="Arial" color="#000000" size="3">+ 1)
</font><font face="Arial" color="#000000" size="3"><sub> <br>
</sub></font><font face="Symbol" color="#000100" size="3">q
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="2"><sub>i3
</sub></font><font face="Arial" color="#000000" size="3"><sub>
</sub></font><font face="Arial" color="#000000" size="3">= log(
</font><font face="Symbol" color="#000100" size="3">-f
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="2"><sub>i3
</sub></font><font face="Arial" color="#000000" size="3">)
</font><font face="Arial" color="#000000" size="3"><sub>
</sub></font><font face="Arial" color="#000000" size="3"><br><br>The BUGS code is as follows<br>
</font><font face="Arial" color="#FF8000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"> model {<br> for (i in 1:K) {<br> for (j in 1:n) {<br> Y[i, j] ~ dnorm(eta[i, j], tauC)<br> eta[i, j] <- phi[i, 1] / (1 + phi[i, 2] * exp(phi[i, 3] * x[j]))<br> &n [...]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Otreesdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><a href="../Examples/Otreesinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Otreesinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="5"> <br><br>
</font><font face="Arial" color="#000100" size="3">The hybrid Metropolis algorithm is used to sample the theta parameters in this model. The step length used for this algorithm adapts for the first 4000 iterations and these samples are discarded from the summary statistics. A further 1000 update burn-in followed by 10000 updates gave the following parameter estimates:<br><center><br><img src="otrees1.bmp" alt="[otrees1]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/OtreesMVN.html b/doc/Examples/OtreesMVN.html
new file mode 100755
index 0000000..0765eb1
--- /dev/null
+++ b/doc/Examples/OtreesMVN.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>OtreesMVN</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="otreesmvn0.bmp" alt="[otreesmvn0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Orange Trees: Non-linear growth<br> curve
</font><font face="Arial" color="#000000" size="5"><br><br>
</font><font face="Arial" color="#000000" size="3">We repeat the Otrees example, replacing the 3 independent univariate Normal priors for each
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="2"><sub>ik
</sub></font><font face="Arial" color="#000000" size="3">, k=1,2,3 by a multivariate Normal prior
</font><font face="Symbol" color="#000100" size="3"><strong>f
</strong></font><font face="Symbol" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="2"><sub>i
</sub></font><font face="Arial" color="#000000" size="3"><sub>
</sub></font><font face="Arial" color="#000000" size="3">~ MNV(
</font><font face="Symbol" color="#000100" size="3"><strong>m
</strong></font><font face="Arial" color="#000000" size="3">,
</font><font face="Symbol" color="#000100" size="3"><strong>T
</strong></font><font face="Arial" color="#000000" size="3">)<br>
</font><font face="Arial" color="#FF8000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"> model {<br> for (i in 1:K) {<br> for (j in 1:n) {<br> Y[i, j] ~ dnorm(eta[i, j], tauC)<br> eta[i, j] <- phi[i, 1] / (1 + phi[i, 2] * exp(phi[i, 3] * x[j]))<br> &n [...]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/OtreesMVNdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><a href="../Examples/OtreesMVNinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/OtreesMVNinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="5"> <br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3">A 4000 iteration Metropolis adaptive phase plus 1000 update burn in followed by a further 10000 updates gave the parameter estimates:<br><center><br><img src="otreesmvn1.bmp" alt="[otreesmvn1]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/OtreesMVNdata.html b/doc/Examples/OtreesMVNdata.html
new file mode 100755
index 0000000..bd453d9
--- /dev/null
+++ b/doc/Examples/OtreesMVNdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>OtreesMVNdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> list(n = 7, K = 5, x = c(118.00, 484.00, 664.00, 1004.00, 1231.00, 1372.00, 1582.00),<br> Y = structure(<br> .Data = c(30.00, 58.00, 87.00, 115.00, 120.00, 142.00, 145.00, <br> 33.00, 69.00, 111.00, 156.00, 172.00, 203.00, 203.00, <br>& [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/OtreesMVNdata.txt b/doc/Examples/OtreesMVNdata.txt
new file mode 100755
index 0000000..127ac09
--- /dev/null
+++ b/doc/Examples/OtreesMVNdata.txt
@@ -0,0 +1,15 @@
+ list(n = 7, K = 5, x = c(118.00, 484.00, 664.00, 1004.00, 1231.00, 1372.00, 1582.00),
+ Y = structure(
+ .Data = c(30.00, 58.00, 87.00, 115.00, 120.00, 142.00, 145.00,
+ 33.00, 69.00, 111.00, 156.00, 172.00, 203.00, 203.00,
+ 30.00, 51.00, 75.00, 108.00, 115.00, 139.00, 140.00,
+ 32.00, 62.00, 112.00, 167.00, 179.00, 209.00, 214.00,
+ 30.00, 49.00, 81.00, 125.00, 142.00, 174.00, 177.00),
+ .Dim = c(5, 7)),
+ mean = c(0, 0, 0),
+ R = structure(.Data = c(0.1, 0, 0,
+ 0, 0.1, 0,
+ 0, 0, 0.1), .Dim = c(3, 3)),
+ prec = structure(.Data = c(1.0E-6, 0, 0,
+ 0, 1.0E-6, 0,
+ 0, 0, 1.0E-6), .Dim = c(3, 3)))
\ No newline at end of file
diff --git a/doc/Examples/OtreesMVNinits.html b/doc/Examples/OtreesMVNinits.html
new file mode 100755
index 0000000..707f3f2
--- /dev/null
+++ b/doc/Examples/OtreesMVNinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>OtreesMVNinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> list(theta = structure(<br> .Data = c(5, 2, -6, <br> 5, 2, -6, <br> 5, 2, -6, <br> 5, 2, -6, <br> &n [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/OtreesMVNinits.txt b/doc/Examples/OtreesMVNinits.txt
new file mode 100755
index 0000000..7553743
--- /dev/null
+++ b/doc/Examples/OtreesMVNinits.txt
@@ -0,0 +1,12 @@
+ list(theta = structure(
+ .Data = c(5, 2, -6,
+ 5, 2, -6,
+ 5, 2, -6,
+ 5, 2, -6,
+ 5, 2, -6),
+ .Dim = c(5, 3)),
+ mu = c(5, 2, -6),
+ tau = structure(.Data = c(0.1, 0, 0,
+ 0, 0.1, 0,
+ 0, 0, 0.1), .Dim = c(3, 3)),
+ tauC = 20)
\ No newline at end of file
diff --git a/doc/Examples/OtreesMVNinits1.html b/doc/Examples/OtreesMVNinits1.html
new file mode 100755
index 0000000..3b639e1
--- /dev/null
+++ b/doc/Examples/OtreesMVNinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>OtreesMVNinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> list(theta = structure(<br> .Data = c(3.0, 1.0, -1.0, <br> 3.0, 1.0, -1.0, <br> 3.0, 1.0, -1.0, <br> 3.0, 1.0, -1.0, <br> &n [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/OtreesMVNinits1.txt b/doc/Examples/OtreesMVNinits1.txt
new file mode 100755
index 0000000..3421eff
--- /dev/null
+++ b/doc/Examples/OtreesMVNinits1.txt
@@ -0,0 +1,12 @@
+ list(theta = structure(
+ .Data = c(3.0, 1.0, -1.0,
+ 3.0, 1.0, -1.0,
+ 3.0, 1.0, -1.0,
+ 3.0, 1.0, -1.0,
+ 3.0, 1.0, -1.0),
+ .Dim = c(5, 3)),
+ mu = c(5, 1.0, -1.0),
+ tau = structure(.Data = c(2.0, 0, 0,
+ 0, 2.0, 0,
+ 0, 0, 2.0), .Dim = c(3, 3)),
+ tauC = 2)
\ No newline at end of file
diff --git a/doc/Examples/OtreesMVNmodel.html b/doc/Examples/OtreesMVNmodel.html
new file mode 100755
index 0000000..9db3684
--- /dev/null
+++ b/doc/Examples/OtreesMVNmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>OtreesMVNmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3"> model {<br> for (i in 1:K) {<br> for (j in 1:n) {<br> Y[i, j] ~ dnorm(eta[i, j], tauC)<br> eta[i, j] <- phi[i, 1] / (1 + phi[i, 2] * exp(phi[i, 3] * x[j]))<br> &nb [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/OtreesMVNmodel.txt b/doc/Examples/OtreesMVNmodel.txt
new file mode 100755
index 0000000..69cab83
--- /dev/null
+++ b/doc/Examples/OtreesMVNmodel.txt
@@ -0,0 +1,18 @@
+ model {
+ for (i in 1:K) {
+ for (j in 1:n) {
+ Y[i, j] ~ dnorm(eta[i, j], tauC)
+ eta[i, j] <- phi[i, 1] / (1 + phi[i, 2] * exp(phi[i, 3] * x[j]))
+ }
+ phi[i, 1] <- exp(theta[i, 1])
+ phi[i, 2] <- exp(theta[i, 2]) - 1
+ phi[i, 3] <- -exp(theta[i, 3])
+ theta[i, 1:3] ~ dmnorm(mu[1:3], tau[1:3, 1:3])
+ }
+ mu[1:3] ~ dmnorm(mean[1:3], prec[1:3, 1:3])
+ tau[1:3, 1:3] ~ dwish(R[1:3, 1:3], 3)
+ sigma2[1:3, 1:3] <- inverse(tau[1:3, 1:3])
+ for (i in 1 : 3) {sigma[i] <- sqrt(sigma2[i, i]) }
+ tauC ~ dgamma(1.0E-3, 1.0E-3)
+ sigmaC <- 1 / sqrt(tauC)
+ }
diff --git a/doc/Examples/Otreesdata.html b/doc/Examples/Otreesdata.html
new file mode 100755
index 0000000..a6f5141
--- /dev/null
+++ b/doc/Examples/Otreesdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Otreesdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(n = 7, K = 5, x = c(118.00, 484.00, 664.00, 1004.00, 1231.00, 1372.00, 1582.00),<br> Y = structure(<br> .Data = c(30.00, 58.00, 87.00, 115.00, 120.00, 142.00, 145.00, <br> 33.00, 69.00, 111.00, 156.00, 172.00, 203.00, 203.00, <br> & [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Otreesdata.txt b/doc/Examples/Otreesdata.txt
new file mode 100755
index 0000000..d561851
--- /dev/null
+++ b/doc/Examples/Otreesdata.txt
@@ -0,0 +1,8 @@
+list(n = 7, K = 5, x = c(118.00, 484.00, 664.00, 1004.00, 1231.00, 1372.00, 1582.00),
+ Y = structure(
+ .Data = c(30.00, 58.00, 87.00, 115.00, 120.00, 142.00, 145.00,
+ 33.00, 69.00, 111.00, 156.00, 172.00, 203.00, 203.00,
+ 30.00, 51.00, 75.00, 108.00, 115.00, 139.00, 140.00,
+ 32.00, 62.00, 112.00, 167.00, 179.00, 209.00, 214.00,
+ 30.00, 49.00, 81.00, 125.00, 142.00, 174.00, 177.00),
+ .Dim = c(5, 7)))
\ No newline at end of file
diff --git a/doc/Examples/Otreesinits.html b/doc/Examples/Otreesinits.html
new file mode 100755
index 0000000..17b6c43
--- /dev/null
+++ b/doc/Examples/Otreesinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Otreesinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(theta = structure(<br> .Data = c(5, 2, -6, <br> 5, 2, -6, <br> 5, 2, -6, <br> 5, 2, -6, <br> &n [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Otreesinits.txt b/doc/Examples/Otreesinits.txt
new file mode 100755
index 0000000..c0f53e5
--- /dev/null
+++ b/doc/Examples/Otreesinits.txt
@@ -0,0 +1,8 @@
+list(theta = structure(
+ .Data = c(5, 2, -6,
+ 5, 2, -6,
+ 5, 2, -6,
+ 5, 2, -6,
+ 5, 2, -6),
+ .Dim = c(5, 3)),
+ mu = c(5, 2, -6), tau = c(20, 20, 20), tauC = 20)
\ No newline at end of file
diff --git a/doc/Examples/Otreesinits1.html b/doc/Examples/Otreesinits1.html
new file mode 100755
index 0000000..9f2828f
--- /dev/null
+++ b/doc/Examples/Otreesinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Otreesinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(theta = structure(<br> .Data = c(3.0, 1.0, -1.0, <br> 3.0, 1.0, -1.0, <br> 3.0, 1.0, -1.0, <br> 3.0, 1.0, -1.0, <br> &n [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Otreesinits1.txt b/doc/Examples/Otreesinits1.txt
new file mode 100755
index 0000000..eb4c2da
--- /dev/null
+++ b/doc/Examples/Otreesinits1.txt
@@ -0,0 +1,8 @@
+list(theta = structure(
+ .Data = c(3.0, 1.0, -1.0,
+ 3.0, 1.0, -1.0,
+ 3.0, 1.0, -1.0,
+ 3.0, 1.0, -1.0,
+ 3.0, 1.0, -1.0),
+ .Dim = c(5, 3)),
+ mu = c(3.0, 1.0, -1.0), tau = c(2, 2, 2), tauC = 2)
\ No newline at end of file
diff --git a/doc/Examples/Otreesmodel.html b/doc/Examples/Otreesmodel.html
new file mode 100755
index 0000000..211fd7a
--- /dev/null
+++ b/doc/Examples/Otreesmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Otreesmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3"> model {<br> for (i in 1:K) {<br> for (j in 1:n) {<br> Y[i, j] ~ dnorm(eta[i, j], tauC)<br> eta[i, j] <- phi[i, 1] / (1 + phi[i, 2] * exp(phi[i, 3] * x[j]))<br> &nb [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Otreesmodel.txt b/doc/Examples/Otreesmodel.txt
new file mode 100755
index 0000000..07d6d40
--- /dev/null
+++ b/doc/Examples/Otreesmodel.txt
@@ -0,0 +1,22 @@
+ model {
+ for (i in 1:K) {
+ for (j in 1:n) {
+ Y[i, j] ~ dnorm(eta[i, j], tauC)
+ eta[i, j] <- phi[i, 1] / (1 + phi[i, 2] * exp(phi[i, 3] * x[j]))
+ }
+ phi[i, 1] <- exp(theta[i, 1])
+ phi[i, 2] <- exp(theta[i, 2]) - 1
+ phi[i, 3] <- -exp(theta[i, 3])
+ for (k in 1:3) {
+ theta[i, k] ~ dnorm(mu[k], tau[k])
+ }
+ }
+ tauC ~ dgamma(1.0E-3, 1.0E-3)
+ sigmaC <- 1 / sqrt(tauC)
+ varC <- 1 / tauC
+ for (k in 1:3) {
+ mu[k] ~ dnorm(0, 1.0E-4)
+ tau[k] ~ dgamma(1.0E-3, 1.0E-3)
+ sigma[k] <- 1 / sqrt(tau[k])
+ }
+ }
diff --git a/doc/Examples/Oxford.html b/doc/Examples/Oxford.html
new file mode 100755
index 0000000..aca5915
--- /dev/null
+++ b/doc/Examples/Oxford.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Oxford</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="oxford0.bmp" alt="[oxford0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Oxford: smooth fit to log-odds<br> ratios
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3">Breslow and Clayton (1993) re-analyse 2 by 2 tables of cases (deaths from childhood cancer) and controls tabulated against maternal exposure to X-rays, one table for each of 120 combinations of age (0-9) and birth year (1944-1964). The data may be arranged to the following form.<br><center><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="oxford1.bmp" alt="[oxford1]">
</font><font face="Arial" color="#000100" size="3"></center>Their most complex model is equivalent to expressing the log(odds-ratio)
</font><font face="Symbol" color="#000100" size="3">y
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> for the table in stratum
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> as<br><br> log
</font><font face="Symbol" color="#000100" size="3">y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">year
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">(year
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> - 22) + b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub><br><br>
</sub></font><font face="Arial" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(0,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">They use a quasi-likelihood approximation of the full hypergeometric likelihood obtained by conditioning on the margins of the tables. <br><br>We let r
</font><font face="Arial" color="#000100" size="2"><sup>0
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> denote number of exposures among the n
</font><font face="Arial" color="#000100" size="2"><sup>0
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> controls in stratum
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">, and r
</font><font face="Arial" color="#000100" size="2"><sup>1
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">denote number of exposures for the n
</font><font face="Arial" color="#000100" size="2"><sup>1
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> cases. The we assume<br><br> r
</font><font face="Arial" color="#000100" size="2"><sup>0
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(p
</font><font face="Arial" color="#000100" size="2"><sup>0
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, n
</font><font face="Arial" color="#000100" size="2"><sup>0
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)
</font><font face="Arial" color="#000100" size="3"><sub><br><br>
</sub></font><font face="Arial" color="#000100" size="3">r
</font><font face="Arial" color="#000100" size="2"><sup>1
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Binomial(p
</font><font face="Arial" color="#000100" size="3"><sup>1
</sup></font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, n
</font><font face="Arial" color="#000100" size="3"><sup>1
</sup></font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br><br> logit(p
</font><font face="Arial" color="#000100" size="2"><sup>0
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><br><br> logit(p
</font><font face="Arial" color="#000100" size="2"><sup>1
</sup></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> + log
</font><font face="Symbol" color="#000100" size="3">y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> <br><br>Assuming this model with independent vague priors for the
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">'s provides the correct conditional likelihood. The appropriate graph is shown below<br>
</font><font face="Arial" color="#0000FF" size="5"><br><center>
</font><font face="Arial" color="#000100" size="2"><img src="oxford2.bmp" alt="[oxford2]"><br><br><br>
</font><font face="Arial" color="#000100" size="3">BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for Oxford example:
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="2"></center>
</font><font face="Arial" color="#000100" size="3"> model<br> {<br> for (i in 1 : K) {<br> r0[i] ~ dbin(p0[i], n0[i])<br> r1[i] ~ dbin(p1[i], n1[i])<br> logit(p0[i]) <- mu[i]<br> logit(p1[i]) <- mu[i] + log [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Oxforddata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><a href="../Examples/Oxfordinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Oxfordinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates <br><center><br><br><img src="oxford3.bmp" alt="[oxford3]"><br></center>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3">These estimates compare well with Breslow and Clayton (1993) PQL estimates of
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000000" size="3"> = 0.566 +/- 0.070,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000000" size="2"><sub>1
</sub></font><font face="Arial" color="#000000" size="3"> = -0.469 +/- 0.0167,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000000" size="2"><sub>2
</sub></font><font face="Arial" color="#000000" size="3"> = 0.0071 +/- 0.0033,
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000000" size="3"> = 0.15 +/- 0.10.<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Oxforddata.html b/doc/Examples/Oxforddata.html
new file mode 100755
index 0000000..9411844
--- /dev/null
+++ b/doc/Examples/Oxforddata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Oxforddata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(r1 = c(3, 5, 2, 7, 7, 2, 5, 3, 5, 11, 6, 6, 11, 4, 4, 2, 8, 8, 6, 5, 15, 4, 9, 9, 4, 12, 8, 8,<br> 6, 8, 12, 4, 7, 16, 12, 9, 4, 7, 8, 11, 5, 12, 8, 17, 9, 3, 2, 7, 6, 5, 11, 14, 13, 8, <br> 6, 4, 8, 4, 8, 7, 15, 15, 9, 9, 5, 6, 3, 9, 12, 14, 16, 17, 8, 8, 9, 5, 9, 11, 6, 14, <br> 21, 16, 6, 9, 8, 9, 8, 4, 11, 11, 6, 9, [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Oxforddata.txt b/doc/Examples/Oxforddata.txt
new file mode 100755
index 0000000..b091a80
--- /dev/null
+++ b/doc/Examples/Oxforddata.txt
@@ -0,0 +1,25 @@
+list(r1 = c(3, 5, 2, 7, 7, 2, 5, 3, 5, 11, 6, 6, 11, 4, 4, 2, 8, 8, 6, 5, 15, 4, 9, 9, 4, 12, 8, 8,
+ 6, 8, 12, 4, 7, 16, 12, 9, 4, 7, 8, 11, 5, 12, 8, 17, 9, 3, 2, 7, 6, 5, 11, 14, 13, 8,
+ 6, 4, 8, 4, 8, 7, 15, 15, 9, 9, 5, 6, 3, 9, 12, 14, 16, 17, 8, 8, 9, 5, 9, 11, 6, 14,
+ 21, 16, 6, 9, 8, 9, 8, 4, 11, 11, 6, 9, 4, 4, 9, 9, 10, 14, 6, 3, 4, 6, 10, 4, 3, 3,
+ 10, 4, 10, 5, 4, 3, 13, 1, 7, 5, 7, 6, 3, 7),
+ n1 = c(28, 21, 32, 35, 35, 38, 30, 43, 49, 53, 31, 35, 46, 53, 61, 40, 29, 44, 52, 55, 61, 31, 48, 44, 42, 53, 56, 71,
+ 43, 43, 43, 40, 44, 70, 75, 71, 37, 31, 42, 46, 47, 55, 63, 91, 43, 39, 35, 32, 53, 49, 75, 64, 69, 64,
+ 49, 29, 40, 27, 48, 43, 61, 77, 55, 60, 46, 28, 33, 32, 46, 57, 56, 78, 58, 52, 31, 28, 46,42 , 45, 63,
+ 71, 69, 43, 50, 31, 34, 54, 46, 58, 62, 52, 41, 34, 52, 63, 59, 88, 62, 47, 53, 57, 74, 68, 61, 45, 45,
+ 62, 73, 53, 39, 45, 51, 55, 41, 53, 51, 42, 46, 54, 32),
+ r0 = c(0, 2, 2, 1, 2, 0, 1, 1, 1, 2, 4, 4, 2, 1, 7, 4, 3, 5, 3, 2, 4, 1, 4, 5, 2, 7, 5, 8,
+ 2, 3, 5, 4, 1, 6, 5, 11, 5, 2, 5, 8, 5, 6, 6, 10, 7, 5, 5, 2, 8, 1, 13, 9, 11, 9,
+ 4, 4, 8, 6, 8, 6, 8, 14, 6, 5, 5, 2, 4, 2, 9, 5, 6, 7, 5, 10, 3, 2, 1, 7, 9, 13,
+ 9, 11, 4, 8, 2, 3, 7, 4, 7, 5, 6, 6, 5, 6, 9, 7, 7, 7, 4, 2, 3, 4, 10, 3, 4, 2,
+ 10, 5, 4, 5, 4, 6, 5, 3, 2, 2, 4, 6, 4, 1),
+ n0 = c(28, 21, 32, 35, 35, 38, 30, 43, 49, 53, 31, 35, 46, 53, 61, 40, 29, 44, 52, 55, 61, 31, 48, 44, 42, 53, 56, 71,
+ 43, 43, 43, 40, 44, 70, 75, 71, 37, 31, 42, 46, 47, 55, 63, 91, 43, 39, 35, 32, 53, 49, 75, 64, 69, 64,
+ 49, 29, 40, 27, 48, 43, 61, 77, 55, 60, 46, 28, 33, 32, 46, 57, 56, 78, 58, 52, 31, 28, 46, 42, 45, 63,
+ 71, 69, 43, 50, 31, 34, 54, 46, 58, 62, 52, 41, 34, 52, 63, 59, 88, 62, 47, 53, 57, 74, 68, 61, 45, 45,
+ 62, 73, 53, 39, 45, 51, 55, 41, 53, 51, 42, 46, 54, 32),
+ year = c(-10, -9, -9, -8, -8, -8, -7, -7, -7, -7, -6, -6, -6, -6, -6, -5, -5, -5, -5, -5, -5, -4, -4, -4, -4, -4, -4, -4,
+ -3, -3, -3, -3, -3, -3, -3, -3, -2, -2, -2, -2, -2, -2, -2, -2, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2,
+ 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 6,
+ 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 9, 9, 10), K = 120)
\ No newline at end of file
diff --git a/doc/Examples/Oxfordinits.html b/doc/Examples/Oxfordinits.html
new file mode 100755
index 0000000..49ab419
--- /dev/null
+++ b/doc/Examples/Oxfordinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Oxfordinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha=0,beta1=0,beta2=0,tau=1,<br>mu=c(0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0, <br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0),<br>b=c(0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0 [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Oxfordinits.txt b/doc/Examples/Oxfordinits.txt
new file mode 100755
index 0000000..bbd42bc
--- /dev/null
+++ b/doc/Examples/Oxfordinits.txt
@@ -0,0 +1,26 @@
+list(alpha=0,beta1=0,beta2=0,tau=1,
+ mu=c(0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0),
+ b=c(0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0)
+ )
\ No newline at end of file
diff --git a/doc/Examples/Oxfordinits1.html b/doc/Examples/Oxfordinits1.html
new file mode 100755
index 0000000..9bf918b
--- /dev/null
+++ b/doc/Examples/Oxfordinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Oxfordinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha=1.0,beta1=1.0,beta2=1.0,tau=0.1,<br>mu=c(0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0, <br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0),<br>b=c(0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0 [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Oxfordinits1.txt b/doc/Examples/Oxfordinits1.txt
new file mode 100755
index 0000000..5fe4748
--- /dev/null
+++ b/doc/Examples/Oxfordinits1.txt
@@ -0,0 +1,26 @@
+list(alpha=1.0,beta1=1.0,beta2=1.0,tau=0.1,
+ mu=c(0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0),
+ b=c(0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0)
+ )
\ No newline at end of file
diff --git a/doc/Examples/Oxfordmodel.html b/doc/Examples/Oxfordmodel.html
new file mode 100755
index 0000000..8840bdd
--- /dev/null
+++ b/doc/Examples/Oxfordmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Oxfordmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for (i in 1 : K) {<br> r0[i] ~ dbin(p0[i], n0[i])<br> r1[i] ~ dbin(p1[i], n1[i])<br> logit(p0[i]) <- mu[i]<br> logit(p1[i]) <- mu[i] + logPsi[i]< [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Oxfordmodel.txt b/doc/Examples/Oxfordmodel.txt
new file mode 100755
index 0000000..f5812fc
--- /dev/null
+++ b/doc/Examples/Oxfordmodel.txt
@@ -0,0 +1,17 @@
+ model
+ {
+ for (i in 1 : K) {
+ r0[i] ~ dbin(p0[i], n0[i])
+ r1[i] ~ dbin(p1[i], n1[i])
+ logit(p0[i]) <- mu[i]
+ logit(p1[i]) <- mu[i] + logPsi[i]
+ logPsi[i] <- alpha + beta1 * year[i] + beta2 * (year[i] * year[i] - 22) + b[i]
+ b[i] ~ dnorm(0, tau)
+ mu[i] ~ dnorm(0.0, 1.0E-6)
+ }
+ alpha ~ dnorm(0.0, 1.0E-6)
+ beta1 ~ dnorm(0.0, 1.0E-6)
+ beta2 ~ dnorm(0.0, 1.0E-6)
+ tau ~ dgamma(1.0E-3, 1.0E-3)
+ sigma <- 1 / sqrt(tau)
+ }
diff --git a/doc/Examples/Pigs.html b/doc/Examples/Pigs.html
new file mode 100755
index 0000000..751c1aa
--- /dev/null
+++ b/doc/Examples/Pigs.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pigs</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="pigs0.bmp" alt="[pigs0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Pigs: genetic counseling and<br> pedigree analysis
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3">Spiegelhalter (1990) uses exact methods to analyse a small pedigree. This pedigree was previously used by Cannings and Thompson (1981) to illustrate their 'peeling' procedure to provide likelihoods for gene frequencies and probabilities for individuals being affected or carriers. We assume the pedigree refers to pigs which have the possibility of carrying a recessive gene: thus each pig has a genotype a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">, a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> or a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">, in which only those with a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> are affected with the trait, while those with a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> are carriers of the defective allele a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">. We assume that Ian (the consequence of a mating between Fred and his Aunt Clare) is yet to be born, and all that is known is that Fred's niece Jane has the trait. We wish to estimate the prevalence p of the allele a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">, and predict the chance of Ian being affected. The conditional probability distributions are as follows. For the genotype of the founder nodes Ann, Brian, Eric and Henry we assume a binomial distribution<br><br> Founder ~ Binomial(q, 2)<br><br>where Founder takes values 0, 1 or 2 for genotypes a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">, a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> and a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> respectively, and q = 1
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">p is the prevalence of the allele a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">. This is equivalent to assuming Hardy Weinberg equilibrium, giving P(a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">) = q
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">, P(a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">) =2 q (1
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">q) , P(a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">) = (1
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">q)
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">.<br><br>For the genotype of offspring we have the standard Mendelian inheritance probabilities given by the following table. <br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="pigs1.bmp" alt="[pigs1]"><br></center>
</font><font face="Arial" color="#000100" size="3"><br>For a recessive gene the genotype-to-phenotype penetrance probabilities are given by:<br><center><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="pigs2.bmp" alt="[pigs2]"><br>
</font><font face="Arial" color="#000100" size="3"></center>The necessary inheritance probabilities are read in from the data file as an array<br><br>BUGS code for Pigs model:
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">q ~ dunif(0,1) # prevalence of a1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">p <- 1 - q # prevalence of a2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Ann1 ~ dbin(q,2); Ann <- Ann1 + 1 # geno. dist. for founder<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Brian1 ~ dbin(q,2); Brian <- Brian1 + 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Clare ~ dcat(p.mendelian[Ann,Brian,]) # geno. dist. for child<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Diane ~ dcat(p.mendelian[Ann,Brian,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Eric1 ~ dbin(q,2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Eric <- Eric1 + 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Fred ~ dcat(p.mendelian[Diane,Eric,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Gene ~ dcat(p.mendelian[Diane,Eric,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Henry1 ~ dbin(q,2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Henry <- Henry1 + 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Ian ~ dcat(p.mendelian[Clare,Fred,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Jane ~ dcat(p.mendelian[Gene,Henry,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">A1 ~ dcat(p.recessive[Ann,]) # phenotype distribution<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">B1 ~ dcat(p.recessive[Brian,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">C1 ~ dcat(p.recessive[Clare,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">D1 ~ dcat(p.recessive[Diane,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">E1 ~ dcat(p.recessive[Eric,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">F1 ~ dcat(p.recessive[Fred,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">G1 ~ dcat(p.recessive[Gene,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">H1 ~ dcat(p.recessive[Henry,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">I1 ~ dcat(p.recessive[Ian,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">J1 ~ dcat(p.recessive[Jane,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">a <- equals(Ann, 2) # event that Ann is carrier<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">b <- equals(Brian, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">c <- equals(Clare, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">d <- equals(Diane, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">e <- equals(Eric, 2) ;<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">f <- equals(Fred, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">g <- equals(Gene, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">h <- equals(Henry, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (J in 1:3) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">i[J] <- equals(Ian, J) # i[1] = a1 a1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># i[2] = a1 a2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># i[3] = a2 a2 (i.e. Ian affected)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"> }
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Pigsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><a href="../Examples/Pigsinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Pigsinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br>
</font><font face="Arial" color="#000000" size="3"><br>Time for 100000 updates 18s on 200MHz Pentium Pro. A 10000 update burn in followed by a further 100000 updates gave the parameter estimates<br><center><br><img src="pigs3.bmp" alt="[pigs3]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="3"></center>We note a number of important tricks. First, each genotype is a 3-valued categorical variable with conditional probabilities either determined by the binomial (Hardy-Weinberg equilibrium) distribution (for founder nodes) or from the Mendelian inheritance probabilities which are stored as a 3-dimensional array
</font><font face="Courier" color="#000100" size="3">p.mendelian
</font><font face="Arial" color="#000100" size="3">. In the latter case, the genotype of the parents picks which row of the matrix is used for the distribution. However, the rows of this matrix are indexed by values 1, 2 or 3, whilst the genotypes of the founder nodes take values 0, 1 or 2. Since BUGS does not allow subscripts to be functions of variables, we must first add 1 to the genotype of the parents (for example,
</font><font face="Courier" color="#000100" size="3">Ann = Ann1 + 1
</font><font face="Arial" color="#000100" size="3">) and use these new variables as subscripts to the matrix
</font><font face="Courier" color="#000100" size="3">p.mendelian
</font><font face="Arial" color="#000100" size="3">. The genotype-to-phenotype distribution is handled similarly in a matrix
</font><font face="Courier" color="#000100" size="3">p.recessive
</font><font face="Arial" color="#000100" size="3">. Second, the
</font><font face="Courier" color="#000100" size="3">equals
</font><font face="Arial" color="#000100" size="3"> function
</font><font face="Courier" color="#000100" size="3">equals(Ann, 2)
</font><font face="Arial" color="#000100" size="3"> allows the calculation of P(Ann's genotype = 2) (i.e. a carrier), whilst
</font><font face="Courier" color="#000100" size="3">equals(Ian, J)
</font><font face="Arial" color="#000100" size="3"> calculates P(Ian's genotype = J), where J=3 implies that Ian is affected.
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Pigsdata.html b/doc/Examples/Pigsdata.html
new file mode 100755
index 0000000..6395f80
--- /dev/null
+++ b/doc/Examples/Pigsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pigsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(p.mendelian = structure(.Data=c(1.0, 0.0, 0.0,<br> 0.5, 0.5, 0.0,<br> 0.0, 1.0, 0.0, <br> &nb [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Pigsdata.txt b/doc/Examples/Pigsdata.txt
new file mode 100755
index 0000000..93648f5
--- /dev/null
+++ b/doc/Examples/Pigsdata.txt
@@ -0,0 +1,13 @@
+list(p.mendelian = structure(.Data=c(1.0, 0.0, 0.0,
+ 0.5, 0.5, 0.0,
+ 0.0, 1.0, 0.0,
+ 0.5, 0.5, 0.0,
+ 0.25, 0.5, 0.25,
+ 0.0, 0.5, 0.5,
+ 0.0, 1.0, 0.0,
+ 0.0, 0.5, 0.5,
+ 0.0, 0.0, 1.0), .Dim=c(3,3,3)),
+ p.recessive = structure(.Data=c(1.0, 0.0,
+ 1.0, 0.0,
+ 0.0, 1.0), .Dim=c(3,2)),
+ A1 = 1, B1 = 1, C1 = 1, D1 = 1, E1 = 1, F1 = 1, G1 = 1, H1 = 1, J1 = 2)
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diff --git a/doc/Examples/Pigsinits.html b/doc/Examples/Pigsinits.html
new file mode 100755
index 0000000..03cba1c
--- /dev/null
+++ b/doc/Examples/Pigsinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pigsinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(Ann1 = 2, Brian1 = 2, Clare = 2, Diane = 2, Eric1 = 2, Fred = 2, Gene = 2, Henry1 = 2, Ian = 2, Jane = 3)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Pigsinits.txt b/doc/Examples/Pigsinits.txt
new file mode 100755
index 0000000..bd1985f
--- /dev/null
+++ b/doc/Examples/Pigsinits.txt
@@ -0,0 +1 @@
+list(Ann1 = 2, Brian1 = 2, Clare = 2, Diane = 2, Eric1 = 2, Fred = 2, Gene = 2, Henry1 = 2, Ian = 2, Jane = 3)
\ No newline at end of file
diff --git a/doc/Examples/Pigsinits1.html b/doc/Examples/Pigsinits1.html
new file mode 100755
index 0000000..8306e97
--- /dev/null
+++ b/doc/Examples/Pigsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pigsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(<br>Ann1 = 2.0,<br>Brian1 = 1.0,<br>Clare = 3.0,<br>Diane = 2.0,<br>Eric1 = 2.0,<br>Fred = 3.0,<br>Gene = 3.0,<br>Henry1 = 2.0,<br>I1 = 2.0,<br>Ian = 3.0,<br>Jane = 3.0,<br>q = 0.7381)<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Pigsinits1.txt b/doc/Examples/Pigsinits1.txt
new file mode 100755
index 0000000..bcd91be
--- /dev/null
+++ b/doc/Examples/Pigsinits1.txt
@@ -0,0 +1,13 @@
+list(
+Ann1 = 2.0,
+Brian1 = 1.0,
+Clare = 3.0,
+Diane = 2.0,
+Eric1 = 2.0,
+Fred = 3.0,
+Gene = 3.0,
+Henry1 = 2.0,
+I1 = 2.0,
+Ian = 3.0,
+Jane = 3.0,
+q = 0.7381)
diff --git a/doc/Examples/Pigsmodel.html b/doc/Examples/Pigsmodel.html
new file mode 100755
index 0000000..c5266f2
--- /dev/null
+++ b/doc/Examples/Pigsmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pigsmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">q ~ dunif(0,1) # prevalence of a1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">p <- 1 - q # prevalence of a2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Ann1 ~ dbin(q,2); Ann <- Ann1 + 1 # geno. dist. for founder<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Brian1 ~ dbin(q,2); Brian <- Brian1 + 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Clare ~ dcat(p.mendelian[Ann,Brian,]) # geno. dist. for child<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Diane ~ dcat(p.mendelian[Ann,Brian,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Eric1 ~ dbin(q,2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Eric <- Eric1 + 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Fred ~ dcat(p.mendelian[Diane,Eric,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Gene ~ dcat(p.mendelian[Diane,Eric,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Henry1 ~ dbin(q,2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Henry <- Henry1 + 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Ian ~ dcat(p.mendelian[Clare,Fred,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Jane ~ dcat(p.mendelian[Gene,Henry,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">A1 ~ dcat(p.recessive[Ann,]) # phenotype distribution<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">B1 ~ dcat(p.recessive[Brian,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">C1 ~ dcat(p.recessive[Clare,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">D1 ~ dcat(p.recessive[Diane,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">E1 ~ dcat(p.recessive[Eric,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">F1 ~ dcat(p.recessive[Fred,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">G1 ~ dcat(p.recessive[Gene,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">H1 ~ dcat(p.recessive[Henry,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">I1 ~ dcat(p.recessive[Ian,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">J1 ~ dcat(p.recessive[Jane,]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">a <- equals(Ann, 2) # event that Ann is carrier<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">b <- equals(Brian, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">c <- equals(Clare, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">d <- equals(Diane, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">e <- equals(Eric, 2) ;<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">f <- equals(Fred, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">g <- equals(Gene, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">h <- equals(Henry, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (J in 1:3) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">i[J] <- equals(Ian, J) # i[1] = a1 a1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># i[2] = a1 a2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># i[3] = a2 a2 (i.e. Ian affected)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"> }
</font><font face="Arial" color="#000100" size="1"><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Pigsmodel.txt b/doc/Examples/Pigsmodel.txt
new file mode 100755
index 0000000..1bf4035
--- /dev/null
+++ b/doc/Examples/Pigsmodel.txt
@@ -0,0 +1,40 @@
+ model
+ {
+ q ~ dunif(0,1) # prevalence of a1
+ p <- 1 - q # prevalence of a2
+ Ann1 ~ dbin(q,2); Ann <- Ann1 + 1 # geno. dist. for founder
+ Brian1 ~ dbin(q,2); Brian <- Brian1 + 1
+ Clare ~ dcat(p.mendelian[Ann,Brian,]) # geno. dist. for child
+ Diane ~ dcat(p.mendelian[Ann,Brian,])
+ Eric1 ~ dbin(q,2)
+ Eric <- Eric1 + 1
+ Fred ~ dcat(p.mendelian[Diane,Eric,])
+ Gene ~ dcat(p.mendelian[Diane,Eric,])
+ Henry1 ~ dbin(q,2)
+ Henry <- Henry1 + 1
+ Ian ~ dcat(p.mendelian[Clare,Fred,])
+ Jane ~ dcat(p.mendelian[Gene,Henry,])
+ A1 ~ dcat(p.recessive[Ann,]) # phenotype distribution
+ B1 ~ dcat(p.recessive[Brian,])
+ C1 ~ dcat(p.recessive[Clare,])
+ D1 ~ dcat(p.recessive[Diane,])
+ E1 ~ dcat(p.recessive[Eric,])
+ F1 ~ dcat(p.recessive[Fred,])
+ G1 ~ dcat(p.recessive[Gene,])
+ H1 ~ dcat(p.recessive[Henry,])
+ I1 ~ dcat(p.recessive[Ian,])
+ J1 ~ dcat(p.recessive[Jane,])
+ a <- equals(Ann, 2) # event that Ann is carrier
+ b <- equals(Brian, 2)
+ c <- equals(Clare, 2)
+ d <- equals(Diane, 2)
+ e <- equals(Eric, 2) ;
+ f <- equals(Fred, 2)
+ g <- equals(Gene, 2)
+ h <- equals(Henry, 2)
+ for (J in 1:3) {
+ i[J] <- equals(Ian, J) # i[1] = a1 a1
+ # i[2] = a1 a2
+ # i[3] = a2 a2 (i.e. Ian affected)
+ }
+ }
diff --git a/doc/Examples/Pigweights.html b/doc/Examples/Pigweights.html
new file mode 100755
index 0000000..6575b7d
--- /dev/null
+++ b/doc/Examples/Pigweights.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pigweights</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#0000FF" size="6"><img src="pigweights0.bmp" alt="[pigweights0]">
</font><font face="Courier New" color="#000100" size="6">Pig Weight Gain
</font><font face="Arial" color="#0000FF" size="6"><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">Histogram smoothing adapted from Example 5.9 from Congdon (2001), p 180. The model illustrates a structured precision matrix for a multivariate normal prior on a multinomial logistic regression model. The model can also be formulated in terms of a structured covariance matrix (see the commented out section of the model) which has a form with elements that decay exponentialy with absolute value of difference in index.
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model{ <br> y[1:s] ~ dmulti(th[1 : s] , n)<br> sum.g <- sum(g[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># smoothed frequencies<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1 : s) { <br> Sm[i] <- n * th[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> g[i] <- exp(gam[i]) <br> th[i] <- g[i] / sum.g<br> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># prior on elements of AR Precision Matrix <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> rho ~ dunif(0, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau ~ dunif(0.5, 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># MVN for logit parameters<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> gam[1 : s] ~ dmnorm(mu[], T[ , ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (j in 1:s) { <br> mu[j] <- -log(s)<br> }<br> # Define Precision Matrix<br> for (j in 2 : s - 1) {<br> T[j, j] <- tau * (1 + pow(rho, 2))<br> }<br> T[1, [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Or Could do in terms of covariance, which is simpler to write but slower<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># for (i in 1 : s) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># for (j in 1 : s) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># cov[i, j] <- pow(rho, abs(i - j)) / tau<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># T[1 : s, 1 : s] <- inverse(cov[ , ])<br> }<br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Pigweightsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="5">
</font><font face="Arial" color="#000000" size="3">( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><a href="../Examples/Pigweightsinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Pigweightsinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br><center><br><img src="pigweights1.bmp" alt="[pigweights1]">
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Pigweightsdata.html b/doc/Examples/Pigweightsdata.html
new file mode 100755
index 0000000..e0ed671
--- /dev/null
+++ b/doc/Examples/Pigweightsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pigweightsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(y = c(1,1,0,7,5,10,30,30,41,48,66,72,56,46,45,22,24,12,5,0,1), n = 522, s = 21)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Pigweightsdata.txt b/doc/Examples/Pigweightsdata.txt
new file mode 100755
index 0000000..69f602e
--- /dev/null
+++ b/doc/Examples/Pigweightsdata.txt
@@ -0,0 +1 @@
+list(y = c(1,1,0,7,5,10,30,30,41,48,66,72,56,46,45,22,24,12,5,0,1), n = 522, s = 21)
\ No newline at end of file
diff --git a/doc/Examples/Pigweightsinits.html b/doc/Examples/Pigweightsinits.html
new file mode 100755
index 0000000..70890bc
--- /dev/null
+++ b/doc/Examples/Pigweightsinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pigweightsinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(gam=c(-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Pigweightsinits.txt b/doc/Examples/Pigweightsinits.txt
new file mode 100755
index 0000000..af552ad
--- /dev/null
+++ b/doc/Examples/Pigweightsinits.txt
@@ -0,0 +1 @@
+list(gam=c(-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3,-3))
\ No newline at end of file
diff --git a/doc/Examples/Pigweightsinits1.html b/doc/Examples/Pigweightsinits1.html
new file mode 100755
index 0000000..d02f682
--- /dev/null
+++ b/doc/Examples/Pigweightsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pigweightsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3">list(gam=c(-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Pigweightsinits1.txt b/doc/Examples/Pigweightsinits1.txt
new file mode 100755
index 0000000..104a061
--- /dev/null
+++ b/doc/Examples/Pigweightsinits1.txt
@@ -0,0 +1 @@
+list(gam=c(-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0))
\ No newline at end of file
diff --git a/doc/Examples/Pigweightsmodel.html b/doc/Examples/Pigweightsmodel.html
new file mode 100755
index 0000000..b941f5a
--- /dev/null
+++ b/doc/Examples/Pigweightsmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pigweightsmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model{ <br> y[1:s] ~ dmulti(th[1 : s] , n)<br> sum.g <- sum(g[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># smoothed frequencies<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1 : s) { <br> Sm[i] <- n * th[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> g[i] <- exp(gam[i]) <br> th[i] <- g[i] / sum.g<br> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># prior on elements of AR Precision Matrix <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> rho ~ dunif(0, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> tau ~ dunif(0.5, 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># MVN for logit parameters<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> gam[1 : s] ~ dmnorm(mu[], T[ , ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (j in 1:s) { <br> mu[j] <- -log(s)<br> }<br> # Define Precision Matrix<br> for (j in 2 : s - 1) {<br> T[j, j] <- tau * (1 + pow(rho, 2))<br> }<br> T[1, [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Or Could do in terms of covariance, which is simpler to write but slower<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># for (i in 1 : s) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># for (j in 1 : s) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># cov[i, j] <- pow(rho, abs(i - j)) / tau<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># T[1 : s, 1 : s] <- inverse(cov[ , ])<br> }<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Pigweightsmodel.txt b/doc/Examples/Pigweightsmodel.txt
new file mode 100755
index 0000000..30eec83
--- /dev/null
+++ b/doc/Examples/Pigweightsmodel.txt
@@ -0,0 +1,40 @@
+ model{
+ y[1:s] ~ dmulti(th[1 : s] , n)
+ sum.g <- sum(g[])
+ # smoothed frequencies
+ for (i in 1 : s) {
+ Sm[i] <- n * th[i]
+ g[i] <- exp(gam[i])
+ th[i] <- g[i] / sum.g
+ }
+ # prior on elements of AR Precision Matrix
+ rho ~ dunif(0, 1)
+ tau ~ dunif(0.5, 10)
+ # MVN for logit parameters
+ gam[1 : s] ~ dmnorm(mu[], T[ , ])
+ for (j in 1:s) {
+ mu[j] <- -log(s)
+ }
+ # Define Precision Matrix
+ for (j in 2 : s - 1) {
+ T[j, j] <- tau * (1 + pow(rho, 2))
+ }
+ T[1, 1] <- tau
+ T[s, s] <- tau
+ for (j in 1 : s -1 ) {
+ T[j, j + 1] <- -tau * rho
+ T[j + 1, j] <- T[j, j + 1]
+ }
+ for (i in 1 : s - 1) {
+ for (j in 2 + i : s) {
+ T[i, j] <- 0; T[j, i] <- 0
+ }
+ }
+ # Or Could do in terms of covariance, which is simpler to write but slower
+ # for (i in 1 : s) {
+ # for (j in 1 : s) {
+ # cov[i, j] <- pow(rho, abs(i - j)) / tau
+ # }
+ # }
+ # T[1 : s, 1 : s] <- inverse(cov[ , ])
+ }
diff --git a/doc/Examples/Pines.html b/doc/Examples/Pines.html
new file mode 100755
index 0000000..267add9
--- /dev/null
+++ b/doc/Examples/Pines.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pines</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"><br><img src="pines0.bmp" alt="[pines0]">
</font><font face="Courier New" color="#000100" size="6">Bayes factors using pseudo priors
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#000100" size="3">Bayes factors using the Carlin and Chib method. For full description see Page 47 of Classic BUGS examples Vol 2.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># standardise data<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(i in 1:N){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Ys[i] <- (Y[i] - mean(Y[])) / sd(Y[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">xs[i] <- (x[i] - mean(x[])) / sd(x[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">zs[i] <- (z[i] - mean(z[])) / sd(z[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># model node<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">j ~ dcat(p[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">p[1] <- 0.9995 p[2] <- 1 - p[1] # use for joint modelling<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># p[1] <- 1 p[2] <- 0 # include for estimating Model 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># p[1] <- 0 p[2] <-1 # include for estimating Model 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">pM2 <- step(j - 1.5)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># model structure<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(i in 1 : N){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[1, i] <- alpha + beta * xs[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[2, i] <- gamma + delta*zs[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Ys[i] ~ dnorm(mu[j, i], tau[j])<br> cumulative.Ys[i] <- cumulative(Ys[i], Ys[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Model 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha ~ dnorm(mu.alpha[j], tau.alpha[j])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta ~ dnorm(mu.beta[j], tau.beta[j])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau[1] ~ dgamma(r1[j], l1[j])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># estimation priors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu.alpha[1]<- 0 tau.alpha[1] <- 1.0E-6 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu.beta[1] <- 0 tau.beta[1] <- 1.0E-4<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">r1[1] <- 0.0001 l1[1] <- 0.0001<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># pseudo-priors <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu.alpha[2]<- 0 tau.alpha[2] <- 256<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu.beta[2] <- 1 tau.beta[2] <- 256<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">r1[2] <- 30 l1[2] <- 4.5<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Model 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">gamma ~ dnorm(mu.gamma[j], tau.gamma[j])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">delta ~ dnorm(mu.delta[j], tau.delta[j])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau[2] ~ dgamma(r2[j], l2[j])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># pseudo-priors <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu.gamma[1] <- 0 tau.gamma[1] <- 400<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu.delta[1] <- 1 tau.delta[1] <- 400<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">r2[1] <- 46 l2[1] <- 4.5<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># estimation priors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu.gamma[2] <- 0 tau.gamma[2] <- 1.0E-6<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu.delta[2] <- 0 tau.delta[2] <- 1.0E-4 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">r2[2] <- 0.0001 l2[2] <- 0.0001<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Pinesdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><a href="../Examples/Pinesinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Pinesinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br><center><br><img src="pines1.bmp" alt="[pines1]"><br>
</font><font face="Arial" color="#000100" size="3"><br></center>corresponding to a Bayes factor of 0.6268 / (1 - 0.6268) x 0.9995 / 0.0005 = .3357
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Pinesdata.html b/doc/Examples/Pinesdata.html
new file mode 100755
index 0000000..a368c25
--- /dev/null
+++ b/doc/Examples/Pinesdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pinesdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(N=42,<br>Y = c(3040, 2470, 3610, 3480, 3810, 2330, 1800, 3110, 3160, 2310,<br>4360, 1880, 3670, 1740, 2250, 2650, 4970, 2620, 2900, 1670,<br>2540, 3840, 3800, 4600, 1900, 2530, 2920, 4990, 1670, 3310,<br>3450, 3600, 2850, 1590, 3770, 3850, 2480, 3570, 2620, 1890,<br>3030,3030),<br>x = c(29.2, 24.7, 32.3, 31.3, 31.5, 24.5, 19.9, 27.3, 27.1, 24.0,<br>33.8, 21.5, 32.2, 22.5, 27.5, 25.6, 34.5, 26.2, 26.7, 21.1,<br>24.1, 30.7, 32.7, 32.6, 22.1, [...]
</font><font face="Arial" color="#000100" size="3"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Pinesdata.txt b/doc/Examples/Pinesdata.txt
new file mode 100755
index 0000000..5cedb92
--- /dev/null
+++ b/doc/Examples/Pinesdata.txt
@@ -0,0 +1,16 @@
+list(N=42,
+Y = c(3040, 2470, 3610, 3480, 3810, 2330, 1800, 3110, 3160, 2310,
+ 4360, 1880, 3670, 1740, 2250, 2650, 4970, 2620, 2900, 1670,
+ 2540, 3840, 3800, 4600, 1900, 2530, 2920, 4990, 1670, 3310,
+ 3450, 3600, 2850, 1590, 3770, 3850, 2480, 3570, 2620, 1890,
+ 3030,3030),
+ x = c(29.2, 24.7, 32.3, 31.3, 31.5, 24.5, 19.9, 27.3, 27.1, 24.0,
+ 33.8, 21.5, 32.2, 22.5, 27.5, 25.6, 34.5, 26.2, 26.7, 21.1,
+ 24.1, 30.7, 32.7, 32.6, 22.1, 25.3, 30.8, 38.9, 22.1, 29.2,
+ 30.1, 31.4, 26.7, 22.1, 30.3, 32.0, 23.2, 30.3, 29.9, 20.8,
+ 33.2, 28.2),
+ z = c(25.4, 22.2, 32.2, 31.0, 30.9, 23.9, 19.2, 27.2, 26.3, 23.9,
+ 33.2, 21.0, 29.0, 22.0, 23.8, 25.3, 34.2, 25.7, 26.4, 20.0,
+ 23.9, 30.7, 32.6, 32.5, 20.8, 23.1, 29.8, 38.1, 21.3, 28.5,
+ 29.2, 31.4, 25.9, 21.4, 29.8, 30.6, 22.6, 30.3, 23.8, 18.4,
+ 29.4, 28.2))
diff --git a/doc/Examples/Pinesinits.html b/doc/Examples/Pinesinits.html
new file mode 100755
index 0000000..1b22cd7
--- /dev/null
+++ b/doc/Examples/Pinesinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pinesinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(j = 2, tau = c(1,1), alpha = 0, beta = 0, gamma = 0, delta = 0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Pinesinits.txt b/doc/Examples/Pinesinits.txt
new file mode 100755
index 0000000..3f1a5f8
--- /dev/null
+++ b/doc/Examples/Pinesinits.txt
@@ -0,0 +1 @@
+list(j = 2, tau = c(1,1), alpha = 0, beta = 0, gamma = 0, delta = 0)
\ No newline at end of file
diff --git a/doc/Examples/Pinesinits1.html b/doc/Examples/Pinesinits1.html
new file mode 100755
index 0000000..cd243ac
--- /dev/null
+++ b/doc/Examples/Pinesinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pinesinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(j = 1, tau = c(0.1,0.1), alpha = 1.0, beta = 1.0, gamma = 1.0, delta = 1.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Pinesinits1.txt b/doc/Examples/Pinesinits1.txt
new file mode 100755
index 0000000..2a2f220
--- /dev/null
+++ b/doc/Examples/Pinesinits1.txt
@@ -0,0 +1 @@
+list(j = 1, tau = c(0.1,0.1), alpha = 1.0, beta = 1.0, gamma = 1.0, delta = 1.0)
\ No newline at end of file
diff --git a/doc/Examples/Pumps.html b/doc/Examples/Pumps.html
new file mode 100755
index 0000000..cf886e2
--- /dev/null
+++ b/doc/Examples/Pumps.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pumps</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="pumps0.bmp" alt="[pumps0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Pumps: conjugate gamma-Poisson<br> hierarchical model
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>George
</font><font face="Arial" color="#000100" size="3"><em>et al
</em></font><font face="Arial" color="#000100" size="3"> (1993) discuss Bayesian analysis of hierarchical models where the conjugate prior is adopted at the first level, but for any given prior distribution of the hyperparameters, the joint posterior is not of closed form. The example they consider relates to 10 power plant pumps. The number of failures x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is assumed to follow a Poisson distribution<br><br> x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Poisson(
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) i = 1,...,10 <br><br>where
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is the failure rate for pump
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> and t
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is the length of operation time of the pump (in 1000s of hours). The data are shown below.<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="pumps1.bmp" alt="[pumps1]">
</font><font face="Arial" color="#000100" size="3"><br></center>A conjugate gamma prior distribution is adopted for the failure rates:<br><br>
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Gamma(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">), i = 1,...,10<br><br>George
</font><font face="Arial" color="#000100" size="3"><em>et al
</em></font><font face="Arial" color="#000100" size="3"> (1993) assume the following prior specification for the hyperparameters
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">~ Exponential(1.0)<br>
</font><font face="Symbol" color="#000100" size="3">b ~
</font><font face="Arial" color="#000100" size="3">Gamma(0.1, 1.0)<br><br>They show that this gives a posterior for
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> which is a gamma distribution, but leads to a non-standard posterior for
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">. Consequently, they use the Gibbs sampler to simulate the required posterior densities. <br>
</font><font face="Arial" color="#000100" size="2"><br><br><br><center>
</font><font face="Arial" color="#000100" size="3"><em>Graphical model for pump example:
</em></font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="pumps2.bmp" alt="[pumps2]"><br><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3">BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for pump example:
</em></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="2"></center>
</font><font face="Arial" color="#000100" size="3"><br> model<br> {<br> for (i in 1 : N) {<br> theta[i] ~ dgamma(alpha, beta)<br> lambda[i] <- theta[i] * t[i]<br> x[i] ~ dpois(lambda[i])<br> }<br> & [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Pumpsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><a href="../Examples/Pumpsinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Pumpsinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>A burn in of 1000 updates followed by a futher 10000 updates gave the parameter estimates:<br><center>
</font><font face="Arial" color="#000000" size="3"><br><img src="pumps3.bmp" alt="[pumps3]">
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Pumpsdata.html b/doc/Examples/Pumpsdata.html
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index 0000000..770b11e
--- /dev/null
+++ b/doc/Examples/Pumpsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pumpsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(t = c(94.3, 15.7, 62.9, 126, 5.24, 31.4, 1.05, 1.05, 2.1, 10.5),<br> x = c( 5, 1, 5, 14, 3, 19, 1, 1, 4, 22), N = 10)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Pumpsdata.txt b/doc/Examples/Pumpsdata.txt
new file mode 100755
index 0000000..f92f702
--- /dev/null
+++ b/doc/Examples/Pumpsdata.txt
@@ -0,0 +1,2 @@
+list(t = c(94.3, 15.7, 62.9, 126, 5.24, 31.4, 1.05, 1.05, 2.1, 10.5),
+ x = c( 5, 1, 5, 14, 3, 19, 1, 1, 4, 22), N = 10)
\ No newline at end of file
diff --git a/doc/Examples/Pumpsinits.html b/doc/Examples/Pumpsinits.html
new file mode 100755
index 0000000..6eea1aa
--- /dev/null
+++ b/doc/Examples/Pumpsinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pumpsinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = 1, beta = 1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Pumpsinits.txt b/doc/Examples/Pumpsinits.txt
new file mode 100755
index 0000000..4725772
--- /dev/null
+++ b/doc/Examples/Pumpsinits.txt
@@ -0,0 +1 @@
+list(alpha = 1, beta = 1)
\ No newline at end of file
diff --git a/doc/Examples/Pumpsinits1.html b/doc/Examples/Pumpsinits1.html
new file mode 100755
index 0000000..5092937
--- /dev/null
+++ b/doc/Examples/Pumpsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pumpsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = 10, beta = 10)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Pumpsinits1.txt b/doc/Examples/Pumpsinits1.txt
new file mode 100755
index 0000000..8497141
--- /dev/null
+++ b/doc/Examples/Pumpsinits1.txt
@@ -0,0 +1 @@
+list(alpha = 10, beta = 10)
\ No newline at end of file
diff --git a/doc/Examples/RCdata.html b/doc/Examples/RCdata.html
new file mode 100755
index 0000000..a148dc9
--- /dev/null
+++ b/doc/Examples/RCdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>RCdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"># data used here is 1993 calibration curve<br>calBP[] C14BP[]<br>0 0 <br>10 178 <br>30 126 <br>50 85 <br>70 113 <br>90 120 <br>110 118 <br>125 101 <br>140 148 <br>160 219 <br>180 176 <br>200 169 <br>220 136 <br>240 110 <br>260 136 <br>280 207 <br>300 272 <br>320 334 <br>340 371 <br>360 349 <br>380 341 <br>400 322 <br>420 319 <br>440 362 <br>460 365 <br>480 405 <br>490 411 <br>500 425 <br>520 502 <br>540 540 <br>560 622 <br>580 654 <br>600 625 <b [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/RCdata.txt b/doc/Examples/RCdata.txt
new file mode 100755
index 0000000..9402ecf
--- /dev/null
+++ b/doc/Examples/RCdata.txt
@@ -0,0 +1,788 @@
+# data used here is 1993 calibration curve
+calBP[] C14BP[]
+ 0 0
+ 10 178
+ 30 126
+ 50 85
+ 70 113
+ 90 120
+ 110 118
+ 125 101
+ 140 148
+ 160 219
+ 180 176
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<html>
<head>
<title>Rats-drop</title>
</head>
<body>
<p>
<font face="Arial" color="#0000FF" size="5"><strong><img src="rats-drop0.bmp" alt="[rats-drop0]"> Rats-drop: the rats example, illustrating the<br> effect of different dropout assumptions<br>
</strong></font><font face="Arial" color="#000100" size="2"><br>This example is taken from section 6 of Gelfand
</font><font face="Arial" color="#000100" size="2"><em>et al
</em></font><font face="Arial" color="#000100" size="2"> (1990), and concerns 30 young rats whose weights were measured weekly for five weeks. Part of the data is shown below, where Y
</font><font face="Arial" color="#000100" size="1"><sub>ij
</sub></font><font face="Arial" color="#000100" size="2">is the weight of the ith rat measured at age x
</font><font face="Arial" color="#000100" size="1"><sub>j
</sub></font><font face="Arial" color="#000100" size="2">. <br><br> Weights Y
</font><font face="Arial" color="#000100" size="1"><sub>ij
</sub></font><font face="Arial" color="#000100" size="2"> of rat i on day x
</font><font face="Arial" color="#000100" size="1"><sub>j
</sub></font><font face="Arial" color="#000100" size="2"><br> x
</font><font face="Arial" color="#000100" size="1"><sub>j
</sub></font><font face="Arial" color="#000100" size="2"> = 8 15 22 29 36 <br> __________________________________ <br> Rat 1 151 199 246 283 320<br> Rat 2 145 199 249 293 &nb [...]
</font><font face="Arial" color="#000100" size="3">Y
</font><font face="Arial" color="#000100" size="1"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(x
</font><font face="Arial" color="#000100" size="1"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> - x
</font><font face="Arial" color="#000100" size="1"><sub>bar
</sub></font><font face="Arial" color="#000100" size="3">),
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="1"><sub>c
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br>
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="1"><sub>c
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Symbol" color="#000100" size="1"><sub>a
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br>
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="1"><sub>c
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Symbol" color="#000100" size="1"><sub>b
</sub></font><font face="Arial" color="#000100" size="3">)
</font><font face="Arial" color="#000100" size="2"><br> <br>where x
</font><font face="Arial" color="#000100" size="1"><sub>bar
</sub></font><font face="Arial" color="#000100" size="2"> = 22, and
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"> represents the
</font><font face="Arial" color="#000100" size="2"><em>precision
</em></font><font face="Arial" color="#000100" size="2"> (1/variance) of a normal distribution. We note the absence of a parameter representing correlation between
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="2"> and
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="2"> unlike in Gelfand
</font><font face="Arial" color="#000100" size="2"><em>et al
</em></font><font face="Arial" color="#000100" size="2"> 1990. However, see the
</font><font face="Courier" color="#000100" size="2">Birats
</font><font face="Arial" color="#000100" size="2"> example in Volume 2 which does explicitly model the covariance between
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="2">and
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="2">. For now, we standardise the x
</font><font face="Arial" color="#000100" size="1"><sub>j
</sub></font><font face="Arial" color="#000100" size="2">'s around their mean to reduce dependence between
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="2"> and
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="2"> in their likelihood: in fact for the full balanced data, complete independence is achieved. (Note that, in general, prior independence does not force the posterior distributions to be independent).<br><br>
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="1"><sub>c
</sub></font><font face="Arial" color="#000100" size="2"> ,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Symbol" color="#000100" size="1"><sub>a
</sub></font><font face="Arial" color="#000100" size="2">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="1"><sub>c
</sub></font><font face="Arial" color="#000100" size="2">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Symbol" color="#000100" size="1"><sub>b
</sub></font><font face="Arial" color="#000100" size="2">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="1"><sub>c
</sub></font><font face="Arial" color="#000100" size="2">are given independent ``noninformative'' priors. Interest particularly focuses on the intercept at zero time (birth), denoted
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="1"><sub>0
</sub></font><font face="Arial" color="#000100" size="2"> =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="1"><sub>c
</sub></font><font face="Arial" color="#000100" size="2"> -
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="1"><sub>c
</sub></font><font face="Arial" color="#000100" size="2"> x
</font><font face="Arial" color="#000100" size="1"><sub>bar
</sub></font><font face="Arial" color="#000100" size="2">. <br><br>
</font><font face="Arial" color="#000100" size="3"><center>
</font><font face="Arial" color="#000100" size="3"><em>Graphical model for rats example:
</em></font><font face="Arial" color="#0000FF" size="5"><strong><br><img src="rats-drop1.bmp" alt="[rats-drop1]">
</strong></font><font face="Arial" color="#000100" size="3"><br><br>BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for rats example:
</em></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2"><br><img src="rats-drop2.bmp" alt="[rats-drop2]"><br><br><br></center><br>Note the use of a very flat but conjugate prior for the population effects: a locally uniform prior could also have been used.
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Data
</font><font face="Arial" color="#000100" size="2"> click on one of the arrows to open the data <br><br>(Note: the response data (Y) for the rats example can also be found in the file ratsy.odc in rectangular format. The covariate data (X) can be found in S-Plus format in file ratsx.odc. To load data from each of these files, focus the window containing the open data file before clicking on "Data" from the "Model" menu.)<br><br>
</font><font face="Arial" color="#0000FF" size="5">Inits
</font><font face="Arial" color="#000100" size="2">list( alpha.c = 150, beta.c = 10, <br> tau.c = 1, alpha.tau = 1, beta.tau = 1)<br>
</font><font face="Arial" color="#000100" size="2"><br>Gelfand
</font><font face="Arial" color="#000100" size="2"><em>et al
</em></font><font face="Arial" color="#000100" size="2"> 1990 also consider the problem of missing data, and delete the last observation of cases 6-10, the last two from 11-20, the last 3 from 21-25 and the last 4 from 26-30. The appropriate data file is obtained by simply replacing data values by NA (see below). The model specification is unchanged, since the distinction between observed and unobserved quantities is made in the data file and not the model specification.<br>
</font><font face="Arial" color="#000100" size="2"><br> click on one of the arrows to open the data for the missing value analysis <br> <br>Missing at random gives beta.c estimate of 6.54 (6.26 to 6.84)<br> <br> &n [...]
</font><font face="Arial" color="#000100" size="3"> Extra data list for sensitivity analysis in informative dropout model
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#FF0000" size="5"> list(k=0.02)
</font><font face="Arial" color="#000100" size="2"><br> <img src="rats-drop9.bmp" alt="[rats-drop9]"><br>
</font><font face="Arial" color="#000100" size="2"><br>Initial values for informative dropout model, probability of missing depending on Y[i,j] with a as intercept<br>
</font><font face="Arial" color="#0000FF" size="5">Inits
</font><font face="Arial" color="#000100" size="2">list( alpha.c = 250, beta.c =6, tau.c = 1, alpha.tau = 1, beta.tau = 1, a = 0)
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3">Second set of initial values
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="2">list( alpha.c = 100, beta.c =4, tau.c = .1, alpha.tau = .1, beta.tau = .1, a = 1)
</font><font face="Arial" color="#000100" size="2"><br><br><br><br>With k=.02, get estimate of beta.c
</font><font face="Arial" color="#000100" size="1"><strong> <br><br>node mean sd MC error 2.5% median 97.5% start sample<br>
</strong></font><font face="Arial" color="#000100" size="1"> beta.c 6.273 0.15 0.009028 5.976 6.276 6.561 1001 3000<br> <br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Rats.html b/doc/Examples/Rats.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Rats</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="rats0.bmp" alt="[rats0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Rats: a normal hierarchical model
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><br>This example is taken from section 6 of Gelfand
</font><font face="Arial" color="#000100" size="3"><em>et al
</em></font><font face="Arial" color="#000100" size="3"> (1990), and concerns 30 young rats whose weights were measured weekly for five weeks. Part of the data is shown below, where Y
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">is the weight of the ith rat measured at age x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">. <br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="rats1.bmp" alt="[rats1]"><br></center>
</font><font face="Arial" color="#000100" size="3"><br>A plot of the 30 growth curves suggests some evidence of downward curvature.<br><br>The model is essentially a random effects linear growth curve<br><br> Y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">(x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> - x
</font><font face="Arial" color="#000100" size="2"><sub>bar
</sub></font><font face="Arial" color="#000100" size="3">),
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Symbol" color="#000100" size="2"><sub>a
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Symbol" color="#000100" size="2"><sub>b
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>where x
</font><font face="Arial" color="#000100" size="2"><sub>ba
</sub></font><font face="Arial" color="#000100" size="3"><sub>r
</sub></font><font face="Arial" color="#000100" size="3"> = 22, and
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> represents the
</font><font face="Arial" color="#000100" size="3"><em>precision
</em></font><font face="Arial" color="#000100" size="3"> (1/variance) of a normal distribution. We note the absence of a parameter representing correlation between
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> unlike in Gelfand
</font><font face="Arial" color="#000100" size="3"><em>et al
</em></font><font face="Arial" color="#000100" size="3"> 1990. However, see the
</font><font face="Courier" color="#000100" size="3">Birats
</font><font face="Arial" color="#000100" size="3"> example in Volume 2 which does explicitly model the covariance between
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">. For now, we standardise the x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">'s around their mean to reduce dependence between
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> in their likelihood: in fact for the full balanced data, complete independence is achieved. (Note that, in general, prior independence does not force the posterior distributions to be independent).<br><br>
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3"> ,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Symbol" color="#000100" size="2"><sub>a
</sub></font><font face="Symbol" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Symbol" color="#000100" size="2"><sub>b
</sub></font><font face="Symbol" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">are given independent ``noninformative'' priors. Interest particularly focuses on the intercept at zero time (birth), denoted
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3"> -
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3"> x
</font><font face="Arial" color="#000100" size="2"><sub>bar
</sub></font><font face="Arial" color="#000100" size="3">. <br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><em><center>Graphical model for rats example:
</em></font><font face="Arial" color="#0000FF" size="5"><strong><br><img src="rats2.bmp" alt="[rats2]">
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br><br>BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for rats example:
</em></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br></center><br>
</font><font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : N ) {<br> for( j in 1 : T ) {<br> Y[i , j] ~ dnorm(mu[i , j],tau.c)<br> mu[i , j] <- alpha[i] + beta[i] * (x[j] - xbar)<br> &nb [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Note the use of a very flat but conjugate prior for the population effects: a locally uniform prior could also have been used.<br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Ratsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><a href="../Examples/Ratsinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Ratsinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="3"><br>(Note: the response data (Y) for the rats example can also be found in the file ratsy.odc in rectangular format. The covariate data (x) can be found in S-Plus format in file ratsx.odc. To load data from each of these files, focus the window containing the open data file before clicking on "load data" from the "Specification" dialog.)<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates:<br><center>
</font><font face="Arial" color="#000000" size="2"><br><img src="rats3.bmp" alt="[rats3]"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"></center>
</font><font face="Arial" color="#000100" size="3">These results may be compared with Figure 5 of Gelfand
</font><font face="Arial" color="#000100" size="3"><em>et al
</em></font><font face="Arial" color="#000100" size="3"> 1990 --- we note that the mean gradient of independent fitted straight lines is 6.19.<br><br>Gelfand
</font><font face="Arial" color="#000100" size="3"><em>et al
</em></font><font face="Arial" color="#000100" size="3"> 1990 also consider the problem of missing data, and delete the last observation of cases 6-10, the last two from 11-20, the last 3 from 21-25 and the last 4 from 26-30. The appropriate data file is obtained by simply replacing data values by NA (see below). The model specification is unchanged, since the distinction between observed and unobserved quantities is made in the data file and not the model specification.<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Ratsmissdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Gelfand
</font><font face="Arial" color="#000100" size="3"><em>et al
</em></font><font face="Arial" color="#000100" size="3"> 1990 focus on the parameter estimates and the predictions for the final 4 observations on rat 26. These predictions are obtained automatically in
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> by monitoring the relevant Y[] nodes. The following estimates were obtained:<br><center>
</font><font face="Arial" color="#000100" size="2"><br><img src="rats4.bmp" alt="[rats4]"></center>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">We note that our estimate 6.58 of
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>c
</sub></font><font face="Arial" color="#000100" size="3"> is substantially greater than that shown in Figure 6 of Gelfand
</font><font face="Arial" color="#000100" size="3"><em>et
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><em>al
</em></font><font face="Arial" color="#000100" size="3">1990. However, plotting the growth curves indicates some curvature with steeper gradients at the beginning: the mean of the estimated gradients of the reduced data is 6.66, compared to 6.19 for the full data. Hence we are inclined to believe our analysis. The observed weights for rat 26 were 207, 257, 303 and 345, compared to our predictions of 204, 250, 295 and 341.
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Ratsdata.html b/doc/Examples/Ratsdata.html
new file mode 100755
index 0000000..db89fb8
--- /dev/null
+++ b/doc/Examples/Ratsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ratsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(x = c(8.0, 15.0, 22.0, 29.0, 36.0), xbar = 22, N = 30, T = 5, <br> Y = structure(<br> .Data = c(151, 199, 246, 283, 320,<br> 145, 199, 249, 293, 354,<br> & [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Ratsdata.txt b/doc/Examples/Ratsdata.txt
new file mode 100755
index 0000000..d51a88f
--- /dev/null
+++ b/doc/Examples/Ratsdata.txt
@@ -0,0 +1,33 @@
+list(x = c(8.0, 15.0, 22.0, 29.0, 36.0), xbar = 22, N = 30, T = 5,
+ Y = structure(
+ .Data = c(151, 199, 246, 283, 320,
+ 145, 199, 249, 293, 354,
+ 147, 214, 263, 312, 328,
+ 155, 200, 237, 272, 297,
+ 135, 188, 230, 280, 323,
+ 159, 210, 252, 298, 331,
+ 141, 189, 231, 275, 305,
+ 159, 201, 248, 297, 338,
+ 177, 236, 285, 350, 376,
+ 134, 182, 220, 260, 296,
+ 160, 208, 261, 313, 352,
+ 143, 188, 220, 273, 314,
+ 154, 200, 244, 289, 325,
+ 171, 221, 270, 326, 358,
+ 163, 216, 242, 281, 312,
+ 160, 207, 248, 288, 324,
+ 142, 187, 234, 280, 316,
+ 156, 203, 243, 283, 317,
+ 157, 212, 259, 307, 336,
+ 152, 203, 246, 286, 321,
+ 154, 205, 253, 298, 334,
+ 139, 190, 225, 267, 302,
+ 146, 191, 229, 272, 302,
+ 157, 211, 250, 285, 323,
+ 132, 185, 237, 286, 331,
+ 160, 207, 257, 303, 345,
+ 169, 216, 261, 295, 333,
+ 157, 205, 248, 289, 316,
+ 137, 180, 219, 258, 291,
+ 153, 200, 244, 286, 324),
+ .Dim = c(30,5)))
\ No newline at end of file
diff --git a/doc/Examples/Ratsinits.html b/doc/Examples/Ratsinits.html
new file mode 100755
index 0000000..c64e903
--- /dev/null
+++ b/doc/Examples/Ratsinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ratsinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = c(250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, <br> 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250),<br> beta = c(6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, <br> &n [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Ratsinits.txt b/doc/Examples/Ratsinits.txt
new file mode 100755
index 0000000..8b54873
--- /dev/null
+++ b/doc/Examples/Ratsinits.txt
@@ -0,0 +1,6 @@
+list(alpha = c(250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250,
+ 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250, 250),
+ beta = c(6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
+ 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6),
+ alpha.c = 150, beta.c = 10,
+ tau.c = 1, alpha.tau = 1, beta.tau = 1)
\ No newline at end of file
diff --git a/doc/Examples/Ratsinits1.html b/doc/Examples/Ratsinits1.html
new file mode 100755
index 0000000..da10f98
--- /dev/null
+++ b/doc/Examples/Ratsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ratsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = c(25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, <br> 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0),<br> beta = c(0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, <br> &n [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Ratsinits1.txt b/doc/Examples/Ratsinits1.txt
new file mode 100755
index 0000000..442c0d8
--- /dev/null
+++ b/doc/Examples/Ratsinits1.txt
@@ -0,0 +1,6 @@
+list(alpha = c(25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0,
+ 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0, 25.0),
+ beta = c(0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6,
+ 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6),
+ alpha.c = 15.0, beta.c = 1.0,
+ tau.c = 0.1, alpha.tau = 0.1, beta.tau = 0.1)
\ No newline at end of file
diff --git a/doc/Examples/Ratsmissdata.html b/doc/Examples/Ratsmissdata.html
new file mode 100755
index 0000000..9dbdefe
--- /dev/null
+++ b/doc/Examples/Ratsmissdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ratsmissdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"> list(x = c(8.0, 15.0, 22.0, 29.0, 36.0), xbar = 22, N = 30, T = 5, <br> Y = structure(<br> .Data = c(151, 199, 246, 283, 320,<br> 145, 199, 249, 293, 354,<br> & [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Ratsmissdata.txt b/doc/Examples/Ratsmissdata.txt
new file mode 100755
index 0000000..552f67b
--- /dev/null
+++ b/doc/Examples/Ratsmissdata.txt
@@ -0,0 +1,33 @@
+ list(x = c(8.0, 15.0, 22.0, 29.0, 36.0), xbar = 22, N = 30, T = 5,
+ Y = structure(
+ .Data = c(151, 199, 246, 283, 320,
+ 145, 199, 249, 293, 354,
+ 147, 214, 263, 312, 328,
+ 155, 200, 237, 272, 297,
+ 135, 188, 230, 280, 323,
+ 159, 210, 252, 298, NA,
+ 141, 189, 231, 275, NA,
+ 159, 201, 248, 297, NA,
+ 177, 236, 285, 350, NA,
+ 134, 182, 220, 260, NA,
+ 160, 208, 261, 313, NA,
+ 143, 188, 220, NA, NA,
+ 154, 200, 244, NA, NA,
+ 171, 221, 270, NA, NA,
+ 163, 216, 242, NA, NA,
+ 160, 207, 248, NA, NA,
+ 142, 187, 234, NA, NA,
+ 156, 203, 243, NA, NA,
+ 157, 212, 259, NA, NA,
+ 152, 203, 246, NA, NA,
+ 154, 205, 253, NA, NA,
+ 139, 190, NA, NA, NA,
+ 146, 191, NA, NA, NA,
+ 157, 211, NA, NA, NA,
+ 132, 185, NA, NA, NA,
+ 160, NA, NA, NA, NA,
+ 169, NA, NA, NA, NA,
+ 157, NA, NA, NA, NA,
+ 137, NA, NA, NA, NA,
+ 153, NA, NA, NA, NA),
+ .Dim = c(30,5)))
\ No newline at end of file
diff --git a/doc/Examples/Ratsmodel.html b/doc/Examples/Ratsmodel.html
new file mode 100755
index 0000000..e09e9bf
--- /dev/null
+++ b/doc/Examples/Ratsmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ratsmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : N ) {<br> for( j in 1 : T ) {<br> Y[i , j] ~ dnorm(mu[i , j],tau.c)<br> mu[i , j] <- alpha[i] + beta[i] * (x[j] - xbar)<br> &nbs [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Ratsmodel.txt b/doc/Examples/Ratsmodel.txt
new file mode 100755
index 0000000..cbe7c7a
--- /dev/null
+++ b/doc/Examples/Ratsmodel.txt
@@ -0,0 +1,18 @@
+ model
+ {
+ for( i in 1 : N ) {
+ for( j in 1 : T ) {
+ Y[i , j] ~ dnorm(mu[i , j],tau.c)
+ mu[i , j] <- alpha[i] + beta[i] * (x[j] - xbar)
+ }
+ alpha[i] ~ dnorm(alpha.c,alpha.tau)
+ beta[i] ~ dnorm(beta.c,beta.tau)
+ }
+ tau.c ~ dgamma(0.001,0.001)
+ sigma <- 1 / sqrt(tau.c)
+ alpha.c ~ dnorm(0.0,1.0E-6)
+ alpha.tau ~ dgamma(0.001,0.001)
+ beta.c ~ dnorm(0.0,1.0E-6)
+ beta.tau ~ dgamma(0.001,0.001)
+ alpha0 <- alpha.c - xbar * beta.c
+ }
diff --git a/doc/Examples/Ratsx.html b/doc/Examples/Ratsx.html
new file mode 100755
index 0000000..c523ee1
--- /dev/null
+++ b/doc/Examples/Ratsx.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ratsx</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(x = c(8.0, 15.0, 22.0, 29.0, 36.0), xbar = 22, N = 30, T = 5)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Ratsy.html b/doc/Examples/Ratsy.html
new file mode 100755
index 0000000..c91c6ba
--- /dev/null
+++ b/doc/Examples/Ratsy.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ratsy</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">Y[,1] Y[,2] Y[,3] Y[,4] Y[,5]<br>151 199 246 283 320<br>145 199 249 293 354<br>147 214 263 312 328<br>155 200 237 272 &nb [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Salm.html b/doc/Examples/Salm.html
new file mode 100755
index 0000000..36f12a8
--- /dev/null
+++ b/doc/Examples/Salm.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Salm</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="salm0.bmp" alt="[salm0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Salm: extra - Poisson variation<br> in dose - response study
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><br>Breslow (1984) analyses some mutagenicity assay data (shown below) on salmonella in which three plates have been processed at each dose
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> of quinoline and the number of revertant colonies of TA98 Salmonella measured. A certain dose-response curve is suggested by theory.<br>
</font><font face="Arial" color="#000100" size="2"><br><img src="salm1.bmp" alt="[salm1]">
</font><font face="Arial" color="#000100" size="3"><br>This is assumed to be a random effects Poisson model allowing for over-dispersion. Let x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> be the dose on the plates
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">1,
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">2 and
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3">3. Then we assume<br><br> y
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> ~ Poisson(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">)<br><br> log(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">log(x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> + 10) +
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(0,
</font><font face="Symbol" color="#000100" size="3"> t
</font><font face="Arial" color="#000100" size="3">)<br><br>
</font><font face="Symbol" color="#000100" size="3">a , b , g , t
</font><font face="Arial" color="#000100" size="3">are given independent ``noninformative'' priors. The appropriate graph is shown<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5"><strong><center><br>
</strong></font><font face="Arial" color="#000100" size="3"><em>Graphical model for salm example
</em></font><font face="Arial" color="#000100" size="2"><br><img src="salm2.bmp" alt="[salm2]"><br><br>
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for salm example<br>
</em></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"></center>
</font><font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : doses ) {<br> for( j in 1 : plates ) {<br> y[i , j] ~ dpois(mu[i , j])<br> log(mu[i , j]) <- alpha + beta * log(x[i] + 10) + <br> &nb [...]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Salmdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><a href="../Examples/Salminits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Salminits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center><br><img src="salm3.bmp" alt="[salm3]"><br>
</font><font face="Arial" color="#000100" size="2"><br></center>
</font><font face="Arial" color="#000100" size="3">These estimates can be compared with the quasi-likelihood estimates of Breslow (1984) who reported
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> = 2.203 +/- 0.363,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> = 0.311 +/- 0.099,
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"> = -9.74E-4 +/- 4.37E-4,
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="3"> = 0.268
</font>
</p>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Salmdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(doses = 6, plates = 3,<br> y = structure(.Data = c(15,21,29,16,18,21,16,26,33,27,41,60,33,38,41,20,27,42),<br> .Dim = c(6, 3)),<br> x = c(0, 10, 33, 100, 333, 1000))
</font>
</p>
</body>
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diff --git a/doc/Examples/Salmdata.txt b/doc/Examples/Salmdata.txt
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index 0000000..d12caff
--- /dev/null
+++ b/doc/Examples/Salmdata.txt
@@ -0,0 +1,4 @@
+list(doses = 6, plates = 3,
+ y = structure(.Data = c(15,21,29,16,18,21,16,26,33,27,41,60,33,38,41,20,27,42),
+ .Dim = c(6, 3)),
+ x = c(0, 10, 33, 100, 333, 1000))
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diff --git a/doc/Examples/Salminits.html b/doc/Examples/Salminits.html
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--- /dev/null
+++ b/doc/Examples/Salminits.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Salminits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = 0, beta = 0, gamma = 0, tau = 0.1)
</font>
</p>
</body>
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diff --git a/doc/Examples/Salminits.txt b/doc/Examples/Salminits.txt
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+++ b/doc/Examples/Salminits.txt
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+list(alpha = 0, beta = 0, gamma = 0, tau = 0.1)
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--- /dev/null
+++ b/doc/Examples/Salminits1.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Salminits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = 1.0, beta = 1.0, gamma = 0.01, tau = 1.0)
</font>
</p>
</body>
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diff --git a/doc/Examples/Salminits1.txt b/doc/Examples/Salminits1.txt
new file mode 100755
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--- /dev/null
+++ b/doc/Examples/Salminits1.txt
@@ -0,0 +1 @@
+list(alpha = 1.0, beta = 1.0, gamma = 0.01, tau = 1.0)
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+++ b/doc/Examples/Salmmodel.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Salmmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : doses ) {<br> for( j in 1 : plates ) {<br> y[i , j] ~ dpois(mu[i , j])<br> log(mu[i , j]) <- alpha + beta * log(x[i] + 10) + <br> &nbs [...]
</font>
</p>
</body>
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diff --git a/doc/Examples/Salmmodel.txt b/doc/Examples/Salmmodel.txt
new file mode 100755
index 0000000..04c6daa
--- /dev/null
+++ b/doc/Examples/Salmmodel.txt
@@ -0,0 +1,16 @@
+ model
+ {
+ for( i in 1 : doses ) {
+ for( j in 1 : plates ) {
+ y[i , j] ~ dpois(mu[i , j])
+ log(mu[i , j]) <- alpha + beta * log(x[i] + 10) +
+ gamma * x[i] + lambda[i , j]
+ lambda[i , j] ~ dnorm(0.0, tau)
+ }
+ }
+ alpha ~ dnorm(0.0,1.0E-6)
+ beta ~ dnorm(0.0,1.0E-6)
+ gamma ~ dnorm(0.0,1.0E-6)
+ tau ~ dgamma(0.001, 0.001)
+ sigma <- 1 / sqrt(tau)
+ }
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diff --git a/doc/Examples/Schools.html b/doc/Examples/Schools.html
new file mode 100755
index 0000000..3a78e89
--- /dev/null
+++ b/doc/Examples/Schools.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Schools</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="schools0.bmp" alt="[schools0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Schools: ranking schoolexamination<br> results using multivariate<br> hierarcical models
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="2"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">Goldstein et al. (1993) present an analysis of examination results from inner London schools. They use hierarchical or multilevel models to study the between-school variation, and calculate school-level residuals in an attempt to differentiate between `good' and `bad' schools. Here we analyse a subset of this data and show how to calculate a rank ordering of schools and obtain credible intervals on each rank.<br><br>
</font><font face="Arial" color="#000100" size="3"><em>Data
</em></font><font face="Arial" color="#000100" size="3"><br><br>Standardized mean examination scores (Y) were available for 1978 pupils from 38 different schools. The median number of pupils per school was 48, with a range of 1--198. Pupil-level covariates included gender plus a standardized London Reading Test (LRT) score and a verbal reasoning (VR) test category (1, 2 or 3, where 1 represents the highest ability group) measured when each child was aged 11. Each school was classified by [...]
</font><font face="Arial" color="#000100" size="3"><em>Model
</em></font><font face="Arial" color="#000100" size="3"><br><br>We consider the following model, which essentially corresponds to Goldstein et al.'s model 1. <br><br><br> Y
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>1j
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>2j
</sub></font><font face="Arial" color="#000100" size="3"> LRT
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><sub>3j
</sub></font><font face="Arial" color="#000100" size="3"> VR
</font><font face="Arial" color="#000100" size="2">1
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> LRT
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> VR
</font><font face="Arial" color="#000100" size="2">2
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>3
</sub></font><font face="Arial" color="#000100" size="3"> Girl
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><br> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>4
</sub></font><font face="Arial" color="#000100" size="3"> Girls' school
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>5
</sub></font><font face="Arial" color="#000100" size="3"> Boys' school
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>6
</sub></font><font face="Arial" color="#000100" size="3"> CE school
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><br> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>7
</sub></font><font face="Arial" color="#000100" size="3"> RC school
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>8
</sub></font><font face="Arial" color="#000100" size="3"> other school
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><br> log
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> LRT
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub><br>
</sub></font><font face="Arial" color="#000100" size="3"><br>where i refers to pupil and j indexes school. We wish to specify a regression model for the variance components, and here we model the logarithm of
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> (the inverse of the between-pupil variance) as a linear function of each pupil's LRT score. This differs from Goldstein et al.'s model which allows the
</font><font face="Arial" color="#000100" size="3"><em> variance
</em></font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> to depend linearly on LRT. However, such a parameterization may lead to negative estimates of
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">.<br><br>
</font><font face="Arial" color="#000100" size="3"><em>Prior distributions
</em></font><font face="Arial" color="#000100" size="3"><br><br>The fixed effects
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> (k=1,...,8),
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3"> f
</font><font face="Arial" color="#000100" size="3"> were assumed to follow vague independent Normal distributions with zero mean and low precision = 0.0001. The random school-level coefficients
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>kj
</sub></font><font face="Arial" color="#000100" size="3"> (k = 1,2,3) were assumed to arise from a multivariate normal population distribution with unknown mean
</font><font face="Symbol" color="#000100" size="3"><strong>g
</strong></font><font face="Arial" color="#000100" size="3"> and covariance matrix
</font><font face="Symbol" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3">. A non-informative multivariate normal prior was then specified for the population mean
</font><font face="Symbol" color="#000100" size="3"><strong>g
</strong></font><font face="Arial" color="#000100" size="3">, whilst the inverse covariance matrix
</font><font face="Symbol" color="#000100" size="3"><strong>T
</strong></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="2"><sup>-1
</sup></font><font face="Arial" color="#000100" size="3"> was assumed to follow a Wishart distribution. To represent vague prior knowledge, we chose the degrees of freedom for this distribution to be as small as possible (i.e. 3, the rank of
</font><font face="Symbol" color="#000100" size="3"><strong>T
</strong></font><font face="Arial" color="#000100" size="3">). The scale matrix
</font><font face="Arial" color="#000100" size="3"><strong>R
</strong></font><font face="Arial" color="#000100" size="3"> was specified as<br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="schools1.bmp" alt="[schools1]"><br></center>
</font><font face="Arial" color="#000100" size="3"><br>which represents our prior guess at the order of magnitude of
</font><font face="Symbol" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3">.<br><br>The BUGS code is given below:<br><br>
</font><font face="Arial" color="#000100" size="3"> model<br> {<br> for(p in 1 : N) {<br> Y[p] ~ dnorm(mu[p], tau[p])<br> mu[p] <- alpha[school[p], 1] + alpha[school[p], 2] * LRT[p] <br> + alpha[school[p], 3] * VR[p, 1] + beta[1] * LRT2[p] <br> [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Schoolsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="3">Note that
</font><font face="Courier" color="#000100" size="3">school
</font><font face="Arial" color="#000100" size="3"> is a 1978 x 3 matrix taking value 1 for all pupils in school 1, 2 for all pupils in school 2 and so on. For computational convenience,
</font><font face="Courier" color="#000100" size="3">Y
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Courier" color="#000100" size="3">mu
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Courier" color="#000100" size="3">tau
</font><font face="Arial" color="#000100" size="3"> are indexed over a single dimension
</font><font face="Courier" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="3"> = 1,...,1978 rather than as pupil i within school j as used in equations above. The appropriate school-level coefficients for pupil
</font><font face="Courier" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="3"> are then selected using the school indicator in row
</font><font face="Courier" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="3"> of the data array --- for example
</font><font face="Courier" color="#000100" size="3">alpha[school[p],1]
</font><font face="Arial" color="#000100" size="3">.
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><a href="../Examples/Schoolsinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Schoolsinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="5"> <br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3">A 1000 update burn in followed by a further 10000 updates gave the parameter estimates <br><center><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1"><br><img src="schools2.bmp" alt="[schools2]"><br><br>
</font><font face="Arial" color="#000100" size="3"><em></center>Estimating the ranks
</em></font><font face="Arial" color="#000100" size="3"><br><br>The school-specific intercept
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><sub>j1
</sub></font><font face="Arial" color="#000100" size="3"> measures the 'residual effect' for school j after adjusting for pupil- and school-level covariates. This might represent an appropriate quantity by which to rank schools' performance. We compute the ranks in BUGS using the "rank" option of the "Statistics" menu, which we set for the variable alpha at the same time as we set the "sample monitor" option. Since the rank is a function of stochastic nodes, [...]
</font>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Schoolsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 1978, M = 38, mn = c(0, 0, 0), <br>prec = structure(.Data = c(0.0001, 0, 0, 0, 0.0001, 0, 0,0, 0.0001), .Dim = c(3, 3)),<br>R = structure(.Data = c(0.1, 0.005, 0.005, 0.005, 0.1, 0.005, 0.005, 0.005, 0.1), .Dim = c(3, 3)),<br>school = c(<br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, <br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, <br>1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, <br>2, 2, 2 [...]
</font>
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diff --git a/doc/Examples/Schoolsdata.txt b/doc/Examples/Schoolsdata.txt
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--- /dev/null
+++ b/doc/Examples/Schoolsdata.txt
@@ -0,0 +1,1206 @@
+list(N = 1978, M = 38, mn = c(0, 0, 0),
+prec = structure(.Data = c(0.0001, 0, 0, 0, 0.0001, 0, 0,0, 0.0001), .Dim = c(3, 3)),
+R = structure(.Data = c(0.1, 0.005, 0.005, 0.005, 0.1, 0.005, 0.005, 0.005, 0.1), .Dim = c(3, 3)),
+school = c(
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
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+0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1
+),.Dim = c(1978, 3)),
+Gender = c(
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+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
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+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
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+),
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\ No newline at end of file
diff --git a/doc/Examples/Schoolsinits.html b/doc/Examples/Schoolsinits.html
new file mode 100755
index 0000000..96a9cd2
--- /dev/null
+++ b/doc/Examples/Schoolsinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Schoolsinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(theta = 0, phi = 0.01, gamma = c(0,0,0), beta = c(0,0,0,0,0,0,0,0), <br>T = structure(.Data = c(10, -3, -3,<br>-3, 135, -65,<br>-3, -65, 135), .Dim = c(3, 3)),<br> alpha = structure(.Data = c( 0,0,0,<br> 0,0,0,<br> &nbs [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Schoolsinits.txt b/doc/Examples/Schoolsinits.txt
new file mode 100755
index 0000000..4807be2
--- /dev/null
+++ b/doc/Examples/Schoolsinits.txt
@@ -0,0 +1,43 @@
+list(theta = 0, phi = 0.01, gamma = c(0,0,0), beta = c(0,0,0,0,0,0,0,0),
+ T = structure(.Data = c(10, -3, -3,
+ -3, 135, -65,
+ -3, -65, 135), .Dim = c(3, 3)),
+ alpha = structure(.Data = c( 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
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+ 0,0,0,
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+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0), .Dim = c(38, 3))
+ )
\ No newline at end of file
diff --git a/doc/Examples/Schoolsinits1.html b/doc/Examples/Schoolsinits1.html
new file mode 100755
index 0000000..cc7dcb0
--- /dev/null
+++ b/doc/Examples/Schoolsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Schoolsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(theta = 0.1, phi = 0, gamma = c(1.0,1.0,1.0), beta = c(0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5), <br>T = structure(.Data = c(10, -3, -3,<br>-3, 135, -65,<br>-3, -65, 135), .Dim = c(3, 3)),<br> alpha = structure(.Data = c( 0,0,0,<br> 0,0,0,<br> & [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Schoolsinits1.txt b/doc/Examples/Schoolsinits1.txt
new file mode 100755
index 0000000..6a7a2d2
--- /dev/null
+++ b/doc/Examples/Schoolsinits1.txt
@@ -0,0 +1,43 @@
+list(theta = 0.1, phi = 0, gamma = c(1.0,1.0,1.0), beta = c(0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5),
+ T = structure(.Data = c(10, -3, -3,
+ -3, 135, -65,
+ -3, -65, 135), .Dim = c(3, 3)),
+ alpha = structure(.Data = c( 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0,
+ 0,0,0), .Dim = c(38, 3))
+ )
\ No newline at end of file
diff --git a/doc/Examples/Schoolsmodel.html b/doc/Examples/Schoolsmodel.html
new file mode 100755
index 0000000..7946101
--- /dev/null
+++ b/doc/Examples/Schoolsmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Schoolsmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for(p in 1 : N) {<br> Y[p] ~ dnorm(mu[p], tau[p])<br> mu[p] <- alpha[school[p], 1] + alpha[school[p], 2] * LRT[p] <br> + alpha[school[p], 3] * VR[p, 1] + beta[1] * LRT2[p] <br> & [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Schoolsmodel.txt b/doc/Examples/Schoolsmodel.txt
new file mode 100755
index 0000000..673d257
--- /dev/null
+++ b/doc/Examples/Schoolsmodel.txt
@@ -0,0 +1,34 @@
+ model
+ {
+ for(p in 1 : N) {
+ Y[p] ~ dnorm(mu[p], tau[p])
+ mu[p] <- alpha[school[p], 1] + alpha[school[p], 2] * LRT[p]
+ + alpha[school[p], 3] * VR[p, 1] + beta[1] * LRT2[p]
+ + beta[2] * VR[p, 2] + beta[3] * Gender[p]
+ + beta[4] * School.gender[p, 1] + beta[5] * School.gender[p, 2]
+ + beta[6] * School.denom[p, 1] + beta[7] * School.denom[p, 2]
+ + beta[8] * School.denom[p, 3]
+ log(tau[p]) <- theta + phi * LRT[p]
+ sigma2[p] <- 1 / tau[p]
+ LRT2[p] <- LRT[p] * LRT[p]
+ }
+ min.var <- exp(-(theta + phi * (-34.6193))) # lowest LRT score = -34.6193
+ max.var <- exp(-(theta + phi * (37.3807))) # highest LRT score = 37.3807
+
+ # Priors for fixed effects:
+ for (k in 1 : 8) {
+ beta[k] ~ dnorm(0.0, 0.0001)
+ }
+ theta ~ dnorm(0.0, 0.0001)
+ phi ~ dnorm(0.0, 0.0001)
+
+ # Priors for random coefficients:
+ for (j in 1 : M) {
+ alpha[j, 1 : 3] ~ dmnorm(gamma[1:3 ], T[1:3 ,1:3 ]);
+ alpha1[j] <- alpha[j,1]
+ }
+
+ # Hyper-priors:
+ gamma[1 : 3] ~ dmnorm(mn[1:3 ], prec[1:3 ,1:3 ]);
+ T[1 : 3, 1 : 3 ] ~ dwish(R[1:3 ,1:3 ], 3)
+ }
diff --git a/doc/Examples/Seeds.html b/doc/Examples/Seeds.html
new file mode 100755
index 0000000..eb2029f
--- /dev/null
+++ b/doc/Examples/Seeds.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Seeds</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="seeds0.bmp" alt="[seeds0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Seeds: Random effect logistic<br> regression
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">This example is taken from Table 3 of Crowder (1978), and concerns the proportion of seeds that germinated on each of 21 plates arranged according to a 2 by 2 factorial layout by seed and type of root extract. The data are shown below, where r
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> are the number of germinated and the total number of seeds on the
</font><font face="Arial" color="#000100" size="3"><em> i
</em></font><font face="Arial" color="#000100" size="3">th plate,
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> =1,...,N. These data are also analysed by, for example, Breslow: and Clayton (1993). <br><center><br>
</font><font face="Arial" color="#000100" size="2"><img src="seeds1.bmp" alt="[seeds1]"><br>
</font><font face="Arial" color="#000100" size="3"></center>The model is essentially a random effects logistic, allowing for over-dispersion. If p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is the probability of germination on the
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> th plate, we assume<br><br> r
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br> logit(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>12
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3"> + b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><br> <br> b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Normal(0,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">)<br> <br>where x
</font><font face="Arial" color="#000100" size="2"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3"> , x
</font><font face="Arial" color="#000100" size="2"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3"> are the seed type and root extract of the
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> th plate, and an interaction term
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>12
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3"> is included.
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"> ,
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> ,
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> ,
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>12
</sub></font><font face="Arial" color="#000100" size="3"> ,
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> are given independent "noninformative" priors. <br><br>
</font><font face="Arial" color="#000100" size="3"><center>
</font><font face="Arial" color="#000100" size="3"><em>Graphical model for seeds example<br><br>
</em></font><font face="Arial" color="#000100" size="3"><img src="seeds2.bmp" alt="[seeds2]"><br>BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for seeds example
</em></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"></center>
</font><font face="Arial" color="#000100" size="3"><br> model<br> {<br> for( i in 1 : N ) {<br> r[i] ~ dbin(p[i],n[i])<br> b[i] ~ dnorm(0.0,tau)<br> logit(p[ [...]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Seedsdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><a href="../Examples/Seedsinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Seedsinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>A burn in of 1000 updates followed by a further 10000 updates gave the following parameter estimates:<br><center>
</font><font face="Arial" color="#000000" size="2"><br><br><img src="seeds3.bmp" alt="[seeds3]"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">We may compare simple logistic, maximum likelihood (from EGRET), penalized quasi-likelihood (PQL) Breslow and Clayton (1993) with the
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> results<br>
</font><font face="Arial" color="#000100" size="2"><br><img src="seeds4.bmp" alt="[seeds4]"><br></center><br>
</font><font face="Arial" color="#000100" size="3">Heirarchical centering is an interesting reformulation of random effects models. Introduce the variables<br><br>
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>12
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><sub><br><br>
</sub></font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> + b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub><br><br>
</sub></font><font face="Arial" color="#000100" size="3">the model then becomes<br> r
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br><br> logit(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Normal(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">)<br><br>The graphical model is shown below <center><br>
</font><font face="Arial" color="#000100" size="2"><img src="seeds5.bmp" alt="[seeds5]"><br><br> </center>
</font><font face="Arial" color="#000100" size="3">This formulation of the model has two advantages: the squence of random numbers generated by the Gibbs sampler has better correlation properties and the time per update is reduced because the updating for the
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> parameters is now conjugate.
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/SeedsMixData.html b/doc/Examples/SeedsMixData.html
new file mode 100755
index 0000000..d6a9e2d
--- /dev/null
+++ b/doc/Examples/SeedsMixData.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>SeedsMixData</title>
</head>
<body>
<p>
<font face="Arial" color="#0000FF" size="3"><strong>S-Plus format:<br>
</strong></font><font face="Arial" color="#000100" size="2">list(N = 21)<br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Rectangular format:<br>
</strong></font><font face="Arial" color="#000100" size="2"> r[] n[] x1[] x2[]<br> 10 39 0 0<br> 23 62 0 0<br> 23 81 0 0<br> 26 51 0 0<br> &nb [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Seedsdata.html b/doc/Examples/Seedsdata.html
new file mode 100755
index 0000000..cc7efee
--- /dev/null
+++ b/doc/Examples/Seedsdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Seedsdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(r = c(10, 23, 23, 26, 17, 5, 53, 55, 32, 46, 10, 8, 10, 8, 23, 0, 3, 22, 15, 32, 3),<br> n = c(39, 62, 81, 51, 39, 6, 74, 72, 51, 79, 13, 16, 30, 28, 45, 4, 12, 41, 30, 51, 7),<br> x1 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),<br> x2 = c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1),<br> &nb [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Seedsdata.txt b/doc/Examples/Seedsdata.txt
new file mode 100755
index 0000000..5fa163a
--- /dev/null
+++ b/doc/Examples/Seedsdata.txt
@@ -0,0 +1,5 @@
+list(r = c(10, 23, 23, 26, 17, 5, 53, 55, 32, 46, 10, 8, 10, 8, 23, 0, 3, 22, 15, 32, 3),
+ n = c(39, 62, 81, 51, 39, 6, 74, 72, 51, 79, 13, 16, 30, 28, 45, 4, 12, 41, 30, 51, 7),
+ x1 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
+ x2 = c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1),
+ N = 21)
\ No newline at end of file
diff --git a/doc/Examples/Seedsdataclone.html b/doc/Examples/Seedsdataclone.html
new file mode 100755
index 0000000..692797c
--- /dev/null
+++ b/doc/Examples/Seedsdataclone.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Seedsdataclone</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(r = c(10, 23, 23, 26, 17, 5, 53, 55, 32, 46, 10, 8, 10, 8, 23, 0, 3, 22, 15, 32, 3),<br> n = c(39, 62, 81, 51, 39, 6, 74, 72, 51, 79, 13, 16, 30, 28, 45, 4, 12, 41, 30, 51, 7),<br> x1 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),<br> x2 = c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1),<br> &nb [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Seedsdataclone.txt b/doc/Examples/Seedsdataclone.txt
new file mode 100755
index 0000000..075bab0
--- /dev/null
+++ b/doc/Examples/Seedsdataclone.txt
@@ -0,0 +1,5 @@
+list(r = c(10, 23, 23, 26, 17, 5, 53, 55, 32, 46, 10, 8, 10, 8, 23, 0, 3, 22, 15, 32, 3),
+ n = c(39, 62, 81, 51, 39, 6, 74, 72, 51, 79, 13, 16, 30, 28, 45, 4, 12, 41, 30, 51, 7),
+ x1 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
+ x2 = c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1),
+ N = 21, K = 128)
\ No newline at end of file
diff --git a/doc/Examples/Seedsinits.html b/doc/Examples/Seedsinits.html
new file mode 100755
index 0000000..2d545b0
--- /dev/null
+++ b/doc/Examples/Seedsinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Seedsinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha0 = 0, alpha1 = 0, alpha2 = 0, alpha12 = 0, tau = 10)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Seedsinits.txt b/doc/Examples/Seedsinits.txt
new file mode 100755
index 0000000..bb6ba04
--- /dev/null
+++ b/doc/Examples/Seedsinits.txt
@@ -0,0 +1 @@
+list(alpha0 = 0, alpha1 = 0, alpha2 = 0, alpha12 = 0, tau = 10)
\ No newline at end of file
diff --git a/doc/Examples/Seedsinits1.html b/doc/Examples/Seedsinits1.html
new file mode 100755
index 0000000..e0f0ee1
--- /dev/null
+++ b/doc/Examples/Seedsinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Seedsinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(<br>alpha0 = 0, alpha1 = 0, alpha2 = 0, alpha12 = 0, tau = 1,<br>b = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Seedsinits1.txt b/doc/Examples/Seedsinits1.txt
new file mode 100755
index 0000000..ac311cc
--- /dev/null
+++ b/doc/Examples/Seedsinits1.txt
@@ -0,0 +1,3 @@
+list(
+alpha0 = 0, alpha1 = 0, alpha2 = 0, alpha12 = 0, tau = 1,
+b = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
diff --git a/doc/Examples/Seedsinits2.html b/doc/Examples/Seedsinits2.html
new file mode 100755
index 0000000..524f8cb
--- /dev/null
+++ b/doc/Examples/Seedsinits2.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Seedsinits2</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(<br>alpha0 = 10, alpha1 = 10, alpha2 = 10, alpha12 = 10, tau = 0.1,<br>b = c(0.1, -0.2, 0.25, 0.11, -0.21, 0.3, -0.25, 0.15, -0.31, -0.1,<br>0.1, 0.12, 0.2, -0.2, 0.4, -0.24, 0.14, 0.3, -0.2, 0.1, 0.05))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Seedsinits2.txt b/doc/Examples/Seedsinits2.txt
new file mode 100755
index 0000000..c1196cf
--- /dev/null
+++ b/doc/Examples/Seedsinits2.txt
@@ -0,0 +1,4 @@
+list(
+alpha0 = 10, alpha1 = 10, alpha2 = 10, alpha12 = 10, tau = 0.1,
+b = c(0.1, -0.2, 0.25, 0.11, -0.21, 0.3, -0.25, 0.15, -0.31, -0.1,
+0.1, 0.12, 0.2, -0.2, 0.4, -0.24, 0.14, 0.3, -0.2, 0.1, 0.05))
\ No newline at end of file
diff --git a/doc/Examples/Seedsmodel.html b/doc/Examples/Seedsmodel.html
new file mode 100755
index 0000000..ac5de6d
--- /dev/null
+++ b/doc/Examples/Seedsmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Seedsmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : N ) {<br> r[i] ~ dbin(p[i],n[i])<br> b[i] ~ dnorm(0.0,tau)<br> logit(p[i]) <- a [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Seedsmodel.txt b/doc/Examples/Seedsmodel.txt
new file mode 100755
index 0000000..e649ce0
--- /dev/null
+++ b/doc/Examples/Seedsmodel.txt
@@ -0,0 +1,15 @@
+ model
+ {
+ for( i in 1 : N ) {
+ r[i] ~ dbin(p[i],n[i])
+ b[i] ~ dnorm(0.0,tau)
+ logit(p[i]) <- alpha0 + alpha1 * x1[i] + alpha2 * x2[i] +
+ alpha12 * x1[i] * x2[i] + b[i]
+ }
+ alpha0 ~ dnorm(0.0,1.0E-6)
+ alpha1 ~ dnorm(0.0,1.0E-6)
+ alpha2 ~ dnorm(0.0,1.0E-6)
+ alpha12 ~ dnorm(0.0,1.0E-6)
+ tau ~ dgamma(0.001,0.001)
+ sigma <- 1 / sqrt(tau)
+ }
diff --git a/doc/Examples/Sixcomp.html b/doc/Examples/Sixcomp.html
new file mode 100755
index 0000000..f0a6c6d
--- /dev/null
+++ b/doc/Examples/Sixcomp.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Sixcomp</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="sixcomp0.bmp" alt="[sixcomp0]">
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Six compartments: differential<br> equation model
</font><font face="Arial" color="#000000" size="3"><br><br>A simple pharmokinetic compartmental model. The solution is a constant. <br><br> model <br> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> solution[1:n.grid, 1:dim] <- ode(init[1:dim], grid[1:n.grid], D(C[1:dim], t), 0, tol)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> D(C[1], t) <-
</font><font face="Arial" color="#000000" size="3">PER1 * C[7] - R * kT1 * C[1]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[2], t) <-
</font><font face="Arial" color="#000000" size="3">PER2 * C[8] - R * kT2 * C[2] - CLR * C[8] / V2
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[3], t) <-
</font><font face="Arial" color="#000000" size="3">PER3 * C[8] - R * kT3 * C[3]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[4], t) <-
</font><font face="Arial" color="#000000" size="3">(QHEP * C[8] + R * kT3 * V3 * C[3] - <br> R * kT4 * V4 * C[4] * (1 + CLHEP / (R * Q4 - CLHEP))) / V4
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[5], t) <-
</font><font face="Arial" color="#000000" size="3">PER5 * C[8] - R * kT5 * C[5]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[6], t) <-
</font><font face="Arial" color="#000000" size="3">PER6 * C[8] - R * kT6 * C[6]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[7], t) <-
</font><font face="Arial" color="#000000" size="3">(R * (kT2 * V2 * C[2] + kT4 * V4 * C[4] + kT5 * V5 * C[5] + <br> kT6 * V6 * C[6])
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">- Q1 * C[7]) / VVEN
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[8], t) <-
</font><font face="Arial" color="#000000" size="3">(R * kT1 * V1 * C[1] - Q1 * C[8]) / VART
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">PER1 <- Q1 / V1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">PER2 <- Q2 / V2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">PER3 <- Q3 / V3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">PER5 <- Q5 / V5<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">PER6 <- Q6 / V6<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">Q4 <- Q3 + QHEP<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Sixcompdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br>
</font><font face="Arial" color="#000100" size="2"> <br>solution[1,1] 0.0<br>solution[1,2] 0.0<br>solution[1,3] 0.0<br>solution[1,4] 0.0<br>solution[1,5] 0.0<br>solution[1,6] 0.0<br>solution[1,7] 25.0<br>solution[ [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Sixcompdata.html b/doc/Examples/Sixcompdata.html
new file mode 100755
index 0000000..b5a5296
--- /dev/null
+++ b/doc/Examples/Sixcompdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Sixcompdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(<br>n.grid = 73, dim = 8, tol = 1.0E-3,<br>R = 1
</font><font face="Arial" color="#000000" size="3">, Q1 = 51.2,
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3">Q2 = 14.48, Q3 = 16, QHEP = 4, Q5 = 16.32, Q6 = 0.4,<br>V1 = 1, V2 = 4.8, V3 = 13, V4 = 10.5, V5 = 180.2, V6 = 10, VVEN = 10, VART = 6.67,<br>kT1 = 10.119, kT2 = 0.596, kT3 = 0.223, kT4 = 0.134, kT5 = 0.033, kT6 = 0.004,<br>CLR = 0, CLHEP = 10,<br>init = c(0, 0, 0, 0, 0, 0, 25, 0),<br>grid = c(0, 10, 20, 30, 40, 50, 60, 70, 80, 90,<br>100, 110, 120, 130, 140, 150, 160, 170, 180, 190, <br>200, 210, 220, 230, 240, 250, 260, 270, 280, 280,<b [...]
</font><font face="Arial" color="#000000" size="3">)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Sixcompdata.txt b/doc/Examples/Sixcompdata.txt
new file mode 100755
index 0000000..1e29d93
--- /dev/null
+++ b/doc/Examples/Sixcompdata.txt
@@ -0,0 +1,17 @@
+list(
+n.grid = 73, dim = 8, tol = 1.0E-3,
+R = 1, Q1 = 51.2,
+Q2 = 14.48, Q3 = 16, QHEP = 4, Q5 = 16.32, Q6 = 0.4,
+V1 = 1, V2 = 4.8, V3 = 13, V4 = 10.5, V5 = 180.2, V6 = 10, VVEN = 10, VART = 6.67,
+kT1 = 10.119, kT2 = 0.596, kT3 = 0.223, kT4 = 0.134, kT5 = 0.033, kT6 = 0.004,
+CLR = 0, CLHEP = 10,
+init = c(0, 0, 0, 0, 0, 0, 25, 0),
+grid = c(0, 10, 20, 30, 40, 50, 60, 70, 80, 90,
+100, 110, 120, 130, 140, 150, 160, 170, 180, 190,
+200, 210, 220, 230, 240, 250, 260, 270, 280, 280,
+300, 310, 320, 330, 340, 350, 360, 370, 380, 390,
+400, 410, 420, 430, 440, 450, 460, 470, 480, 490,
+500, 510, 520, 530, 540, 550, 560, 570, 580, 590,
+600, 610, 620, 630, 640, 650, 660, 670, 680, 690,
+700, 710, 720)
+)
\ No newline at end of file
diff --git a/doc/Examples/Sixcompmodel.html b/doc/Examples/Sixcompmodel.html
new file mode 100755
index 0000000..9f25e6c
--- /dev/null
+++ b/doc/Examples/Sixcompmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Sixcompmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3"> model <br> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> solution[1:n.grid, 1:dim] <- ode(init[1:dim], grid[1:n.grid], D(C[1:dim], t), 0, tol)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> D(C[1], t) <-
</font><font face="Arial" color="#000000" size="3">PER1 * C[7] - R * kT1 * C[1]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[2], t) <-
</font><font face="Arial" color="#000000" size="3">PER2 * C[8] - R * kT2 * C[2] - CLR * C[8] / V2
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[3], t) <-
</font><font face="Arial" color="#000000" size="3">PER3 * C[8] - R * kT3 * C[3]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[4], t) <-
</font><font face="Arial" color="#000000" size="3">(QHEP * C[8] + R * kT3 * V3 * C[3] - <br> R * kT4 * V4 * C[4] * (1 + CLHEP / (R * Q4 - CLHEP))) / V4
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[5], t) <-
</font><font face="Arial" color="#000000" size="3">PER5 * C[8] - R * kT5 * C[5]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[6], t) <-
</font><font face="Arial" color="#000000" size="3">PER6 * C[8] - R * kT6 * C[6]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[7], t) <-
</font><font face="Arial" color="#000000" size="3">(R * (kT2 * V2 * C[2] + kT4 * V4 * C[4] + kT5 * V5 * C[5] + <br> kT6 * V6 * C[6])
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">- Q1 * C[7]) / VVEN
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">D(C[8], t) <-
</font><font face="Arial" color="#000000" size="3">(R * kT1 * V1 * C[1] - Q1 * C[8]) / VART
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">PER1 <- Q1 / V1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">PER2 <- Q2 / V2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">PER3 <- Q3 / V3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">PER5 <- Q5 / V5<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">PER6 <- Q6 / V6<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">Q4 <- Q3 + QHEP<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Sixcompmodel.txt b/doc/Examples/Sixcompmodel.txt
new file mode 100755
index 0000000..5779932
--- /dev/null
+++ b/doc/Examples/Sixcompmodel.txt
@@ -0,0 +1,23 @@
+ model
+ {
+ solution[1:n.grid, 1:dim] <- ode(init[1:dim], grid[1:n.grid], D(C[1:dim], t), 0, tol)
+
+ D(C[1], t) <- PER1 * C[7] - R * kT1 * C[1]
+ D(C[2], t) <- PER2 * C[8] - R * kT2 * C[2] - CLR * C[8] / V2
+ D(C[3], t) <- PER3 * C[8] - R * kT3 * C[3]
+ D(C[4], t) <- (QHEP * C[8] + R * kT3 * V3 * C[3] -
+ R * kT4 * V4 * C[4] * (1 + CLHEP / (R * Q4 - CLHEP))) / V4
+ D(C[5], t) <- PER5 * C[8] - R * kT5 * C[5]
+ D(C[6], t) <- PER6 * C[8] - R * kT6 * C[6]
+ D(C[7], t) <- (R * (kT2 * V2 * C[2] + kT4 * V4 * C[4] + kT5 * V5 * C[5] +
+ kT6 * V6 * C[6]) - Q1 * C[7]) / VVEN
+ D(C[8], t) <- (R * kT1 * V1 * C[1] - Q1 * C[8]) / VART
+
+ PER1 <- Q1 / V1
+ PER2 <- Q2 / V2
+ PER3 <- Q3 / V3
+ PER5 <- Q5 / V5
+ PER6 <- Q6 / V6
+
+ Q4 <- Q3 + QHEP
+ }
diff --git a/doc/Examples/Sparrowhawk.html b/doc/Examples/Sparrowhawk.html
new file mode 100755
index 0000000..05f0211
--- /dev/null
+++ b/doc/Examples/Sparrowhawk.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Sparrowhawk</title>
</head>
<body>
<p>
<font face="Arial" color="#0000FF" size="5"><strong><img src="sparrowhawk0.bmp" alt="[sparrowhawk0]">
</strong></font><font face="Courier New" color="#000100" size="6"> Sparrowhawks: Dynamic site-<br> occupancy, or generalised<br> metapopulation, model for the<br> dynamics [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="6"> <br> (contributed by Marc Kery)<br>
</font><font face="Arial" color="#000100" size="3"><br>Modelling the dynamics of species distributions is central to metapopulation ecology, biogeography and other branches of ecology. However, simple analyses that do not account for possible imperfect detection will lead to distorted results; the general distributional extent and patch survival rate will be underestimated and colonisation rates and turnover rates will be overestimated. And worse, the degree of the induced bias may be rel [...]
</font><font face="Arial" color="#000100" size="3"><em>Oikos
</em></font><font face="Arial" color="#000100" size="3">, 2002).<br><br>To model the dynamics of distributions or of metapopulations, i.e., occupancy and patch survival and colonisation rates, free of the biasing effects of imperfect detection, MacKenzie
</font><font face="Arial" color="#000100" size="3"><em>et al.
</em></font><font face="Arial" color="#000100" size="3"> (
</font><font face="Arial" color="#000100" size="3"><em>Ecology
</em></font><font face="Arial" color="#000100" size="3">, 2003; also
</font><font face="Arial" color="#000100" size="3"><em>Academic Press
</em></font><font face="Arial" color="#000100" size="3">, 2006) developed a multi-season version of their site-occupancy model (see example "Gentians") that uses spatially and temporally replicated detection/nondetection (a.k.a."presence/absence") data to model occurrence separately from detection. Royle and Kéry,
</font><font face="Arial" color="#000100" size="3"><em>(Ecology
</em></font><font face="Arial" color="#000100" size="3">, 2007) developed a hierarchical formulation of the dynamic model that can be easily implemented in WinBUGS. This model describes the dynamic biological process of patch occupancy separately from the observation process.<br><br>The data required for this type of modeling consists of the detection/nondetection observations at a number of sites (i) and over a number of years ("seasons", t). Seasons are chosen so that the occu [...]
</font><font face="Arial" color="#000100" size="1"><sub>itk
</sub></font><font face="Arial" color="#000100" size="3"> denotes the binary detection observation at site i, in season t and for replicate observation k. Important assumptions of the model are within-season "closure" and no false-positive errors, i.e., a species can only be overlooked when absent but not falsely detected where it is not present.<br><br>Dynamic site-occupancy models describe the biological process underlying observation y
</font><font face="Arial" color="#000100" size="1"><sub>itk
</sub></font><font face="Arial" color="#000100" size="3"> as a function of initial occupancy in the first year (psi
</font><font face="Arial" color="#000100" size="1"><sub>t=1
</sub></font><font face="Arial" color="#000100" size="3">) and an annual probability of patch survival (phi
</font><font face="Arial" color="#000100" size="1"><sub>t
</sub></font><font face="Arial" color="#000100" size="3">) and patch colonisation (gamma
</font><font face="Arial" color="#000100" size="1"><sub>t
</sub></font><font face="Arial" color="#000100" size="3">). Several other parameterisations are available, e.g. in terms of extinction rather than patch survival rate or the autologistic parameterisation (see Royle and Dorazio,
</font><font face="Arial" color="#000100" size="3"><em>Academic Press
</em></font><font face="Arial" color="#000100" size="3">, 2008). The autologistic is particularly useful when effects of covariates directly on occupancy need to be modellied, rather than on its dynamic components.<br><br>Here is the representation in terms of initial occupancy (z
</font><font face="Arial" color="#000100" size="1"><sub>it
</sub></font><font face="Arial" color="#000100" size="3">) and probabilities of survival (phi) and colonisation (gamma). For clarity, index i (for site) is dropped; however, importantly, all parameters could be made site-specific and modelled as (e.g., logistic) functions of covariates.<br><br>State process:<br> z
</font><font face="Arial" color="#000100" size="1"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli(psi
</font><font face="Arial" color="#000100" size="1"><sub>t=1
</sub></font><font face="Arial" color="#000100" size="3">) Initial occupancy psi, for year j = 1<br> z
</font><font face="Arial" color="#000100" size="1"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"> | z
</font><font face="Arial" color="#000100" size="1"><sub>t -1
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli(z
</font><font face="Arial" color="#000100" size="1"><sub>t -1
</sub></font><font face="Arial" color="#000100" size="3"> * phi
</font><font face="Arial" color="#000100" size="1"><sub>t -1
</sub></font><font face="Arial" color="#000100" size="3"> + (1 - z
</font><font face="Arial" color="#000100" size="1"><sub>t -1
</sub></font><font face="Arial" color="#000100" size="3"> ) *gamma
</font><font face="Arial" color="#000100" size="1"><sub>t -1
</sub></font><font face="Arial" color="#000100" size="3"> ) Occupancy in later years<br><br>Observation process:<br> y
</font><font face="Arial" color="#000100" size="1"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli( z
</font><font face="Arial" color="#000100" size="1"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"> * p
</font><font face="Arial" color="#000100" size="1"><sub>t
</sub></font><font face="Arial" color="#000100" size="3">) Detection conditional on occurrence (z=1)<br><br>Hence, occupancy dynamics is modelled as a Bernoulli process with success probability depending on the previous year's occurrence state (z) and survival and colonisation rates: if a site was occupied (z
</font><font face="Arial" color="#000100" size="1"><sub>t -1
</sub></font><font face="Arial" color="#000100" size="3"> =1), the survival component (phi) in the Bernoulli success probability becomes operative, while if it wasn't (z
</font><font face="Arial" color="#000100" size="1"><sub>t -1
</sub></font><font face="Arial" color="#000100" size="3">=0), the colonisation component (gamma) does.<br><br>A number of useful quantities can be obtained as derived parameters such as the actual number of occupied sites in each year (or alternatively, finite-sample occupancy) or turnover and growth rates. Occupancy for years t>1 is also a derived parameter that can be computed from initial occupancy and survival and colonisation rates. The hierarchical representation of the model is [...]
</font><font face="Arial" color="#000100" size="3"><em>Accipiter nisus
</em></font><font face="Arial" color="#000100" size="3">) collected during 2000-2005 in the Swiss national Breeding Bird Survey (MHB) where three (and sometimes only two) replicate surveys are conducted in each of 267 kilometre square quadrats laid out as a grid over the country. Data from a random subset of 116 quadrats are given in two arrays: x contains the binary "detection/nondetection" data at site i during season j and for replicate k. REPS contains the number of replicat [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">{ # Generalised metapopulation model or dynamic site-occupancy model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Priors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for(i in 1 : nyear -1){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">phi[i] ~ dunif(0,1) # Patch survival rate (one fewer than number of years)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">gamma[i] ~ dunif(0,1) # Patch colonisation rate <br> # (one fewer than number of years)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">p[i]~dunif(0,1) # Detection probability (conditional on occurrence)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">p[nyear]~dunif(0,1) # Detection in last year <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">psi~dunif(0,1) # Occupancy in first year (remainder are derived quantitites)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Model for the parameters describing the observation process: <br> #detection probability<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for(i in 1 : nsite){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for(j in 1 : nyear){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for(k in 1 : REPS[i,j]){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> pmat[j, i, k]<- p[j] # Could also add a linear time trend or add <br> # covariate function<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Initial state and likelihood for year 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for(i in 1 : nsite){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> z[i,1] ~ dbern(psi) # State model for year 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for(k in 1 : REPS[i,1]){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> mu2[1, i, k] <- z[i,1] * pmat[1, i, k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> x[1, i, k] ~ dbern(mu2[1, i, k]) # Observation model for year 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Likelihood for second to final years<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for(i in 1 : nsite){ # State model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for(j in 2 : nyear){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> R[i, j] <- (1 - z[i ,j -1]) * z[i, j] # "recruits"<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> mu[i, j ]<- z[i, j -1] * phi[j -1]+ (1 - z[i, j -1]) * gamma[j -1]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> z[i, j] ~ dbern(mu[i, j])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for(k in 1 : REPS[i, j]){ # Observation model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> mu2[j, i, k] <- z[i, j] * pmat[j, i, k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> x[j, i, k] ~ dbern(mu2[j, i, k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br> # Derived quantities: Annual occupancy, finite-sample occupancy, <br> #growth rate, turnover rate<br> psivec[1] <- psi # Occupancy rate in year 1<br> Nocc[1 ]< -sum(z[1 : nsite,1]) # Number occupied sites in year 1<br> for(t in 2 : nyear){<br> &n [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Sparrowhawkdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Sparrowhawkinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="3"> </a>
</font><font face="Arial" color="#0000FF" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Sparrowhawkinits2.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="3"><br><br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Running 2 chains for 11000 iterations, with 1000 discarded as a burnin, yields these results:
</font><font face="Arial" color="#000100" size="2"><br><center>
</font><font face="Arial" color="#000100" size="3"><br><img src="sparrowhawk1.bmp" alt="[sparrowhawk1]">
</font><font face="Arial" color="#000100" size="2"><br></center>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">Note that normally, detection probability of Swiss Sparrowhawks was only around 15%, so a naive metapopulation model that assumes perfect detection would yield greatly biased inference. Something seemed to have happened in 2005 (see, e.g., Nocc[6]), but we don't know what.<br>
</font>
</p>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Sparrowhawkdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(x= structure(.Data= c(0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, NA, NA, NA, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, NA, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Sparrowhawkdata.txt b/doc/Examples/Sparrowhawkdata.txt
new file mode 100755
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--- /dev/null
+++ b/doc/Examples/Sparrowhawkdata.txt
@@ -0,0 +1 @@
+list(x= structure(.Data= c(0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, NA, NA, NA, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, NA, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 [...]
diff --git a/doc/Examples/Sparrowhawkinits1.html b/doc/Examples/Sparrowhawkinits1.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Sparrowhawkinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(z= structure(.Data= c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, [...]
</font>
</p>
</body>
</html>
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--- /dev/null
+++ b/doc/Examples/Sparrowhawkinits1.txt
@@ -0,0 +1 @@
+list(z= structure(.Data= c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, [...]
diff --git a/doc/Examples/Sparrowhawkinits2.html b/doc/Examples/Sparrowhawkinits2.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Sparrowhawkinits2</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(z= structure(.Data= c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, [...]
</font>
</p>
</body>
</html>
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--- /dev/null
+++ b/doc/Examples/Sparrowhawkinits2.txt
@@ -0,0 +1 @@
+list(z= structure(.Data= c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, [...]
diff --git a/doc/Examples/StVeit.html b/doc/Examples/StVeit.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>StVeit</title>
</head>
<body>
<p>
<font face="Arial" color="#0000FF" size="5"><strong><img src="stveit0.bmp" alt="[stveit0]">
</strong></font><font face="Courier New" color="#000100" size="6">St Veit-Klinglberg, Austria - <br> Radiocarbon calibration with<br> stratification
</font><font face="Arial" color="#0000FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">This example is from the book Buck CE, Cavanagh WG & Litton CD (1996)
</font><font face="Arial" color="#000100" size="3"><em>Bayesian approach to interpreting archaeological data
</em></font><font face="Arial" color="#000100" size="3">. Wiley: Chichester p218-226<br>See also Buck CE, Litton CD & Shennan SJ (1994) A case study in combining radiocarbon and archaeological information: the Early Bronze Age settlement of St Veit-Klinglberg, Lan Salzburg, Austria.
</font><font face="Arial" color="#000100" size="3"><em>Germania
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>2
</strong></font><font face="Arial" color="#000100" size="3"> 427-447. The model was set up by Andrew Millard.
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">© Andrew Millard 2001 <br><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model{ <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[1] ~ dunif(theta[2], theta.max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[2] ~ dunif(theta[3], theta[1])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[3] ~ dunif(theta[9], theta[2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[4] ~ dunif(theta[9], theta.max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[5] ~ dunif(theta[7], theta.max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[6] ~ dunif(theta[7], theta.max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[7] ~ dunif(theta[9], theta7max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta7max <- min(theta[5], theta[6])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[8] ~ dunif(theta[9], theta.max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[9] ~ dunif(theta[10], theta9max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta9max <-min(min(theta[3], theta[4]), min(theta[7], theta[8]))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[10] ~ dunif(theta[11], theta[9])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[11] ~ dunif(0 ,theta[10])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> bound[1] <- ranked(theta[1:8], 8)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> bound[2] <- ranked(theta[1:8], 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> bound[3] <- ranked(theta[9:11], 3)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> bound[4] <- ranked(theta[9:11], 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : 5){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[j + 11] ~ dunif(0, theta.max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> within[j, 1] <- 1 - step(bound[1] - theta[j + 11])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 2 : 4){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> within[j, k] <- step(bound[k - 1] - theta[j + 11]) <br> - step(bound[k] - theta[j + 11])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> within[j, 5] <- step(bound[4] - theta[j + 11])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1:nDate){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> X[i] ~ dnorm(mu[i], tau[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau[i] <- 1/pow(sigma[i],2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[i] <- interp.lin(theta[i], calBP[], C14BP[])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># monitor the following variable to smooth density of theta<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta.smooth[i] <- 10 * round(theta[i] / 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/StVeitdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Examples/RCdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Radio Carbon Calibration Curve
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/StVeitinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/StVeitinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br><center><br><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="stveit1.bmp" alt="[stveit1]"><img src="stveit2.bmp" alt="[stveit2]"><img src="stveit3.bmp" alt="[stveit3]"><img src="stveit4.bmp" alt="[stveit4]"><img src="stveit5.bmp" alt="[stveit5]"><img src="stveit6.bmp" alt="[stveit6]"><img src="stveit7.bmp" alt="[stveit7]"><img src="stveit8.bmp" alt="[stveit8]"><img src="stveit9.bmp" alt="[stveit9]"><img src="stveit10.bmp" alt="[stveit10]"><img src="stveit11.bmp" alt="[stveit11]"><img src= [...]
</font><font face="Arial" color="#0000FF" size="5"><br><br><img src="stveit17.bmp" alt="[stveit17]"></center>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/StVeitdata.html b/doc/Examples/StVeitdata.html
new file mode 100755
index 0000000..d9aa6ae
--- /dev/null
+++ b/doc/Examples/StVeitdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>StVeitdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(nDate=16, theta.max=21000,<br> X= c(3275, 3270, 3400, 3190, 3420, 3370, 3435, 3160, 3340, 3270, 3200, 3390, 3480, 3250, 3115, 3460), <br> sigma=c( 75, 80, 75, 75, 65, 75, 60, 70, 80, 75, 70, 80, 75, 75, 70, 70))
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/StVeitdata.txt b/doc/Examples/StVeitdata.txt
new file mode 100755
index 0000000..5746dba
--- /dev/null
+++ b/doc/Examples/StVeitdata.txt
@@ -0,0 +1,3 @@
+list(nDate=16, theta.max=21000,
+ X= c(3275, 3270, 3400, 3190, 3420, 3370, 3435, 3160, 3340, 3270, 3200, 3390, 3480, 3250, 3115, 3460),
+ sigma=c( 75, 80, 75, 75, 65, 75, 60, 70, 80, 75, 70, 80, 75, 75, 70, 70))
\ No newline at end of file
diff --git a/doc/Examples/StVeitinits.html b/doc/Examples/StVeitinits.html
new file mode 100755
index 0000000..1f31c4b
--- /dev/null
+++ b/doc/Examples/StVeitinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>StVeitinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(theta=c(3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/StVeitinits.txt b/doc/Examples/StVeitinits.txt
new file mode 100755
index 0000000..bf8c728
--- /dev/null
+++ b/doc/Examples/StVeitinits.txt
@@ -0,0 +1 @@
+list(theta=c(3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500, 3500))
\ No newline at end of file
diff --git a/doc/Examples/StVeitinits1.html b/doc/Examples/StVeitinits1.html
new file mode 100755
index 0000000..4c7fcc8
--- /dev/null
+++ b/doc/Examples/StVeitinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>StVeitinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(theta=c(3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/StVeitinits1.txt b/doc/Examples/StVeitinits1.txt
new file mode 100755
index 0000000..6b978ae
--- /dev/null
+++ b/doc/Examples/StVeitinits1.txt
@@ -0,0 +1 @@
+list(theta=c(3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000, 3000))
\ No newline at end of file
diff --git a/doc/Examples/StVeitmodel.html b/doc/Examples/StVeitmodel.html
new file mode 100755
index 0000000..ebd591b
--- /dev/null
+++ b/doc/Examples/StVeitmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>StVeitmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model{ <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[1] ~ dunif(theta[2], theta.max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[2] ~ dunif(theta[3], theta[1])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[3] ~ dunif(theta[9], theta[2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[4] ~ dunif(theta[9], theta.max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[5] ~ dunif(theta[7], theta.max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[6] ~ dunif(theta[7], theta.max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[7] ~ dunif(theta[9], theta7max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta7max <- min(theta[5], theta[6])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[8] ~ dunif(theta[9], theta.max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[9] ~ dunif(theta[10], theta9max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta9max <-min(min(theta[3], theta[4]), min(theta[7], theta[8]))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[10] ~ dunif(theta[11], theta[9])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[11] ~ dunif(0 ,theta[10])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> bound[1] <- ranked(theta[1:8], 8)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> bound[2] <- ranked(theta[1:8], 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> bound[3] <- ranked(theta[9:11], 3)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> bound[4] <- ranked(theta[9:11], 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : 5){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[j + 11] ~ dunif(0, theta.max)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> within[j, 1] <- 1 - step(bound[1] - theta[j + 11])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 2 : 4){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> within[j, k] <- step(bound[k - 1] - theta[j + 11]) <br> - step(bound[k] - theta[j + 11])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> within[j, 5] <- step(bound[4] - theta[j + 11])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1:nDate){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> X[i] ~ dnorm(mu[i], tau[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau[i] <- 1/pow(sigma[i],2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[i] <- interp.lin(theta[i], calBP[], C14BP[])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># monitor the following variable to smooth density of theta<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta.smooth[i] <- 10 * round(theta[i] / 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/StVeitmodel.txt b/doc/Examples/StVeitmodel.txt
new file mode 100755
index 0000000..ce2ee6e
--- /dev/null
+++ b/doc/Examples/StVeitmodel.txt
@@ -0,0 +1,40 @@
+ model{
+ theta[1] ~ dunif(theta[2], theta.max)
+ theta[2] ~ dunif(theta[3], theta[1])
+ theta[3] ~ dunif(theta[9], theta[2])
+ theta[4] ~ dunif(theta[9], theta.max)
+ theta[5] ~ dunif(theta[7], theta.max)
+ theta[6] ~ dunif(theta[7], theta.max)
+ theta[7] ~ dunif(theta[9], theta7max)
+ theta7max <- min(theta[5], theta[6])
+ theta[8] ~ dunif(theta[9], theta.max)
+ theta[9] ~ dunif(theta[10], theta9max)
+ theta9max <-min(min(theta[3], theta[4]), min(theta[7], theta[8]))
+ theta[10] ~ dunif(theta[11], theta[9])
+ theta[11] ~ dunif(0 ,theta[10])
+
+ bound[1] <- ranked(theta[1:8], 8)
+ bound[2] <- ranked(theta[1:8], 1)
+ bound[3] <- ranked(theta[9:11], 3)
+ bound[4] <- ranked(theta[9:11], 1)
+
+ for (j in 1 : 5){
+ theta[j + 11] ~ dunif(0, theta.max)
+ within[j, 1] <- 1 - step(bound[1] - theta[j + 11])
+ for (k in 2 : 4){
+ within[j, k] <- step(bound[k - 1] - theta[j + 11])
+ - step(bound[k] - theta[j + 11])
+ }
+ within[j, 5] <- step(bound[4] - theta[j + 11])
+ }
+
+
+ for (i in 1:nDate){
+ X[i] ~ dnorm(mu[i], tau[i])
+ tau[i] <- 1/pow(sigma[i],2)
+ mu[i] <- interp.lin(theta[i], calBP[], C14BP[])
+
+ # monitor the following variable to smooth density of theta
+ theta.smooth[i] <- 10 * round(theta[i] / 10)
+ }
+ }
diff --git a/doc/Examples/Stacks.html b/doc/Examples/Stacks.html
new file mode 100755
index 0000000..c10e2f2
--- /dev/null
+++ b/doc/Examples/Stacks.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stacks</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="stacks0.bmp" alt="[stacks0]">
</strong></font><font face="Courier New" color="#000100" size="6">Stacks: robust regression
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Birkes and Dodge (1993) apply different regression models to the much-analysed stack-loss data of Brownlee (1965). This features 21 daily responses of stack loss y, the amount of ammonia escaping, with covariates being air flow x
</font><font face="Arial" color="#000100" size="3"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">, temperature x
</font><font face="Arial" color="#000100" size="3"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> and acid concentration x
</font><font face="Arial" color="#000100" size="3"><sub>3
</sub></font><font face="Arial" color="#000100" size="3">. Part of the data is shown below.<br><img src="stacks1.bmp" alt="[stacks1]">
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><sub>
</sub></font><font face="Arial" color="#000100" size="3"><sub><br>
</sub></font><font face="Arial" color="#000100" size="3">We first assume a linear regression on the expectation of y, with a variety of different error structures. Specifically
</font><font face="Arial" color="#000100" size="3"><sub> <br><br>
</sub></font><font face="Arial" color="#000100" size="2"><sub>
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3"><sub>m
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub> =
</sub></font><font face="Symbol" color="#000100" size="3"><sub>b
</sub></font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"><sub> +
</sub></font><font face="Symbol" color="#000100" size="3"><sub>b
</sub></font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"><sub>z
</sub></font><font face="Arial" color="#000100" size="2"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3"><sub> +
</sub></font><font face="Symbol" color="#000100" size="3"><sub>b
</sub></font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"><sub>z
</sub></font><font face="Arial" color="#000100" size="2"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3"><sub> +
</sub></font><font face="Symbol" color="#000100" size="3"><sub>b
</sub></font><font face="Arial" color="#000100" size="2"><sub>3
</sub></font><font face="Arial" color="#000100" size="3"><sub>z
</sub></font><font face="Arial" color="#000100" size="2"><sub>3i
</sub></font><font face="Arial" color="#000100" size="3"><sub><br> <br> y
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub> ~ Normal(
</sub></font><font face="Symbol" color="#000100" size="3"><sub>m
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>,
</sub></font><font face="Symbol" color="#000100" size="3"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>)<br> <br> y
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub> ~ Double exp(
</sub></font><font face="Symbol" color="#000100" size="3"><sub>m
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>,
</sub></font><font face="Symbol" color="#000100" size="3"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>)<br> <br> y
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub> ~ t(
</sub></font><font face="Symbol" color="#000100" size="3"><sub>m
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>,
</sub></font><font face="Symbol" color="#000100" size="3"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>, d)<br> <br>
</sub></font><font face="Arial" color="#000100" size="3">where z
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = (x
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> - xbar
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">) /sd(x
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">) are covariates standardised to have zero mean and unit variance.
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>3
</sub></font><font face="Arial" color="#000100" size="3"> are initially given independent "noninformative" priors. <br><br>Maximum likelihood estimates for the double expontential (Laplace) distribution are essentially equivalent to minimising the sum of absolute deviations (LAD), while the other options are alternative heavy-tailed distributions. A t on 4 degrees of freedom has been chosen, although with more data it would be possible to allow this parameter also to be unknown. [...]
</font><font face="Arial" color="#000100" size="3"><sub> <br><br>
</sub></font><font face="Symbol" color="#000100" size="3"><sub>b
</sub></font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3"><sub>~ Normal(0,
</sub></font><font face="Symbol" color="#000100" size="3"><sub> f
</sub></font><font face="Arial" color="#000100" size="3"><sub>), j = 1, 2, 3.<br> <br>
</sub></font><font face="Arial" color="#000100" size="3">In the following example we extend the work of Birkes and Dodge (1993) by applying this ridge technique to each of the possible error distributions.<br><br>Birkes and Dodge (1993) suggest investigating outliers by examining residuals y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> -
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> greater than 2.5 standard deviations. We can calculate standardised residuals for each of these distributions, and create a variable outlier[i] taking on the value 1 whenever this condition is fulfilled. Mean values of outlier[i] then show the confidence with which this definition of outlier is fulfilled.<br><br>The
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language for all the models is shown below, with all models except the normal linear regression commented out:<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Standardise x's and coefficients<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : p) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> b[j] <- beta[j] / sd(x[ , j ]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> z[i, j] <- (x[i, j] - mean(x[, j])) / sd(x[ , j]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> b0 <- beta0 - b[1] * mean(x[, 1]) - b[2] * mean(x[, 2]) - b[3] * mean(x[, 3])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> d <- 4; # degrees of freedom for t<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y[i] ~ dnorm(mu[i], tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Y[i] ~ ddexp(mu[i], tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Y[i] ~ dt(mu[i], tau, d)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[i] <- beta0 + beta[1] * z[i, 1] + beta[2] * z[i, 2] + beta[3] * z[i, 3]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> stres[i] <- (Y[i] - mu[i]) / sigma<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> outlier[i] <- step(stres[i] - 2.5) + step(-(stres[i] + 2.5) )<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Priors <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta0 ~ dnorm(0, 0.00001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : p) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta[j] ~ dnorm(0, 0.00001) # coeffs independent<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # beta[j] ~ dnorm(0, phi) # coeffs exchangeable (ridge regression)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau ~ dgamma(1.0E-3, 1.0E-3)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> phi ~ dgamma(1.0E-2,1.0E-2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # standard deviation of error distribution<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma <- sqrt(1 / tau) # normal errors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # sigma <- sqrt(2) / tau # double exponential errors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # sigma <- sqrt(d / (tau * (d - 2))); # t errors on d degrees of freedom<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Stacksdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Stacksinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Stacksinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000000" size="3"> ( click to open )
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong>a) Normal error
</strong></font><font face="Arial" color="#000000" size="3"> <br><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center>
</font><font face="Arial" color="#000100" size="3"><br><img src="stacks2.bmp" alt="[stacks2]"><br><br>
</font><font face="Arial" color="#000100" size="3"><strong></center>b) Double exponential error
</strong></font><font face="Arial" color="#000100" size="3"><br><br>A
</font><font face="Arial" color="#000000" size="3">1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center>
</font><font face="Arial" color="#000100" size="3"><br><img src="stacks3.bmp" alt="[stacks3]"><br><br>
</font><font face="Arial" color="#000100" size="3"><strong></center>c) t4 error
</strong></font><font face="Arial" color="#000000" size="3"> <br><br>A 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center>
</font><font face="Arial" color="#000100" size="3"><br><img src="stacks4.bmp" alt="[stacks4]"><br><br>
</font><font face="Arial" color="#000100" size="3"><strong></center>d) Normal eror ridge regression
</strong></font><font face="Arial" color="#000100" size="3"><br><br>A
</font><font face="Arial" color="#000000" size="3"> 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center>
</font><font face="Arial" color="#000100" size="3"><br><img src="stacks5.bmp" alt="[stacks5]"><br><br>
</font><font face="Arial" color="#000100" size="3"><strong></center>e) Double exponential error ridge regression
</strong></font><font face="Arial" color="#000100" size="3"> <br><br>A
</font><font face="Arial" color="#000000" size="3"> 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center>
</font><font face="Arial" color="#000100" size="3"><br><br><img src="stacks6.bmp" alt="[stacks6]"><br>
</font><font face="Arial" color="#000100" size="3"><strong></center>f) t4 error ridge regression
</strong></font><font face="Arial" color="#000100" size="3"> <br><br>A
</font><font face="Arial" color="#000000" size="3"> 1000 update burn in followed by a further 10000 updates gave the parameter estimates<br><center>
</font><font face="Arial" color="#000100" size="3"><br><img src="stacks7.bmp" alt="[stacks7]">
</font><font face="Arial" color="#000100" size="2"><br></center>
</font><font face="Arial" color="#000100" size="3"><br>We note the similar results between the Birkes and Dodge methods and
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3">, and the lack of influence of the ridge technique in this context. <br>
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Stacksdata.html b/doc/Examples/Stacksdata.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stacksdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(p = 3, N = 21, <br> Y = c(42, 37, 37, 28, 18, 18, 19, 20, 15, 14, 14, 13, 11, 12, 8, 7, 8, 8, 9, 15, 15),<br> x = structure(.Data = c( 80, 27, 89,<br> 80, 27, 88,<br>   [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Stacksdata.txt b/doc/Examples/Stacksdata.txt
new file mode 100755
index 0000000..fecc4f8
--- /dev/null
+++ b/doc/Examples/Stacksdata.txt
@@ -0,0 +1,23 @@
+list(p = 3, N = 21,
+ Y = c(42, 37, 37, 28, 18, 18, 19, 20, 15, 14, 14, 13, 11, 12, 8, 7, 8, 8, 9, 15, 15),
+ x = structure(.Data = c( 80, 27, 89,
+ 80, 27, 88,
+ 75, 25, 90,
+ 62, 24, 87,
+ 62, 22, 87,
+ 62, 23, 87,
+ 62, 24, 93,
+ 62, 24, 93,
+ 58, 23, 87,
+ 58, 18, 80,
+ 58, 18, 89,
+ 58, 17, 88,
+ 58, 18, 82,
+ 58, 19, 93,
+ 50, 18, 89,
+ 50, 18, 86,
+ 50, 19, 72,
+ 50, 19, 79,
+ 50, 20, 80,
+ 56, 20, 82,
+ 70, 20, 91), .Dim = c(21, 3)))
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diff --git a/doc/Examples/Stacksinits.html b/doc/Examples/Stacksinits.html
new file mode 100755
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+++ b/doc/Examples/Stacksinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stacksinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(beta0 = 10, beta=c(0,0, 0), tau = 0.1, phi = 0.1)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Stacksinits.txt b/doc/Examples/Stacksinits.txt
new file mode 100755
index 0000000..1332975
--- /dev/null
+++ b/doc/Examples/Stacksinits.txt
@@ -0,0 +1 @@
+list(beta0 = 10, beta=c(0,0, 0), tau = 0.1, phi = 0.1)
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new file mode 100755
index 0000000..9cf3f4d
--- /dev/null
+++ b/doc/Examples/Stacksinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stacksinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(beta0 = 1.0, beta=c(1.0,1.0, 1.0), tau = 1.0, phi = 1.0)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Stacksinits1.txt b/doc/Examples/Stacksinits1.txt
new file mode 100755
index 0000000..48b78c9
--- /dev/null
+++ b/doc/Examples/Stacksinits1.txt
@@ -0,0 +1 @@
+list(beta0 = 1.0, beta=c(1.0,1.0, 1.0), tau = 1.0, phi = 1.0)
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+++ b/doc/Examples/Stacksmodel.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stacksmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Standardise x's and coefficients<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : p) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> b[j] <- beta[j] / sd(x[ , j ]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> z[i, j] <- (x[i, j] - mean(x[, j])) / sd(x[ , j]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> b0 <- beta0 - b[1] * mean(x[, 1]) - b[2] * mean(x[, 2]) - b[3] * mean(x[, 3])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> d <- 4; # degrees of freedom for t<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y[i] ~ dnorm(mu[i], tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Y[i] ~ ddexp(mu[i], tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Y[i] ~ dt(mu[i], tau, d)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[i] <- beta0 + beta[1] * z[i, 1] + beta[2] * z[i, 2] + beta[3] * z[i, 3]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> stres[i] <- (Y[i] - mu[i]) / sigma<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> outlier[i] <- step(stres[i] - 2.5) + step(-(stres[i] + 2.5) )<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Priors <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta0 ~ dnorm(0, 0.00001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : p) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta[j] ~ dnorm(0, 0.00001) # coeffs independent<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # beta[j] ~ dnorm(0, phi) # coeffs exchangeable (ridge regression)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau ~ dgamma(1.0E-3, 1.0E-3)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> phi ~ dgamma(1.0E-2,1.0E-2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # standard deviation of error distribution<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma <- sqrt(1 / tau) # normal errors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # sigma <- sqrt(2) / tau # double exponential errors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # sigma <- sqrt(d / (tau * (d - 2))); # t errors on d degrees of freedom<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }
</font><font face="Arial" color="#000100" size="3"><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Stacksmodel.txt b/doc/Examples/Stacksmodel.txt
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index 0000000..884d306
--- /dev/null
+++ b/doc/Examples/Stacksmodel.txt
@@ -0,0 +1,35 @@
+ model
+ {
+ # Standardise x's and coefficients
+ for (j in 1 : p) {
+ b[j] <- beta[j] / sd(x[ , j ])
+ for (i in 1 : N) {
+ z[i, j] <- (x[i, j] - mean(x[, j])) / sd(x[ , j])
+ }
+ }
+ b0 <- beta0 - b[1] * mean(x[, 1]) - b[2] * mean(x[, 2]) - b[3] * mean(x[, 3])
+
+ # Model
+ d <- 4; # degrees of freedom for t
+ for (i in 1 : N) {
+ Y[i] ~ dnorm(mu[i], tau)
+ # Y[i] ~ ddexp(mu[i], tau)
+ # Y[i] ~ dt(mu[i], tau, d)
+
+ mu[i] <- beta0 + beta[1] * z[i, 1] + beta[2] * z[i, 2] + beta[3] * z[i, 3]
+ stres[i] <- (Y[i] - mu[i]) / sigma
+ outlier[i] <- step(stres[i] - 2.5) + step(-(stres[i] + 2.5) )
+ }
+ # Priors
+ beta0 ~ dnorm(0, 0.00001)
+ for (j in 1 : p) {
+ beta[j] ~ dnorm(0, 0.00001) # coeffs independent
+ # beta[j] ~ dnorm(0, phi) # coeffs exchangeable (ridge regression)
+ }
+ tau ~ dgamma(1.0E-3, 1.0E-3)
+ phi ~ dgamma(1.0E-2,1.0E-2)
+ # standard deviation of error distribution
+ sigma <- sqrt(1 / tau) # normal errors
+ # sigma <- sqrt(2) / tau # double exponential errors
+ # sigma <- sqrt(d / (tau * (d - 2))); # t errors on d degrees of freedom
+ }
diff --git a/doc/Examples/Stagnant.html b/doc/Examples/Stagnant.html
new file mode 100755
index 0000000..419612e
--- /dev/null
+++ b/doc/Examples/Stagnant.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stagnant</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="stagnant0.bmp" alt="[stagnant0]">
</strong></font><font face="Courier New" color="#000100" size="6">Stagnant: a changepoint problem <br> and an illustration of how NOT<br> to do MCMC!)
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3">Carlin, Gelfand and Smith (1992) analyse data from Bacon and Watts (1971) concerning a changepoint in a linear regression.<br><img src="stagnant1.bmp" alt="[stagnant1]">
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><strong><br>Note the repeated x's.
</strong></font><font face="Arial" color="#000100" size="3"><br><br>We assume a model with two straight lines that meet at a certain changepoint x
</font><font face="Arial" color="#000100" size="3"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> --- this is slightly different from the model of Carlin, Gelfand and Smith (1992) who do not constrain the two straight lines to cross at the changepoint. We assume<br><br> Y
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"><sub>J[i]
</sub></font><font face="Arial" color="#000100" size="3"> (x
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> - x
</font><font face="Arial" color="#000100" size="3"><sub>k
</sub></font><font face="Arial" color="#000100" size="3">) J[i]=1 if i <= k J[i]=2 if i > k<br><br>giving E(Y) =
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> at the changepoint, with gradient
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> before, and gradient
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> after the changepoint. We give independent "noninformative'' priors to
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>Note: alpha is E(Y) at the changepoint, so will be highly correlated with k. This may be a very poor parameterisation. <br><br>Note way of constructing a uniform prior on the integer k, and making the regression<br>parameter depend on a random changepoint.<br>
</strong></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : N ) {<br> Y[i] ~ dnorm(mu[i],tau)<br> mu[i] <- alpha + beta[J[i]] * (x[i] - x[k])<br> J[i] <- 1 + step(i - k - 0.5)<br> punif[i] <- 1/N<br> }<br> tau ~ dgamma(0.001,0.001)<br>&n [...]
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Stagnantdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Stagnantinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Stagnantinits2.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#000100" size="3"><br>Traces of two chains shows complete dependence on starting values<br><br><img src="stagnant2.bmp" alt="[stagnant2]"><br><img src="stagnant3.bmp" alt="[stagnant3]">
</font><font face="Arial" color="#00FF00" size="5"><strong><br>
</strong></font><font face="Arial" color="#FF0000" size="5"><strong>Results are hopeless - no mixing at all.
</strong></font><font face="Arial" color="#00FF00" size="5"><strong>
</strong></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><strong>Note: alpha is E(Y) at the changepoint, so will be highly correlated with k. This may be a very poor parameterisation. <br><br>TRY USING CONTINUOUS PARAMETERISATION<br>
</strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">{<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Y[i] ~ dnorm(mu[i], tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i] <- alpha + beta[J[i]] * (x[i] - x.change) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">J[i] <- 1 + step(x[i] - x.change)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau ~ dgamma(0.001, 0.001)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha ~ dnorm(0.0,1.0E-6)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(j in 1 : 2) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta[j] ~ dnorm(0.0,1.0E-6)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma <- 1 / sqrt(tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">x.change ~ dunif(-1.3,1.1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Stagnantcdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Stagnantcinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Stagnantcinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="5"> <br><img src="stagnant4.bmp" alt="[stagnant4]"><br><center><img src="stagnant5.bmp" alt="[stagnant5]"><br>
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Stagnantcdata.html b/doc/Examples/Stagnantcdata.html
new file mode 100755
index 0000000..f530862
--- /dev/null
+++ b/doc/Examples/Stagnantcdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stagnantcdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"> list(Y = c(1.12, 1.12, 0.99, 1.03, 0.92, 0.90, 0.81, 0.83, 0.65, 0.67, 0.60, 0.59, 0.51, 0.44, 0.43,<br>0.43, 0.33, 0.30, 0.25, 0.24, 0.13, -0.01, -0.13, -0.14, -0.30, -0.33, -0.46, -0.43, -0.65),<br>x = c(-1.39, -1.39, -1.08, -1.08, -0.94, -0.80, -0.63, -0.63, -0.25, -0.25, -0.12, -0.12, 0.01, 0.11, 0.11, <br>0.11, 0.25, 0.25, 0.34, 0.34, 0.44, 0.59, 0.70, 0.70, 0.85, 0.85, 0.99, 0.99, 1.19),<br>N = 29)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Stagnantcdata.txt b/doc/Examples/Stagnantcdata.txt
new file mode 100755
index 0000000..38cd02b
--- /dev/null
+++ b/doc/Examples/Stagnantcdata.txt
@@ -0,0 +1,5 @@
+ list(Y = c(1.12, 1.12, 0.99, 1.03, 0.92, 0.90, 0.81, 0.83, 0.65, 0.67, 0.60, 0.59, 0.51, 0.44, 0.43,
+ 0.43, 0.33, 0.30, 0.25, 0.24, 0.13, -0.01, -0.13, -0.14, -0.30, -0.33, -0.46, -0.43, -0.65),
+ x = c(-1.39, -1.39, -1.08, -1.08, -0.94, -0.80, -0.63, -0.63, -0.25, -0.25, -0.12, -0.12, 0.01, 0.11, 0.11,
+ 0.11, 0.25, 0.25, 0.34, 0.34, 0.44, 0.59, 0.70, 0.70, 0.85, 0.85, 0.99, 0.99, 1.19),
+N = 29)
\ No newline at end of file
diff --git a/doc/Examples/Stagnantcinits.html b/doc/Examples/Stagnantcinits.html
new file mode 100755
index 0000000..4fdae91
--- /dev/null
+++ b/doc/Examples/Stagnantcinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stagnantcinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha = 0.47, beta = c(-0.45, -1.0), tau = 5, x.change = 0.5)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Stagnantcinits.txt b/doc/Examples/Stagnantcinits.txt
new file mode 100755
index 0000000..0853772
--- /dev/null
+++ b/doc/Examples/Stagnantcinits.txt
@@ -0,0 +1 @@
+list(alpha = 0.47, beta = c(-0.45, -1.0), tau = 5, x.change = 0.5)
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diff --git a/doc/Examples/Stagnantcinits1.html b/doc/Examples/Stagnantcinits1.html
new file mode 100755
index 0000000..70fab0a
--- /dev/null
+++ b/doc/Examples/Stagnantcinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stagnantcinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"> list(alpha = 0.47, beta = c(-0.45, -1.0), tau = 5, x.change = -0.5)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Stagnantcinits1.txt b/doc/Examples/Stagnantcinits1.txt
new file mode 100755
index 0000000..e8f2e8b
--- /dev/null
+++ b/doc/Examples/Stagnantcinits1.txt
@@ -0,0 +1 @@
+ list(alpha = 0.47, beta = c(-0.45, -1.0), tau = 5, x.change = -0.5)
\ No newline at end of file
diff --git a/doc/Examples/Stagnantcinits2.html b/doc/Examples/Stagnantcinits2.html
new file mode 100755
index 0000000..fa3deea
--- /dev/null
+++ b/doc/Examples/Stagnantcinits2.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stagnantcinits2</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"> list(alpha = 0.47, beta = c(-0.45, -1.0), tau = 5, x.change = -0.5)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Stagnantcinits2.txt b/doc/Examples/Stagnantcinits2.txt
new file mode 100755
index 0000000..e8f2e8b
--- /dev/null
+++ b/doc/Examples/Stagnantcinits2.txt
@@ -0,0 +1 @@
+ list(alpha = 0.47, beta = c(-0.45, -1.0), tau = 5, x.change = -0.5)
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diff --git a/doc/Examples/Stagnantcmodel.html b/doc/Examples/Stagnantcmodel.html
new file mode 100755
index 0000000..b3268dc
--- /dev/null
+++ b/doc/Examples/Stagnantcmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stagnantcmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for(i in 1 : N) {<br> Y[i] ~ dnorm(mu[i], tau)<br>mu[i] <- alpha + beta[J[i]] * (x[i] - x.change) <br>J[i] <- 1 + step(x[i] - x.change)<br> }<br> tau ~ dgamma(0.001, 0.001)<br> alpha ~ dnorm(0.0,1.0E-6)<br> for(j in 1 : 2) {<br> &nb [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Stagnantcmodel.txt b/doc/Examples/Stagnantcmodel.txt
new file mode 100755
index 0000000..5d7a1ab
--- /dev/null
+++ b/doc/Examples/Stagnantcmodel.txt
@@ -0,0 +1,15 @@
+ model
+ {
+ for(i in 1 : N) {
+ Y[i] ~ dnorm(mu[i], tau)
+ mu[i] <- alpha + beta[J[i]] * (x[i] - x.change)
+ J[i] <- 1 + step(x[i] - x.change)
+ }
+ tau ~ dgamma(0.001, 0.001)
+ alpha ~ dnorm(0.0,1.0E-6)
+ for(j in 1 : 2) {
+ beta[j] ~ dnorm(0.0,1.0E-6)
+ }
+ sigma <- 1 / sqrt(tau)
+ x.change ~ dunif(-1.3,1.1)
+ }
diff --git a/doc/Examples/Stagnantdata.html b/doc/Examples/Stagnantdata.html
new file mode 100755
index 0000000..e09bae4
--- /dev/null
+++ b/doc/Examples/Stagnantdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stagnantdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"> list(Y = c(1.12, 1.12, 0.99, 1.03, 0.92, 0.90, 0.81, 0.83, 0.65, 0.67, 0.60, 0.59, 0.51, 0.44, 0.43,<br>0.43, 0.33, 0.30, 0.25, 0.24, 0.13, -0.01, -0.13, -0.14, -0.30, -0.33, -0.46, -0.43, -0.65),<br>x = c(-1.39, -1.39, -1.08, -1.08, -0.94, -0.80, -0.63, -0.63, -0.25, -0.25, -0.12, -0.12, 0.01, 0.11, 0.11, <br>0.11, 0.25, 0.25, 0.34, 0.34, 0.44, 0.59, 0.70, 0.70, 0.85, 0.85, 0.99, 0.99, 1.19),<br>N = 29)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Stagnantdata.txt b/doc/Examples/Stagnantdata.txt
new file mode 100755
index 0000000..38cd02b
--- /dev/null
+++ b/doc/Examples/Stagnantdata.txt
@@ -0,0 +1,5 @@
+ list(Y = c(1.12, 1.12, 0.99, 1.03, 0.92, 0.90, 0.81, 0.83, 0.65, 0.67, 0.60, 0.59, 0.51, 0.44, 0.43,
+ 0.43, 0.33, 0.30, 0.25, 0.24, 0.13, -0.01, -0.13, -0.14, -0.30, -0.33, -0.46, -0.43, -0.65),
+ x = c(-1.39, -1.39, -1.08, -1.08, -0.94, -0.80, -0.63, -0.63, -0.25, -0.25, -0.12, -0.12, 0.01, 0.11, 0.11,
+ 0.11, 0.25, 0.25, 0.34, 0.34, 0.44, 0.59, 0.70, 0.70, 0.85, 0.85, 0.99, 0.99, 1.19),
+N = 29)
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diff --git a/doc/Examples/Stagnantinits1.html b/doc/Examples/Stagnantinits1.html
new file mode 100755
index 0000000..d2b0dc6
--- /dev/null
+++ b/doc/Examples/Stagnantinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stagnantinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"> list(alpha = 0.2, beta = c(-0.45, -1.0), tau = 5, k = 16)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Stagnantinits1.txt b/doc/Examples/Stagnantinits1.txt
new file mode 100755
index 0000000..63f3ba5
--- /dev/null
+++ b/doc/Examples/Stagnantinits1.txt
@@ -0,0 +1 @@
+ list(alpha = 0.2, beta = c(-0.45, -1.0), tau = 5, k = 16)
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diff --git a/doc/Examples/Stagnantinits2.html b/doc/Examples/Stagnantinits2.html
new file mode 100755
index 0000000..d2dfc8a
--- /dev/null
+++ b/doc/Examples/Stagnantinits2.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Stagnantinits2</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha = 0.6, beta = c(-0.45, -1.0), tau = 5, k = 8)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Stagnantinits2.txt b/doc/Examples/Stagnantinits2.txt
new file mode 100755
index 0000000..9fdabce
--- /dev/null
+++ b/doc/Examples/Stagnantinits2.txt
@@ -0,0 +1 @@
+list(alpha = 0.6, beta = c(-0.45, -1.0), tau = 5, k = 8)
\ No newline at end of file
diff --git a/doc/Examples/Surgical.html b/doc/Examples/Surgical.html
new file mode 100755
index 0000000..b40aa8c
--- /dev/null
+++ b/doc/Examples/Surgical.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Surgical</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="surgical0.bmp" alt="[surgical0]">
</strong></font><font face="Courier New" color="#000100" size="6">Surgical: Institutional ranking
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3">This example considers mortality rates in 12 hospitals performing cardiac surgery in babies. The data are shown below.<br><center>
</font><font face="Arial" color="#000100" size="2"><br><img src="surgical1.bmp" alt="[surgical1]"><br></center>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">The number of deaths r
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> for hospital
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"> are modelled as a binary response variable with `true' failure probability p
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">:<br><br> r
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>We first assume that the true failure probabilities are
</font><font face="Arial" color="#000100" size="3"><em>independent
</em></font><font face="Arial" color="#000100" size="3"> (
</font><font face="Arial" color="#000100" size="3"><em>i.e
</em></font><font face="Arial" color="#000100" size="3">.fixed effects) for each hospital. This is equivalent to assuming a standard non-informative prior distribution for the p
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">'s, namely:<br><br> p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Beta(1.0, 1.0)<br><br><center><br><br>
</font><font face="Arial" color="#000100" size="3"><em>Graphical model for fixed effects surgical example:
</em></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><img src="surgical2.bmp" alt="[surgical2]"><br> <br> <br>
</font><font face="Arial" color="#000100" size="3">BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for fixed effects surgical model:
</em></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2"></center>
</font><font face="Arial" color="#000100" size="3"><br> model<br> {<br> for( i in 1 : N ) {<br> p[i] ~ dbeta(1.0, 1.0)<br> r[i] ~ dbin(p[i], n[i])<br> }<br> }<br>
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Surgicaldata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Surgicalinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Surgicalinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">A more realistic model for the surgical data is to assume that the failure rates across hospitals are
</font><font face="Arial" color="#000100" size="3"><em>similar
</em></font><font face="Arial" color="#000100" size="3"> in some way. This is equivalent to specifying a
</font><font face="Arial" color="#000100" size="3"><em>random effects
</em></font><font face="Arial" color="#000100" size="3"> model for the true failure probabilities p
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> as follows:<br><br> logit(p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) = b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><br> <br> b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Normal(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">)<br> <br>Standard non-informative priors are then specified for the population mean (logit) probability of failure,
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="3">, and precision,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">.<br>
</font><font face="Arial" color="#000100" size="2"><br><br><center>
</font><font face="Arial" color="#000100" size="3"><em>Graphical model for random effects surgical example:
</em></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><img src="surgical3.bmp" alt="[surgical3]"><br><br><br>
</font><font face="Arial" color="#000100" size="3">BUGS
</font><font face="Arial" color="#000100" size="3"><em> language for random effects surgical model:<br></center>
</em></font><font face="Arial" color="#000100" size="3"> <br> <br> model<br> {<br> for( i in 1 : N ) {<br> b[i] ~ dnorm(mu,tau)<br> r[i] ~ dbin(p[i],n[i])<br> [...]
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Surgicaldata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Surgicalrandinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1</a>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="5"><a href="../Examples/Surgicalrandinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="5">Results
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>A burn in of 1000 updates followed by a further 10000 updates gave the following estimates of surgical mortality in each hospital for the fixed effect analysis<br><center>
</font><font face="Arial" color="#0000FF" size="3"><br><br><img src="surgical4.bmp" alt="[surgical4]"><br></center>
</font><font face="Arial" color="#000100" size="3"><br>and for the random effects analysis<br><center><br><img src="surgical5.bmp" alt="[surgical5]">
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="2"><br></center>
</font><font face="Arial" color="#000100" size="3">A particular strength of the Markov chain Monte Carlo (Gibbs sampling) approach implemented in
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> is the ability to make inferences on arbitrary functions of unknown model parameters. For example, we may compute the
</font><font face="Arial" color="#000100" size="3"><em>rank
</em></font><font face="Arial" color="#000100" size="3"> probabilty of failure for each hospital at each iteration. This yields a sample from the posterior distribution of the ranks. <br><br>The figures below show the posterior ranks for the estimated surgical mortality rate in each hospital for the random effect models. These are obtained by setting the rank monitor for variable p (select the "Rank" option from the "Statistics" menu) after the burn-in phase, and then [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><em>Plots of distribution of ranks of true failure probability for random effects model:
</em></font><font face="Arial" color="#000100" size="3"><br><br><center>
</font><font face="Arial" color="#000100" size="2"><img src="surgical6.bmp" alt="[surgical6]"><img src="surgical7.bmp" alt="[surgical7]"><img src="surgical8.bmp" alt="[surgical8]"><img src="surgical9.bmp" alt="[surgical9]"><img src="surgical10.bmp" alt="[surgical10]"><img src="surgical11.bmp" alt="[surgical11]"><img src="surgical12.bmp" alt="[surgical12]"><img src="surgical13.bmp" alt="[surgical13]"><img src="surgical14.bmp" alt="[surgical14]"><img src="surgical15.bmp" alt="[surgical15]"> [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Examples/Surgicaldata.html b/doc/Examples/Surgicaldata.html
new file mode 100755
index 0000000..73f3576
--- /dev/null
+++ b/doc/Examples/Surgicaldata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Surgicaldata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(n = c(47, 148, 119, 810, 211, 196, 148, 215, 207, 97, 256, 360),<br> r = c(0, 18, 8, 46, 8, 13, 9, 31, 14, 8, 29, 24),<br> N = 12)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Surgicaldata.txt b/doc/Examples/Surgicaldata.txt
new file mode 100755
index 0000000..b54814d
--- /dev/null
+++ b/doc/Examples/Surgicaldata.txt
@@ -0,0 +1,3 @@
+list(n = c(47, 148, 119, 810, 211, 196, 148, 215, 207, 97, 256, 360),
+ r = c(0, 18, 8, 46, 8, 13, 9, 31, 14, 8, 29, 24),
+ N = 12)
\ No newline at end of file
diff --git a/doc/Examples/Surgicalinits.html b/doc/Examples/Surgicalinits.html
new file mode 100755
index 0000000..94e797a
--- /dev/null
+++ b/doc/Examples/Surgicalinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Surgicalinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"> list(p = c(0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1))
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Surgicalinits.txt b/doc/Examples/Surgicalinits.txt
new file mode 100755
index 0000000..e165b6e
--- /dev/null
+++ b/doc/Examples/Surgicalinits.txt
@@ -0,0 +1 @@
+ list(p = c(0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1))
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diff --git a/doc/Examples/Surgicalinits1.html b/doc/Examples/Surgicalinits1.html
new file mode 100755
index 0000000..59e50df
--- /dev/null
+++ b/doc/Examples/Surgicalinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Surgicalinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"> list(p = c(0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5))
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Surgicalinits1.txt b/doc/Examples/Surgicalinits1.txt
new file mode 100755
index 0000000..ce06764
--- /dev/null
+++ b/doc/Examples/Surgicalinits1.txt
@@ -0,0 +1 @@
+ list(p = c(0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5))
\ No newline at end of file
diff --git a/doc/Examples/Surgicalmodel.html b/doc/Examples/Surgicalmodel.html
new file mode 100755
index 0000000..5b5387c
--- /dev/null
+++ b/doc/Examples/Surgicalmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Surgicalmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : N ) {<br> p[i] ~ dbeta(1.0, 1.0)<br> r[i] ~ dbin(p[i], n[i])<br> }<br> }<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Surgicalmodel.txt b/doc/Examples/Surgicalmodel.txt
new file mode 100755
index 0000000..8df5dd5
--- /dev/null
+++ b/doc/Examples/Surgicalmodel.txt
@@ -0,0 +1,7 @@
+ model
+ {
+ for( i in 1 : N ) {
+ p[i] ~ dbeta(1.0, 1.0)
+ r[i] ~ dbin(p[i], n[i])
+ }
+ }
diff --git a/doc/Examples/Surgicalranddata.html b/doc/Examples/Surgicalranddata.html
new file mode 100755
index 0000000..be77bbd
--- /dev/null
+++ b/doc/Examples/Surgicalranddata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Surgicalranddata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(n = c(47, 148, 119, 810, 211, 196, 148, 215, 207, 97, 256, 360),<br> r = c(0, 18, 8, 46, 8, 13, 9, 31, 14, 8, 29, 24),<br> N = 12)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Surgicalranddata.txt b/doc/Examples/Surgicalranddata.txt
new file mode 100755
index 0000000..b54814d
--- /dev/null
+++ b/doc/Examples/Surgicalranddata.txt
@@ -0,0 +1,3 @@
+list(n = c(47, 148, 119, 810, 211, 196, 148, 215, 207, 97, 256, 360),
+ r = c(0, 18, 8, 46, 8, 13, 9, 31, 14, 8, 29, 24),
+ N = 12)
\ No newline at end of file
diff --git a/doc/Examples/Surgicalrandinits.html b/doc/Examples/Surgicalrandinits.html
new file mode 100755
index 0000000..cd9b061
--- /dev/null
+++ b/doc/Examples/Surgicalrandinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Surgicalrandinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(b = c( 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1), <br> tau = 1, mu = 0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/Surgicalrandinits.txt b/doc/Examples/Surgicalrandinits.txt
new file mode 100755
index 0000000..5814694
--- /dev/null
+++ b/doc/Examples/Surgicalrandinits.txt
@@ -0,0 +1,2 @@
+list(b = c( 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1),
+ tau = 1, mu = 0)
\ No newline at end of file
diff --git a/doc/Examples/Surgicalrandinits1.html b/doc/Examples/Surgicalrandinits1.html
new file mode 100755
index 0000000..ed66577
--- /dev/null
+++ b/doc/Examples/Surgicalrandinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Surgicalrandinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(b = c( 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5), <br> tau = 0.1, mu = 1.0)
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Surgicalrandinits1.txt b/doc/Examples/Surgicalrandinits1.txt
new file mode 100755
index 0000000..31e902f
--- /dev/null
+++ b/doc/Examples/Surgicalrandinits1.txt
@@ -0,0 +1,2 @@
+list(b = c( 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5),
+ tau = 0.1, mu = 1.0)
\ No newline at end of file
diff --git a/doc/Examples/Surgicalrandmodel.html b/doc/Examples/Surgicalrandmodel.html
new file mode 100755
index 0000000..48b9dd2
--- /dev/null
+++ b/doc/Examples/Surgicalrandmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Surgicalrandmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model<br> {<br> for( i in 1 : N ) {<br> b[i] ~ dnorm(mu,tau)<br> r[i] ~ dbin(p[i],n[i])<br> logit(p[i]) <- b[ [...]
</font><font face="Arial" color="#000100" size="3"><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Examples/Surgicalrandmodel.txt b/doc/Examples/Surgicalrandmodel.txt
new file mode 100755
index 0000000..cf31b26
--- /dev/null
+++ b/doc/Examples/Surgicalrandmodel.txt
@@ -0,0 +1,12 @@
+ model
+ {
+ for( i in 1 : N ) {
+ b[i] ~ dnorm(mu,tau)
+ r[i] ~ dbin(p[i],n[i])
+ logit(p[i]) <- b[i]
+ }
+ pop.mean <- exp(mu) / (1 + exp(mu))
+ mu ~ dnorm(0.0,1.0E-6)
+ sigma <- 1 / sqrt(tau)
+ tau ~ dgamma(0.001,0.001)
+ }
diff --git a/doc/Examples/Voles.html b/doc/Examples/Voles.html
new file mode 100755
index 0000000..573b10b
--- /dev/null
+++ b/doc/Examples/Voles.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Voles</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"><br><img src="voles0.bmp" alt="[voles0]">
</font><font face="Arial" color="#0000FF" size="3"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Voles: estimating the size of a <br> closed population using the data<br> augmentation technique
</font><font face="Arial" color="#0000FF" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="6"> <br> (contributed by Andy Royle)<br>
</font><font face="Arial" color="#000100" size="3"><br>Estimating the size of a closed population is a classical problem in statistical ecology. We consider the simplest of a huge class of models, referred to colloquially as "Model M0" in the jargon of capture-recapture. We provide a Bayesian analysis of this model based on data augmentation. Data augmentation can be used to analyze any capture-recapture model in which the population size, N, is unknown.<br><br>The standard desi [...]
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> for i =1, 2,..., nind. The problem is to estimate the size of the population N = nind + n0, where n0 is the number of individuals not captured. <br><br>If we knew N, then the model for the observed data y
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">would simply be that:<br><br>y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(p, J) for i= 1, 2,...., N<br><br>In practice N is not known, and there are a number of ways for handling that in the model formulation, i.e., so that estimates of population size, N, can be obtained.<br><br>
</font><font face="Courier New" color="#000100" size="6">Classical solution
</font><font face="Arial" color="#000100" size="3"><br><br>Since there are J +1 mutually exclusive outcomes (y = 0, 1, 2,..., J), the classical solution to the problem is to formulate the model for the encounter frequencies as a multinomial with unknown sample size N = nind + n0. The cell probabilities are binomial cell probabilities of the form p
</font><font face="Arial" color="#000100" size="2"><sup>j
</sup></font><font face="Arial" color="#000100" size="3">(1 - p)
</font><font face="Arial" color="#000100" size="2"><sup>J - j
</sup></font><font face="Arial" color="#000100" size="3">. <br><br>We do not know if the multinomial model can be implemented directly in WinBUGS. Here we provide an analysis of this simplest of models for estimation of population size by a technique called data augmentation (see Royle, Dorazio and Link, 2007, J. Comp. and Graph. Stats.).<br><br>
</font><font face="Courier New" color="#000100" size="6">Bayesian analysis based on data augmentation
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="3"><br>The two parameters are p and N (or n0) for which a natural prior specification is:<br> <br> p ~ uniform(0,1) and <br> N ~ uniform(0, M) for some large M.<br> <br>For implem [...]
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernouli(psi) for i = 1, 2, ...., M such that N =
</font><font face="Symbol" color="#000100" size="5">S
</font><font face="Arial" color="#000100" size="3">z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">. To implement this model in WinBUGS we introduce excess zero "observations" y
</font><font face="Arial" color="#000100" size="2"><sub>nind +1
</sub></font><font face="Arial" color="#000100" size="3"> = 0,....., y
</font><font face="Arial" color="#000100" size="2"><sub>M
</sub></font><font face="Arial" color="#000100" size="3"> = 0, the set of latent indicator variables z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernouli(psi) and the model for the augmented data is:<br><br> z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Bernoulli(psi) for i = 1, 2,..... M [note M here not N]<br> y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial( z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> * p, J) for i = 1, 2, .... M [note M here not N]<br> psi ~ uniform(0, 1)<br> p ~ uniform(0, 1)<br><br>Interestingly, this is precisely a zero-inflated binomial model (see "Gentians" example). The population size [...]
</font><font face="Symbol" color="#000100" size="5">S
</font><font face="Arial" color="#000100" size="3">z
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">.<br><br>Some discussion of data augmentation in this context can be found in Royle, Dorazio and Link (JCGS, 2007) as well as in Royle and Dorazio (Academic Press, 2008). Care should be taken in choice of M -- a value too small will cause posterior mass to pile up on the boundary N=M. As the intent of the discrete uniform prior is to express the absence of prior information, M should be increased in such cases. But note that too lar [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000000" size="3"># prior distributions<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">psi ~ dunif(0, 1)<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">p ~ dunif(0,1)<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"># zero-inflated binomial model for the augmented data<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">for(i in 1 : nind + nz){<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">z[i] ~ dbern(psi)<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">mu[i] <- z[i ]* p<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">y[i] ~ dbin(mu[i], J)<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"># N is a derived parameter under data augmentation
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">N<-sum(z[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Courier New" color="#000100" size="6">Example analysis
</font><font face="Arial" color="#0000FF" size="5"><br>
</font><font face="Arial" color="#000100" size="3"><br>The data are capture-recapture data on voles
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">(Microtus) (see Williams, Nichols and Conroy, Academic Press, 2002, for additional details and more extensive data). The study was conducted over J = 5 days and yielded encounter histories on nind = 56 individuals. For this analysis, the data set was augmented with nz = 60 individuals. This example comes from Chapter 5 of Royle and Dorazio (Academic Press, 2008). <br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Volesdata.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Data
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Volesinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="3"> </a>
</font><font face="Arial" color="#0000FF" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Examples/Volesinits2.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#000100" size="3">( click to open )
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#0000FF" size="5">Results<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3">Two chains were run for 11000 iterations which produced the following estimates. Note that the posterior mode of N is on the boundary N = nind, a result of the high per sample detection probability (posterior mean of p = 0.63).<br><center>
</font><font face="Arial" color="#000100" size="1"><br><img src="voles1.bmp" alt="[voles1]">
</font><font face="Arial" color="#000100" size="3"><br></center><br><br><img src="voles2.bmp" alt="[voles2]"><img src="voles3.bmp" alt="[voles3]"><br><img src="voles4.bmp" alt="[voles4]">
</font>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Volesdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">##note that the "data" contain nz = 60 y = 0 "augmented" observations<br>list(y=<br>c(2, 3, 4, 5, 1, 3, 5, 5, 4, 2, 5, 3, 5, 4, 4, 3, 5, 1, 2, 3, <br>2, 4, 5, 5, 1, 1, 2, 4, 4, 5, 4, 1, 3, 1, 1, 2, 5, 5, 4, 1, 5, <br>4, 1, 4, 3, 5, 4, 1, 3, 1, 1, 2, 5, 3, 5, 2, 0, 0, 0, 0, 0, 0, <br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, <br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, <br>0, 0, 0, 0, [...]
</font>
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diff --git a/doc/Examples/Volesdata.txt b/doc/Examples/Volesdata.txt
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+##note that the "data" contain nz = 60 y = 0 "augmented" observations
+list(y=
+c(2, 3, 4, 5, 1, 3, 5, 5, 4, 2, 5, 3, 5, 4, 4, 3, 5, 1, 2, 3,
+2, 4, 5, 5, 1, 1, 2, 4, 4, 5, 4, 1, 3, 1, 1, 2, 5, 5, 4, 1, 5,
+4, 1, 4, 3, 5, 4, 1, 3, 1, 1, 2, 5, 3, 5, 2, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
+nind = 56,
+nz = 60,
+J = 5)
diff --git a/doc/Examples/Volesinits1.html b/doc/Examples/Volesinits1.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Volesinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(p = 0.985380, psi = 0.559106, z = c(<br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1))<br>
</font>
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diff --git a/doc/Examples/Volesinits1.txt b/doc/Examples/Volesinits1.txt
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+list(p = 0.985380, psi = 0.559106, z = c(
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
diff --git a/doc/Examples/Volesinits2.html b/doc/Examples/Volesinits2.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Volesinits2</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(p = 0.4, psi = 0.3, z = c(<br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,<br>1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0,<br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,<br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,<br>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))<br>
</font>
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diff --git a/doc/Examples/Volesinits2.txt b/doc/Examples/Volesinits2.txt
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+++ b/doc/Examples/Volesinits2.txt
@@ -0,0 +1,7 @@
+list(p = 0.4, psi = 0.3, z = c(
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
diff --git a/doc/Examples/Volesmodel.html b/doc/Examples/Volesmodel.html
new file mode 100755
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--- /dev/null
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Volesmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000000" size="3"># prior distributions<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">psi ~ dunif(0, 1)<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">p ~ dunif(0,1)<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"># zero-inflated binomial model for the augmented data<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">for(i in 1 : nind + nz){<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">z[i] ~ dbern(psi)<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">mu[i] <- z[i ]* p<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">y[i] ~ dbin(mu[i], J)<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000000" size="1">
</font><font face="Arial" color="#000000" size="3"># N is a derived parameter under data augmentation
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">N<-sum(z[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font>
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diff --git a/doc/Examples/Volesmodel.txt b/doc/Examples/Volesmodel.txt
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+
+ model {
+ # prior distributions
+ psi ~ dunif(0, 1)
+ p ~ dunif(0,1)
+ # zero-inflated binomial model for the augmented data
+ for(i in 1 : nind + nz){
+ z[i] ~ dbern(psi)
+ mu[i] <- z[i ]* p
+ y[i] ~ dbin(mu[i], J)
+ }
+ # N is a derived parameter under data augmentation
+ N<-sum(z[])
+ }
diff --git a/doc/Examples/VolumeEco.html b/doc/Examples/VolumeEco.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>VolumeEco</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="volumeeco0.bmp" alt="[volumeeco0]">
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Ecology Examples<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <br> <a href="../Examples/Gentians.html">Gentians: imperfect detection in site occppancy</a><br> <br> <a href="../Examples/Sparrowhawk.html">Sparrowhawks: generalised metapopulation model</a><br> <br> <a href="../Examples/Birds.html">Birds: estimating species richness</a><br> <br> &nbs [...]
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#0000FF" size="3"><u><br>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000000" size="3"><strong>References
</strong></font><font face="Arial" color="#000000" size="3">: <br> Sorry - an on-line version of the references is currently unavailable. <br> Please refer to the existing
</font><font face="Arial" color="#000100" size="3"> Examples documentation available from<br>
</font><font face="Courier" color="#000100" size="3"> http://www.mrc-bsu.cam.ac.uk/bugs
</font><font face="Arial" color="#000100" size="3">.
</font>
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diff --git a/doc/Examples/Volumei.html b/doc/Examples/Volumei.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Volumei</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="volumei0.bmp" alt="[volumei0]">
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Examples Volume 1<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="../Examples/Rats.html">Rats: Normal hierarchical model</a><br> <br> <a href="../Examples/Pumps.html">Pump: conjugate gamma-Poisson hierarchical model</a><br> <br> <a href="../Examples/Dogs.html">Dogs: log linear binary model</a><br> <br> <a href=". [...]
</font><font face="Arial" color="#0000FF" size="1"><u><br>
</u></font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><strong>References
</strong></font><font face="Arial" color="#000000" size="3">: <br>
</font><font face="Arial" color="#000000" size="2">Sorry - an on-line version of the references is currently unavailable. <br>
</font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000000" size="2">Please refer to the existing
</font><font face="Arial" color="#000100" size="2"> Examples documentation available from<br>
</font><font face="Courier" color="#000100" size="3"> http://www.mrc-bsu.cam.ac.uk/bugs
</font><font face="Arial" color="#000100" size="3">.
</font>
</p>
</body>
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<head>
<title>Volumeii</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="volumeii0.bmp" alt="[volumeii0]">
</strong></font><font face="Arial" color="#000100" size="6">
</font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Examples Volume 2
</font><font face="Arial" color="#000100" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Examples/Dugongs.html">Dugongs: a nonconjugate, nonlinear model</a><br> <br> <a href="../Examples/Otrees.html">Orange trees: a hierarchical, nonlinear model</a><br> <br> <a href="../Examples/OtreesMVN.html">Multivariate Orange trees: <br> a&nb [...]
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#0000FF" size="3"><u><br>
</u></font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000000" size="3"><strong><br> References
</strong></font><font face="Arial" color="#000000" size="3">: <br> Sorry - an on-line version of the references is currently unavailable. <br> Please refer to the existing
</font><font face="Arial" color="#000100" size="3"> Examples documentation available from<br>
</font><font face="Courier" color="#000100" size="3"> http://www.mrc-bsu.cam.ac.uk/bugs
</font><font face="Arial" color="#000100" size="3">.
</font>
</p>
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<html>
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<title>Volumeiii</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><strong><img src="volumeiii0.bmp" alt="[volumeiii0]">
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Examples Volume 3<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="../Examples/Camel.html">Camel: multivariate normal with structured missing data</a><br> <br> <a href="../Examples/Eye-tracking.html">Eye Tracking: dirichlet process prior</a><br> <br> <a href="../Examples/Fire.html">Fire insurance claims: data distribution using dloglik</a><br>&nbs [...]
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#0000FF" size="3"><u><br>
</u></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000000" size="3"><strong>References
</strong></font><font face="Arial" color="#000000" size="3">: <br> Sorry - an on-line version of the references is currently unavailable. <br> Please refer to the existing
</font><font face="Arial" color="#000100" size="3"> Examples documentation available from<br>
</font><font face="Courier" color="#000100" size="3"> http://www.mrc-bsu.cam.ac.uk/bugs
</font><font face="Arial" color="#000100" size="3">.
</font>
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</body>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>t-df</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="5"><strong><img src="t-df0.bmp" alt="[t-df0]">
</strong></font><font face="Courier New" color="#000100" size="6">Simulating data: learning about the<br> degrees of freedom of a <br> t-distribution
</font><font face="Arial" color="#000000" size="5"><strong><br>
</strong></font><font face="Arial" color="#000000" size="2"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3">This example uses simulated data: we generate n = 1000 observations from a (standard) t distribution with
</font><font face="Arial" color="#000000" size="3"><em>d = 4
</em></font><font face="Arial" color="#000000" size="3"> degrees of freedom:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> d <- 4<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1 : 1000) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> y[i] ~ dt(0, 1, d)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br>We let the sampler run for a while (just to check that we're simulating from the correct distribution) and then we save a set of simulated data using the 'save state' facility (select
</font><font face="Arial" color="#000000" size="3"><em>Save State
</em></font><font face="Arial" color="#000000" size="3"> from the
</font><font face="Arial" color="#000000" size="3"><em>Model
</em></font><font face="Arial" color="#000000" size="3"> menu).<br><br>Check: should have mean 0, variance 2, etc.<br><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> y[1] 0.01129 1.383 0.01415 -2.645 -0.01056 2.843 1001 10000<br> <br>
</font><font face="Arial" color="#000000" size="3"><br> <img src="t-df1.bmp" alt="[t-df1]">
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000000" size="3">To analyse the simulated data: first we try a model for learning about the degrees of freedom as a continuous quantity:<br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Model:<br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1:1000) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> y[i] ~ dt(0, 1, d)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> d ~ dunif(2, 100) # degrees of freedom must be at least two<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> d 4.282 0.4398 0.01448 3.493 4.252 5.217 1001 10000<br><br>
</font><font face="Arial" color="#0000FF" size="2"><img src="t-df2.bmp" alt="[t-df2]"><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000000" size="3">Now we attempt to model the degrees of freedom parameter with a discrete uniform prior on {2, 3, 4, ..., 50}. The sampler soon converges to
</font><font face="Arial" color="#000000" size="3"><em>d
</em></font><font face="Arial" color="#000000" size="3"> = 4 but mixes poorly.<br>
</font><font face="Arial" color="#0000FF" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Model:<br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (j in 1:49) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> p[j] <- 1 / 49<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> d.value[j] <- j + 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1:1000) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> y[i] ~ dt(0, 1, d)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> K ~ dcat(p[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> d <- d.value[K]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> d 4.204 0.4102 0.03144 4.0 4.0 5.0 1001 10000<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><img src="t-df3.bmp" alt="[t-df3]"><br>
</strong></font><font face="Arial" color="#000000" size="3"><br>We should get better mixing if we specify the prior for
</font><font face="Arial" color="#000000" size="3"><em>d
</em></font><font face="Arial" color="#000000" size="3"> on a finer grid, e.g. {2.0, 2.1, 2.2, ..., 6.0}:<br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Model:<br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1:41) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> p[j] <- 1 / 41<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> d.value[j] <- 2 + (j - 1) * 0.1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1:1000) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y[i] ~ dt(0, 1, d)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> K ~ dcat(p[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> d <- d.value[K]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> d 4.277 0.4162 0.01194 3.5 4.3 5.1 1001 10000<br><br><br><img src="t-df4.bmp" alt="[t-df4]">
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Simulated data:<br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000000" size="2"> click to opensimulated t4 data
</font><font face="Arial" color="#000100" size="2">
</font>
</p>
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</html>
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+++ b/doc/Examples/t-dfdata.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>t-dfdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(<br>y = c(<br>0.6198,0.909,1.214,-0.2378,2.471,<br>0.8881,4.526,-3.048,-0.4039,0.1464,<br>0.8168,0.3377,1.244,-0.5036,-3.275,<br>0.2038,0.2198,0.02984,-1.591,1.219,<br>0.456,0.8206,-0.8904,0.5116,1.709,<br>-0.1632,-0.1556,-0.9488,0.2658,-0.2757,<br>-0.7156,0.3891,-0.3972,1.126,-0.04562,<br>-1.023,-0.2997,-1.529,-1.304,-0.3963,<br>-1.342,0.2707,-0.7539,1.075,-1.236,<br>0.2686,-0.7793,0.247,-0.1234,1.096,<br>0.3949,0.2669,-0.3347,0.9494,1.075 [...]
</font>
</p>
</body>
</html>
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@@ -0,0 +1,202 @@
+list(
+y = c(
+0.6198,0.909,1.214,-0.2378,2.471,
+0.8881,4.526,-3.048,-0.4039,0.1464,
+0.8168,0.3377,1.244,-0.5036,-3.275,
+0.2038,0.2198,0.02984,-1.591,1.219,
+0.456,0.8206,-0.8904,0.5116,1.709,
+-0.1632,-0.1556,-0.9488,0.2658,-0.2757,
+-0.7156,0.3891,-0.3972,1.126,-0.04562,
+-1.023,-0.2997,-1.529,-1.304,-0.3963,
+-1.342,0.2707,-0.7539,1.075,-1.236,
+0.2686,-0.7793,0.247,-0.1234,1.096,
+0.3949,0.2669,-0.3347,0.9494,1.075,
+4.86,0.5967,0.5605,-1.331,-0.2925,
+0.404,-0.09936,-1.799,-0.3873,1.323,
+0.2479,0.2486,-1.114,-0.3774,-0.3704,
+1.497,1.736,-1.657,-0.02219,-0.8786,
+1.362,1.282,0.709,-1.443,0.5774,
+-0.2957,0.9289,5.142,0.9784,-1.774,
+1.034,0.3699,-1.665,-0.199,1.119,
+-1.474,-0.2979,1.268,-2.396,-1.626,
+2.185,0.1846,0.7285,-1.627,-2.699,
+0.5002,0.2033,0.7209,-0.4287,-0.2053,
+-0.4245,-0.6676,1.381,-1.259,0.5434,
+-1.013,0.5165,0.2755,0.9312,-0.7799,
+2.601,2.51,-0.3427,1.048,0.4806,
+-3.194,-0.6113,-1.234,0.6285,0.02296,
+0.4129,0.1305,-0.9421,-1.277,-0.31,
+-0.5866,0.2431,-0.3949,-0.3085,0.4198,
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\ No newline at end of file
diff --git a/doc/Examples/t-dfmodel.html b/doc/Examples/t-dfmodel.html
new file mode 100755
index 0000000..c1dbe17
--- /dev/null
+++ b/doc/Examples/t-dfmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>t-dfmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1:1000) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> y[i] ~ dt(0, 1, d)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> d ~ dunif(2, 100) # degrees of freedom must be at least two<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Examples/t-dfmodel.txt b/doc/Examples/t-dfmodel.txt
new file mode 100755
index 0000000..51005b6
--- /dev/null
+++ b/doc/Examples/t-dfmodel.txt
@@ -0,0 +1,6 @@
+ model {
+ for (i in 1:1000) {
+ y[i] ~ dt(0, 1, d)
+ }
+ d ~ dunif(2, 100) # degrees of freedom must be at least two
+ }
diff --git a/doc/Examples/voles0.bmp b/doc/Examples/voles0.bmp
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diff --git a/doc/Examples/voles2.bmp b/doc/Examples/voles2.bmp
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diff --git a/doc/Examples/voles4.bmp b/doc/Examples/voles4.bmp
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diff --git a/doc/Examples/volumei0.bmp b/doc/Examples/volumei0.bmp
new file mode 100755
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diff --git a/doc/Examples/volumeii0.bmp b/doc/Examples/volumeii0.bmp
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diff --git a/doc/Examples/volumeiii0.bmp b/doc/Examples/volumeiii0.bmp
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diff --git a/doc/GeoBUGS/Examples/Elevation.html b/doc/GeoBUGS/Examples/Elevation.html
new file mode 100755
index 0000000..300464a
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Elevation.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Elevation</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="elevation0.bmp" alt="[elevation0]">
</font><font face="Courier New" color="#000100" size="6">Bayesian kriging and spatial<br> prediction:Surface elevation
</font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3"><br>The data for this example are taken from Diggle and Riberio (2000) (and came originally from Davis (1973)). The data file contains the variables height, x and y, giving surface elevation at each of 52 locations (x, y) within a 310-foot square. The unit of distance is 50 feet, whereas one unit of height represents 10 feet of elevation. A Gaussian kriging model can be fitted to these data in OpenBUGS using either the
</font><font face="Arial" color="#000100" size="3"><strong><em><a href="../GeoBUGS/Manuals/Manual.html#spatial.exp">
</em></strong></font><font face="Arial" color="#0000FF" size="3"><strong><em><u>spatial.exp
</u></em></strong></font><font face="Arial" color="#000100" size="3"><strong><em></a>
</em></strong></font><font face="Arial" color="#000000" size="3"> or
</font><font face="Arial" color="#000100" size="3"><strong><em><a href="../GeoBUGS/Manuals/Manual.html#spatial.exp">
</em></strong></font><font face="Arial" color="#0000FF" size="3"><strong><em><u>spatial.disc
</u></em></strong></font><font face="Arial" color="#000100" size="3"><strong><em></a>
</em></strong></font><font face="Arial" color="#000000" size="3"> distributions. The data file also contains a set of locations x.pred and y.pred representing a 15 x 15 grid of points at which we wish to predict surface elevation. Predictions can be obtained using either the
</font><font face="Arial" color="#000100" size="3"><strong><em><a href="../GeoBUGS/Manuals/Manual.html#spatial.exp.pred">
</em></strong></font><font face="Arial" color="#0000FF" size="3"><strong><em><u>spatial.pred
</u></em></strong></font><font face="Arial" color="#000100" size="3"><strong><em></a>
</em></strong></font><font face="Arial" color="#000000" size="3"> or
</font><font face="Arial" color="#000100" size="3"><strong><em><a href="../GeoBUGS/Manuals/Manual.html#spatial.exp.pred">
</em></strong></font><font face="Arial" color="#0000FF" size="3"><strong><em><u>spatial.unipred
</u></em></strong></font><font face="Arial" color="#000100" size="3"><strong><em></a>
</em></strong></font><font face="Arial" color="#000000" size="3"> predictive distributions in OpenBUGS<br>
</font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong>Model
</strong></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Spatially structured multivariate normal likelihood
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3"># exponential correlation function<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> height[1:N] ~ spatial.exp(mu[], x[], y[], tau, phi, kappa)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # disc correlation function <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># height[1:N] ~ spatial.disc(mu[], x[], y[], tau, alpha)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[i] <- beta<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Priors
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta ~ dflat()<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau ~ dgamma(0.001, 0.001) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma2 <- 1/tau<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># priors for spatial.exp parameters<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # prior range for correlation at min distance (0.2 x 50 ft) is 0.02 to 0.99<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> phi ~ dunif(0.05, 20)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># prior range for correlation at max distance (8.3 x 50 ft) is 0 to 0.66<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> kappa ~ dunif(0.05,1.95)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># priors for spatial.disc parameter<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # prior range for correlation at min distance (0.2 x 50 ft) is 0.07 to 0.96<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># alpha ~ dunif(0.25, 48)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># prior range for correlation at max distance (8.3 x 50 ft) is 0 to 0.63<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Spatial prediction
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Single site prediction<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(j in 1:M) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> height.pred[j] ~ spatial.unipred(beta, x.pred[j], y.pred[j], height[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Only use joint prediction for small subset of points, due to length of time it takes to run<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(j in 1:10) { mu.pred[j] <- beta }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> height.pred.multi[1:10] ~ spatial.pred(mu.pred[], x.pred[1:10], y.pred[1:10], height[]) <br> }<br> }<br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Elevationdata.html">Data</a>
</u></strong></font><font face="Arial" color="#0000FF" size="3"><u>
</u></font><font face="Arial" color="#000100" size="3">(Click to open)<br><br>Initial values for exponential model<br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Elevationinits.html">Inits for chain 1</a> <a href="../GeoBUGS/Examples/Elevationinits1.html">Inits for chain 2</a>
</u></strong></font><font face="Arial" color="#000100" size="3">(Click to open)
</font><font face="Arial" color="#0000FF" size="3"><u><br><br><br>
</u></font><font face="Arial" color="#000100" size="3">Initial values for disc model
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/ElevationDiscinits.html">Inits for chain 1</a> <a href="../GeoBUGS/Examples/ElevationDiscinits1.html">Inits for chain 2</a>
</u></strong></font><font face="Arial" color="#000100" size="3">(Click to open)
</font><font face="Arial" color="#0000FF" size="3"><u><br><br>
</u></font><font face="Arial" color="#000100" size="3">Results for exponential model
</font><font face="Arial" color="#0000FF" size="3"><br><center>
</font><font face="Arial" color="#000100" size="3"><br> <img src="elevation1.bmp" alt="[elevation1]"><br> <br> <img src="elevation2.bmp" alt="[elevation2]"><br><br></center>
</font><font face="Arial" color="#0000FF" size="3"><u><br>
</u></font><font face="Arial" color="#000100" size="3">Results for disc model<br>
</font><font face="Arial" color="#0000FF" size="3"><br><center><img src="elevation3.bmp" alt="[elevation3]"><br><br><br><img src="elevation4.bmp" alt="[elevation4]"><br></center>
</font><font face="Arial" color="#000100" size="3"><br>The GeoBUGS map tool can be used to produce an approximate map of the posterior mean predicted surface elevation. It is not possible to map point locations using GeoBUGS. However, a map file called
</font><font face="Arial" color="#000100" size="3"><strong><em>elevation
</em></strong></font><font face="Arial" color="#000100" size="3"> is already loaded in the GeoBUGS Map Tool --- this is a 15 x 15 grid with the centroids of the grid cell corresponding to the locations of each of the prediction points. You can use this to produce a map of the posterior mean (or other posterior summaries) of the vector of predicted values
</font><font face="Arial" color="#000100" size="3"><strong><em>height.pred
</em></strong></font><font face="Arial" color="#000100" size="3">. <br><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/ElevationDiscinits.html b/doc/GeoBUGS/Examples/ElevationDiscinits.html
new file mode 100755
index 0000000..30bee78
--- /dev/null
+++ b/doc/GeoBUGS/Examples/ElevationDiscinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ElevationDiscinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(tau=0.001, phi = 0.1, beta=820, alpha=5,<br>height.pred=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, <br>0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/ElevationDiscinits.txt b/doc/GeoBUGS/Examples/ElevationDiscinits.txt
new file mode 100755
index 0000000..92bce15
--- /dev/null
+++ b/doc/GeoBUGS/Examples/ElevationDiscinits.txt
@@ -0,0 +1,8 @@
+list(tau=0.001, phi = 0.1, beta=820, alpha=5,
+height.pred=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0),
+height.pred.multi=c(0,0,0,0,0,0,0,0,0,0))
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/ElevationDiscinits1.html b/doc/GeoBUGS/Examples/ElevationDiscinits1.html
new file mode 100755
index 0000000..e33ef2d
--- /dev/null
+++ b/doc/GeoBUGS/Examples/ElevationDiscinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ElevationDiscinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(tau=0.1, phi=0.1, beta=1000, alpha = 1,<br>height.pred=c(100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100, <br>100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,<br>100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,10 [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/ElevationDiscinits1.txt b/doc/GeoBUGS/Examples/ElevationDiscinits1.txt
new file mode 100755
index 0000000..e6b5d02
--- /dev/null
+++ b/doc/GeoBUGS/Examples/ElevationDiscinits1.txt
@@ -0,0 +1,8 @@
+list(tau=0.1, phi=0.1, beta=1000, alpha = 1,
+height.pred=c(100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,
+ 100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,
+100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,
+100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,
+100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,
+ 100,100,100,100,100,100,100,100,100,100,100,100,100,100,100),
+height.pred.multi=c(100,100,100,100,100,100,100,100,100,100))
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Elevationdata.html b/doc/GeoBUGS/Examples/Elevationdata.html
new file mode 100755
index 0000000..ccf5cfc
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Elevationdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Elevationdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N=52, M= 225, <br>x = c(0.3, 1.4, 2.4, 3.6, 5.7, 1.6, 2.9, 3.4, 3.4, 4.8, 5.3, 6.2, <br> 0.2, 0.9, 2.3, 2.5, 3, 3.5, 4.1, 4.9, 6.3, 0.9, 1.7, 2.4, 3.7, 4.5, 5.2,<br> 6.3, 0.3, 2, 3.8, 6.3, 0.6, 1.5, 2.1, 2.1, 3.1, 4.5, 5.5, 5.7, 6.2, 0.4,<br> 1.4, 1.4, 2.1, 2.3, 3.1, 4.1, 5.4, 6, 5.7, 3.6), <br> y = c(6.1, 6.2, 6.1, 6.2, 6.2, 5.2, 5.1, 5.3, 5.7, 5.6, 5, 5.2, 4.3, <br> [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Elevationdata.txt b/doc/GeoBUGS/Examples/Elevationdata.txt
new file mode 100755
index 0000000..c013bca
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Elevationdata.txt
@@ -0,0 +1,52 @@
+list(N=52, M= 225,
+ x = c(0.3, 1.4, 2.4, 3.6, 5.7, 1.6, 2.9, 3.4, 3.4, 4.8, 5.3, 6.2,
+ 0.2, 0.9, 2.3, 2.5, 3, 3.5, 4.1, 4.9, 6.3, 0.9, 1.7, 2.4, 3.7, 4.5, 5.2,
+ 6.3, 0.3, 2, 3.8, 6.3, 0.6, 1.5, 2.1, 2.1, 3.1, 4.5, 5.5, 5.7, 6.2, 0.4,
+ 1.4, 1.4, 2.1, 2.3, 3.1, 4.1, 5.4, 6, 5.7, 3.6),
+ y = c(6.1, 6.2, 6.1, 6.2, 6.2, 5.2, 5.1, 5.3, 5.7, 5.6, 5, 5.2, 4.3,
+ 4.2, 4.8, 4.5, 4.5, 4.5, 4.6, 4.2, 4.3, 3.2, 3.8, 3.8, 3.5, 3.2, 3.2,
+ 3.4, 2.4, 2.7, 2.3, 2.2, 1.7, 1.8, 1.8, 1.1, 1.1, 1.8, 1.7, 1, 1, 0.5,
+ 0.6, 0.1, 0.7, 0.3, 0, 0.8, 0.4, 0.1, 3, 6),
+ height = c(870, 793, 755, 690, 800, 800, 730, 728,
+ 710, 780, 804, 855, 830, 813, 762, 765, 740, 765, 760, 790, 820, 855,
+ 812, 773, 812, 827, 805, 840, 890, 820, 873, 875, 873, 865, 841, 862,
+ 908, 855, 850, 882, 910, 940, 915, 890, 880, 870, 880, 960, 890, 860,
+ 830, 705),
+ x.pred=c(0.21, 0.21, 0.21, 0.21, 0.21, 0.21, 0.21, 0.21, 0.21, 0.21, 0.21, 0.21, 0.21,
+ 0.21, 0.21, 0.63, 0.63, 0.63, 0.63, 0.63, 0.63, 0.63, 0.63, 0.63, 0.63,
+ 0.63, 0.63, 0.63, 0.63, 0.63, 1.05, 1.05, 1.05, 1.05, 1.05, 1.05, 1.05,
+ 1.05, 1.05, 1.05, 1.05, 1.05, 1.05, 1.05, 1.05, 1.47, 1.47, 1.47, 1.47,
+ 1.47, 1.47, 1.47, 1.47, 1.47, 1.47, 1.47, 1.47, 1.47, 1.47, 1.47, 1.89,
+ 1.89, 1.89, 1.89, 1.89, 1.89, 1.89, 1.89, 1.89, 1.89, 1.89, 1.89, 1.89,
+ 1.89, 1.89, 2.31, 2.31, 2.31, 2.31, 2.31, 2.31, 2.31, 2.31, 2.31, 2.31,
+ 2.31, 2.31, 2.31, 2.31, 2.31, 2.73, 2.73, 2.73, 2.73, 2.73, 2.73, 2.73,
+ 2.73, 2.73, 2.73, 2.73, 2.73, 2.73, 2.73, 2.73, 3.15, 3.15, 3.15, 3.15,
+ 3.15, 3.15, 3.15, 3.15, 3.15, 3.15, 3.15, 3.15, 3.15, 3.15, 3.15, 3.57,
+ 3.57, 3.57, 3.57, 3.57, 3.57, 3.57, 3.57, 3.57, 3.57, 3.57, 3.57, 3.57,
+ 3.57, 3.57, 3.99, 3.99, 3.99, 3.99, 3.99, 3.99, 3.99, 3.99, 3.99, 3.99,
+ 3.99, 3.99, 3.99, 3.99, 3.99, 4.41, 4.41, 4.41, 4.41, 4.41, 4.41, 4.41,
+ 4.41, 4.41, 4.41, 4.41, 4.41, 4.41, 4.41, 4.41, 4.83, 4.83, 4.83, 4.83,
+ 4.83, 4.83, 4.83, 4.83, 4.83, 4.83, 4.83, 4.83, 4.83, 4.83, 4.83, 5.25,
+ 5.25, 5.25, 5.25, 5.25, 5.25, 5.25, 5.25, 5.25, 5.25, 5.25, 5.25, 5.25,
+ 5.25, 5.25, 5.67, 5.67, 5.67, 5.67, 5.67, 5.67, 5.67, 5.67, 5.67, 5.67,
+ 5.67, 5.67, 5.67, 5.67, 5.67, 6.09, 6.09, 6.09, 6.09, 6.09, 6.09, 6.09,
+ 6.09, 6.09, 6.09, 6.09, 6.09, 6.09, 6.09, 6.09),
+y.pred=c(6.09, 5.67, 5.25, 4.83, 4.41, 3.99, 3.57, 3.15, 2.73, 2.31, 1.89, 1.47, 1.05,
+ 0.63, 0.21, 6.09, 5.67, 5.25, 4.83, 4.41, 3.99, 3.57, 3.15, 2.73, 2.31,
+ 1.89, 1.47, 1.05, 0.63, 0.21, 6.09, 5.67, 5.25, 4.83, 4.41, 3.99, 3.57,
+ 3.15, 2.73, 2.31, 1.89, 1.47, 1.05, 0.63, 0.21, 6.09, 5.67, 5.25, 4.83,
+ 4.41, 3.99, 3.57, 3.15, 2.73, 2.31, 1.89, 1.47, 1.05, 0.63, 0.21, 6.09,
+ 5.67, 5.25, 4.83, 4.41, 3.99, 3.57, 3.15, 2.73, 2.31, 1.89, 1.47, 1.05,
+ 0.63, 0.21, 6.09, 5.67, 5.25, 4.83, 4.41, 3.99, 3.57, 3.15, 2.73, 2.31,
+ 1.89, 1.47, 1.05, 0.63, 0.21, 6.09, 5.67, 5.25, 4.83, 4.41, 3.99, 3.57,
+ 3.15, 2.73, 2.31, 1.89, 1.47, 1.05, 0.63, 0.21, 6.09, 5.67, 5.25, 4.83,
+ 4.41, 3.99, 3.57, 3.15, 2.73, 2.31, 1.89, 1.47, 1.05, 0.63, 0.21, 6.09,
+ 5.67, 5.25, 4.83, 4.41, 3.99, 3.57, 3.15, 2.73, 2.31, 1.89, 1.47, 1.05,
+ 0.63, 0.21, 6.09, 5.67, 5.25, 4.83, 4.41, 3.99, 3.57, 3.15, 2.73, 2.31,
+ 1.89, 1.47, 1.05, 0.63, 0.21, 6.09, 5.67, 5.25, 4.83, 4.41, 3.99, 3.57,
+ 3.15, 2.73, 2.31, 1.89, 1.47, 1.05, 0.63, 0.21, 6.09, 5.67, 5.25, 4.83,
+ 4.41, 3.99, 3.57, 3.15, 2.73, 2.31, 1.89, 1.47, 1.05, 0.63, 0.21, 6.09,
+ 5.67, 5.25, 4.83, 4.41, 3.99, 3.57, 3.15, 2.73, 2.31, 1.89, 1.47, 1.05,
+ 0.63, 0.21, 6.09, 5.67, 5.25, 4.83, 4.41, 3.99, 3.57, 3.15, 2.73, 2.31,
+ 1.89, 1.47, 1.05, 0.63, 0.21, 6.09, 5.67, 5.25, 4.83, 4.41, 3.99, 3.57,
+ 3.15, 2.73, 2.31, 1.89, 1.47, 1.05, 0.63, 0.21))
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Elevationinits.html b/doc/GeoBUGS/Examples/Elevationinits.html
new file mode 100755
index 0000000..b28de92
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Elevationinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Elevationinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(tau=0.001, phi=0.4, beta=820, kappa=1,<br>height.pred=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, <br>0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,<br>0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Elevationinits.txt b/doc/GeoBUGS/Examples/Elevationinits.txt
new file mode 100755
index 0000000..ed46c68
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Elevationinits.txt
@@ -0,0 +1,8 @@
+list(tau=0.001, phi=0.4, beta=820, kappa=1,
+height.pred=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0),
+height.pred.multi=c(0,0,0,0,0,0,0,0,0,0))
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Elevationinits1.html b/doc/GeoBUGS/Examples/Elevationinits1.html
new file mode 100755
index 0000000..293291c
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Elevationinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Elevationinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(tau=0.1, phi=0.1, beta=1000, kappa=0.1,<br>height.pred=c(100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100, <br>100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,<br>100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,10 [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Elevationinits1.txt b/doc/GeoBUGS/Examples/Elevationinits1.txt
new file mode 100755
index 0000000..b32e789
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Elevationinits1.txt
@@ -0,0 +1,8 @@
+list(tau=0.1, phi=0.1, beta=1000, kappa=0.1,
+height.pred=c(100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,
+ 100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,
+100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,
+100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,
+100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,100,
+ 100,100,100,100,100,100,100,100,100,100,100,100,100,100,100),
+height.pred.multi=c(100,100,100,100,100,100,100,100,100,100))
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Elevationmodel.html b/doc/GeoBUGS/Examples/Elevationmodel.html
new file mode 100755
index 0000000..38ad6e8
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Elevationmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Elevationmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Spatially structured multivariate normal likelihood
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3"># exponential correlation function<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> height[1:N] ~ spatial.exp(mu[], x[], y[], tau, phi, kappa)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # disc correlation function <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># height[1:N] ~ spatial.disc(mu[], x[], y[], tau, alpha)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[i] <- beta<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Priors
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">beta ~ dflat()<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau ~ dgamma(0.001, 0.001) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma2 <- 1/tau<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># priors for spatial.exp parameters<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # prior range for correlation at min distance (0.2 x 50 ft) is 0.02 to 0.99<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> phi ~ dunif(0.05, 20)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># prior range for correlation at max distance (8.3 x 50 ft) is 0 to 0.66<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> kappa ~ dunif(0.05,1.95)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># priors for spatial.disc parameter<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # prior range for correlation at min distance (0.2 x 50 ft) is 0.07 to 0.96<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># alpha ~ dunif(0.25, 48)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># prior range for correlation at max distance (8.3 x 50 ft) is 0 to 0.63<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Spatial prediction
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Single site prediction<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(j in 1:M) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> height.pred[j] ~ spatial.unipred(beta, x.pred[j], y.pred[j], height[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Only use joint prediction for small subset of points, due to length of time it takes to run<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(j in 1:10) { mu.pred[j] <- beta }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> height.pred.multi[1:10] ~ spatial.pred(mu.pred[], x.pred[1:10], y.pred[1:10], height[]) <br> }<br> }<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/GeoBUGS/Examples/Elevationmodel.txt b/doc/GeoBUGS/Examples/Elevationmodel.txt
new file mode 100755
index 0000000..9eae2cf
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Elevationmodel.txt
@@ -0,0 +1,40 @@
+ model {
+
+ # Spatially structured multivariate normal likelihood
+ # exponential correlation function
+ height[1:N] ~ spatial.exp(mu[], x[], y[], tau, phi, kappa)
+ # disc correlation function
+ # height[1:N] ~ spatial.disc(mu[], x[], y[], tau, alpha)
+
+ for(i in 1:N) {
+ mu[i] <- beta
+ }
+
+ # Priors
+ beta ~ dflat()
+ tau ~ dgamma(0.001, 0.001)
+ sigma2 <- 1/tau
+
+ # priors for spatial.exp parameters
+ # prior range for correlation at min distance (0.2 x 50 ft) is 0.02 to 0.99
+ phi ~ dunif(0.05, 20)
+ # prior range for correlation at max distance (8.3 x 50 ft) is 0 to 0.66
+ kappa ~ dunif(0.05,1.95)
+
+ # priors for spatial.disc parameter
+ # prior range for correlation at min distance (0.2 x 50 ft) is 0.07 to 0.96
+ # alpha ~ dunif(0.25, 48)
+ # prior range for correlation at max distance (8.3 x 50 ft) is 0 to 0.63
+
+ # Spatial prediction
+
+ # Single site prediction
+ for(j in 1:M) {
+ height.pred[j] ~ spatial.unipred(beta, x.pred[j], y.pred[j], height[])
+ }
+
+ # Only use joint prediction for small subset of points, due to length of time it takes to run
+ for(j in 1:10) { mu.pred[j] <- beta }
+ height.pred.multi[1:10] ~ spatial.pred(mu.pred[], x.pred[1:10], y.pred[1:10], height[])
+ }
+ }
diff --git a/doc/GeoBUGS/Examples/Examples.html b/doc/GeoBUGS/Examples/Examples.html
new file mode 100755
index 0000000..1cea9d8
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Examples.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Examples</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="examples0.bmp" alt="[examples0]">
</font><font face="Courier New" color="#000100" size="6">GeoBUGS Examples
</font><font face="Arial" color="#000100" size="6"><strong><sup><br><br>
</sup></strong></font><font face="Arial" color="#0000FF" size="3"><u><br>
</u></font><font face="Courier New" color="#0000FF" size="3"> <a href="../GeoBUGS/Examples/Scotland.html">Conditional Autoregressive (CAR) models for disease mapping: <br> Lip cancer in Scotland</a><br><br> <a href="../GeoBUGS/Examples/LHA.html">Convolution priors: Lung cancer in a London Health A [...]
</font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font>
</p>
</body>
</html>
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diff --git a/doc/GeoBUGS/Examples/Forest.html b/doc/GeoBUGS/Examples/Forest.html
new file mode 100755
index 0000000..a732403
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Forest.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Forest</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="forest0.bmp" alt="[forest0]">
</font><font face="Courier New" color="#000100" size="6">Poisson-gamma spatial moving<br> average (convolution)model: <br> Distribution of hickory trees<br> &nbs [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Ickstadt and Wolpert (1998) and Wolpert and Ickstadt (1998) analyse the spatial distribution of hickory trees (a subdominant species) in a 140 metre x 140 metre research plot in Duke Forest, North Carolina, USA, with the aim of investigating the regularity of the distribution of trees: spatial clustering would reveal that the subdominant species is receding from, or encroaching into, a stand recovering from a disturbance, while regula [...]
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, in each of i=1,...,16 30m x 30m quadrats (each having area A
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = 900 m
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">) on a 4x4 grid covering the research plot (excluding a 10m boundary region to minimise edge effects), together with the x and y co-ordinates of the centroid of each plot (relative to the south-west corner of the research plot). Ickstadt and Wolpert (1998) fit a Poisson-gamma spatial moving average model as follows:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">~ Poisson(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">) i = 1,...,16<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"> m
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">= A
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> *
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"> l
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><sub>j<br>
</sub></font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3">where
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">can be thought of as latent unobserved risk factors associated with locations or sub-regions of the study region indexed by j, and k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> is a kernel matrix of 'weights' which depend on the distance or proximity between latent location j and quadrat i of the study region (see
</font><font face="Arial" color="#000000" size="3"><a href="../GeoBUGS/Manuals//Manual.html#Appendix 2">
</font><font face="Arial" color="#0000FF" size="3"><u>Appendix 2
</u></font><font face="Arial" color="#000100" size="3"></a> for further details of this convolution model). Ickstadt and Wolpert (1998) take the locations of the latent
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">to be the same as the partition of the study region used for the observed data i.e. j = 1,....16 with latent sub-region j being the same as quadrat i of the study region. Note that it is not necessary for the latent partition to be the same as the observed partition - see
</font><font face="Arial" color="#000000" size="3"><a href="../GeoBUGS/Examples/Huddersfield.html">
</font><font face="Arial" color="#0000FF" size="3"><u>Hudersfield
</u></font><font face="Arial" color="#000100" size="3"></a>. The
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> are assigned independent gamma prior distributions<br><br>
</font><font face="Symbol" color="#000100" size="3"> g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Gamma(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">) j = 1,....,16. <br><br>Ickstadt and Wolpert (1998) consider two alternative kernel functions: an adjacency-based kernel and a distance-based kernel. The adjacency based kernel is defined as:<br><br> k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = 1 if i = j<br> k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = exp(
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">)/n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> if j is a nearest neighbour of i (only north-south and east-west<br> neighbours considered) and n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is the number of neighbours of area i<br> k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = 0 otherwise<br><br>The distance based kernel is defined as:<br><br>k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = exp(
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">[d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">/ exp(
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">)]
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">) where d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> is the distance between the centroid of areas i and j<br><br>For both kernels, the parameter exp(
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">) reflects the degree of spatial dependence or clustering in the data, with large values of
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">suggesting spatial correlation and irregular distribution of hickory trees.<br><br>Ickstadt and Wolpert (1998) elicit expert prior opinion concerning the unknown hyperparameters
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">= log(
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">),
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3"><sub>1
</sub></font><font face="Symbol" color="#000100" size="3">= -
</font><font face="Arial" color="#000100" size="3">log(
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">) and
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> and translate this information into Normal prior distributions for
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">and
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">.<br><br>This model may be implemented in WinBUGS 1.4 using the
</font><font face="Arial" color="#000000" size="3"><a href="../GeoBUGS/Manuals/Manual.html#pois.conv">
</font><font face="Arial" color="#0000FF" size="3"><strong><em><u>pois.conv
</u></em></strong></font><font face="Arial" color="#000100" size="3"><strong><em></a>
</em></strong></font><font face="Arial" color="#000100" size="3"> distribution. The code is given below. <br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Model
</strong></font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># likelihood
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y[i] ~ dpois.conv(mu[i,])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1:J) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[i, j] <- A[i] * lambda[i, j]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> lambda[i, j] <- k[i, j] * gamma[j]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># priors (see Ickstadt and Wolpert (1998) for details of prior elicitation)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1:J) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma[j] ~ dgamma(alpha, beta)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha <- exp(theta0)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta <- exp(-theta1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta0 ~ dnorm(-0.383, 1) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta1 ~ dnorm(-5.190, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta2 ~ dnorm(-1.775, 1) # prior on theta2 for adjacency-based kernel<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # theta2 ~ dnorm(1.280, 1) # prior on theta2 for distance-based kernel<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># compute adjacency-based kernel
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Note N = J in this example (necessary for adjacency-based kernel)
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> k[i, i] <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1:J) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># distance between areas i and j<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> d[i, j] <- sqrt((x[i] - x[j])*(x[i] - x[j]) + (y[i] - y[j])*(y[i] - y[j]))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># (only needed to help compute nearest neighbour weights;<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># alternatively, read matrix w from file)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> w[i, j] <- step(30.1 - d[i, j]) # nearest neighbour weights:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># areas are 30 sq m, so any pair of areas with centroids > 30m apart are not <br> # nearest neighbours (0.1 added to account for numeric imprecision in d)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in (i+1):J) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> k[i, j] <- w[i, j] * exp(theta2) / (sum(w[i,]) - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> k[j, i] <- w[j, i] * exp(theta2) / (sum(w[j,]) - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># alternatively, compute distance-based kernel
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for (i in 1:N) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># k[i, i] <- 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for (j in 1:J) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># distance between areas i and j<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># d[i, j] <- sqrt((x[i] - x[j])*(x[i] - x[j]) + (y[i] - y[j])*(y[i] - y[j]))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for (j in (i+1):J) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># k[i, j] <- exp(-pow(d[i, j]/exp(theta2), 2))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># k[j, i] <- exp(-pow(d[j, i]/exp(theta2), 2))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># summary quantities for posterior inference
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># smoothed density of hickory trees (per sq metre) in area i<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> density[i] <- sum(lambda[i, ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># observed density of hickory trees (per sq metre) in area i<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> obs.density[i] <- Y[i]/A[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># large values indicate strong spatial dependence;<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># spatial.effect -> 0 indicates spatial independence<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> spatial.effect <- exp(theta2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Forestdata.html">Data</a>
</u></strong></font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000100" size="3">(Click to open)
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Forestinits.html">Inits for chain 1</a>
</u></strong></font><font face="Arial" color="#000000" size="2"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Forestinits1.html">Inits for chain 2</a>
</u></strong></font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000100" size="3">(Click to open)
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Results
</strong></font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">Assuming adjacency-based kernel (equivalent to Ickstadt and Wolpert's model M
</font><font face="Arial" color="#000000" size="3"><sub>S
</sub></font><font face="Arial" color="#000000" size="3">):
</font><font face="Arial" color="#000100" size="3"><strong> <br><center><br><img src="forest1.bmp" alt="[forest1]"></center>
</strong></font><font face="Arial" color="#000100" size="3"><br>Ickstadt and Wolpert report a posterior mean (sd) of 0.281 (0.156) for the spatial effect, exp(
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">), from their analysis using a 4x4 partition of the study region (Table 1.3).<br><br><br>
</font><font face="Arial" color="#000000" size="3">Assuming distance-based kernel (equivalent to Ickstadt and Wolpert's model M
</font><font face="Arial" color="#000000" size="3"><sub>D
</sub></font><font face="Arial" color="#000000" size="3">):
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><center><img src="forest2.bmp" alt="[forest2]"><br></center> <br> <br>Ickstadt and Wolpert report a posterior mean (sd) of 7.449 (6.764) for the spatial effect, exp(
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">), from their analysis using a 4x4 partition of the study region (Table 1.3), and posterior means of -0.02, -5.28 and 1.54 respectively for theta0, theta1 and theta2. Ickstadt and Wolpert noted that the posterior for the spatial effect was multi-modal:<br><br>Note however that convergence of this distance-based model is not very good, and the results reported above are not particularly stable (the adjacency-based model appears to co [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/GeoBUGS/Examples/Forestdata.html b/doc/GeoBUGS/Examples/Forestdata.html
new file mode 100755
index 0000000..fe047bb
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+++ b/doc/GeoBUGS/Examples/Forestdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Forestdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(N = 16, J = 16,<br>Y = c(4, 3, 0, 2, 3, 2, 0, 0, 2, 1, 2, 3, 17, 3, 2, 13),<br>A = c(900, 900, 900, 900, 900, 900, 900, 900, 900, 900, 900, 900, 900, 900, 900, 900), <br>x = c(15, 45, 75, 105, 15, 45, 75, 105, 15, 45, 75, 105, 15, 45, 75, 105),<br>y = c(15, 15, 15, 15, 45, 45, 45, 45, 75, 75, 75, 75, 105, 105, 105, 105)<br>)
</font>
</p>
</body>
</html>
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diff --git a/doc/GeoBUGS/Examples/Forestdata.txt b/doc/GeoBUGS/Examples/Forestdata.txt
new file mode 100755
index 0000000..be5ae21
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Forestdata.txt
@@ -0,0 +1,6 @@
+list(N = 16, J = 16,
+ Y = c(4, 3, 0, 2, 3, 2, 0, 0, 2, 1, 2, 3, 17, 3, 2, 13),
+ A = c(900, 900, 900, 900, 900, 900, 900, 900, 900, 900, 900, 900, 900, 900, 900, 900),
+ x = c(15, 45, 75, 105, 15, 45, 75, 105, 15, 45, 75, 105, 15, 45, 75, 105),
+ y = c(15, 15, 15, 15, 45, 45, 45, 45, 75, 75, 75, 75, 105, 105, 105, 105)
+)
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diff --git a/doc/GeoBUGS/Examples/Forestinits.html b/doc/GeoBUGS/Examples/Forestinits.html
new file mode 100755
index 0000000..a08c3b3
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Forestinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Forestinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(theta0 = -1, theta1 = -3, theta2 = 0, <br>gamma = c(0.00406, 0.00518, 0.00916, 0.0117, 0.0101, 0.00249, 0.0178, 0.00112, 0.000703, <br>0.00427, 0.0112, 0.00599, 0.00131, 0.00599, 0.000738, 0.00259))
</font>
</p>
</body>
</html>
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diff --git a/doc/GeoBUGS/Examples/Forestinits.txt b/doc/GeoBUGS/Examples/Forestinits.txt
new file mode 100755
index 0000000..266b9d4
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Forestinits.txt
@@ -0,0 +1,3 @@
+list(theta0 = -1, theta1 = -3, theta2 = 0,
+ gamma = c(0.00406, 0.00518, 0.00916, 0.0117, 0.0101, 0.00249, 0.0178, 0.00112, 0.000703,
+ 0.00427, 0.0112, 0.00599, 0.00131, 0.00599, 0.000738, 0.00259))
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diff --git a/doc/GeoBUGS/Examples/Forestinits1.html b/doc/GeoBUGS/Examples/Forestinits1.html
new file mode 100755
index 0000000..44f6253
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Forestinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Forestinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(theta0 = -0.1, theta1 = -0.3, theta2 = 1.0, <br>gamma = c(0.0406, 0.0518, 0.0916, 0.117, 0.101, 0.0249, 0.178, 0.0112, 0.00703, <br>0.0427, 0.112, 0.0599, 0.0131, 0.0599, 0.00738, 0.0259))
</font>
</p>
</body>
</html>
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diff --git a/doc/GeoBUGS/Examples/Forestinits1.txt b/doc/GeoBUGS/Examples/Forestinits1.txt
new file mode 100755
index 0000000..a35ae33
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Forestinits1.txt
@@ -0,0 +1,3 @@
+list(theta0 = -0.1, theta1 = -0.3, theta2 = 1.0,
+ gamma = c(0.0406, 0.0518, 0.0916, 0.117, 0.101, 0.0249, 0.178, 0.0112, 0.00703,
+ 0.0427, 0.112, 0.0599, 0.0131, 0.0599, 0.00738, 0.0259))
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diff --git a/doc/GeoBUGS/Examples/Forestmodel.html b/doc/GeoBUGS/Examples/Forestmodel.html
new file mode 100755
index 0000000..44e5e90
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Forestmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Forestmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># likelihood
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y[i] ~ dpois.conv(mu[i,])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1:J) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[i, j] <- A[i] * lambda[i, j]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> lambda[i, j] <- k[i, j] * gamma[j]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># priors (see Ickstadt and Wolpert (1998) for details of prior elicitation)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1:J) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma[j] ~ dgamma(alpha, beta)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha <- exp(theta0)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta <- exp(-theta1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta0 ~ dnorm(-0.383, 1) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta1 ~ dnorm(-5.190, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta2 ~ dnorm(-1.775, 1) # prior on theta2 for adjacency-based kernel<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # theta2 ~ dnorm(1.280, 1) # prior on theta2 for distance-based kernel<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># compute adjacency-based kernel
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Note N = J in this example (necessary for adjacency-based kernel)
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> k[i, i] <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1:J) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># distance between areas i and j<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> d[i, j] <- sqrt((x[i] - x[j])*(x[i] - x[j]) + (y[i] - y[j])*(y[i] - y[j]))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># (only needed to help compute nearest neighbour weights;<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># alternatively, read matrix w from file)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> w[i, j] <- step(30.1 - d[i, j]) # nearest neighbour weights:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># areas are 30 sq m, so any pair of areas with centroids > 30m apart are not <br> # nearest neighbours (0.1 added to account for numeric imprecision in d)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in (i+1):J) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> k[i, j] <- w[i, j] * exp(theta2) / (sum(w[i,]) - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> k[j, i] <- w[j, i] * exp(theta2) / (sum(w[j,]) - 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># alternatively, compute distance-based kernel
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for (i in 1:N) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># k[i, i] <- 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for (j in 1:J) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># distance between areas i and j<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># d[i, j] <- sqrt((x[i] - x[j])*(x[i] - x[j]) + (y[i] - y[j])*(y[i] - y[j]))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for (j in (i+1):J) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># k[i, j] <- exp(-pow(d[i, j]/exp(theta2), 2))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># k[j, i] <- exp(-pow(d[j, i]/exp(theta2), 2))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># summary quantities for posterior inference
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># smoothed density of hickory trees (per sq metre) in area i<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> density[i] <- sum(lambda[i, ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># observed density of hickory trees (per sq metre) in area i<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> obs.density[i] <- Y[i]/A[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># large values indicate strong spatial dependence;<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># spatial.effect -> 0 indicates spatial independence<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> spatial.effect <- exp(theta2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Forestmodel.txt b/doc/GeoBUGS/Examples/Forestmodel.txt
new file mode 100755
index 0000000..8a4bac3
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Forestmodel.txt
@@ -0,0 +1,67 @@
+ model {
+
+ # likelihood
+ for (i in 1:N) {
+ Y[i] ~ dpois.conv(mu[i,])
+ for (j in 1:J) {
+ mu[i, j] <- A[i] * lambda[i, j]
+ lambda[i, j] <- k[i, j] * gamma[j]
+ }
+ }
+
+ # priors (see Ickstadt and Wolpert (1998) for details of prior elicitation)
+ for (j in 1:J) {
+ gamma[j] ~ dgamma(alpha, beta)
+ }
+ alpha <- exp(theta0)
+ beta <- exp(-theta1)
+
+ theta0 ~ dnorm(-0.383, 1)
+ theta1 ~ dnorm(-5.190, 1)
+ theta2 ~ dnorm(-1.775, 1) # prior on theta2 for adjacency-based kernel
+ # theta2 ~ dnorm(1.280, 1) # prior on theta2 for distance-based kernel
+
+
+ # compute adjacency-based kernel
+ # Note N = J in this example (necessary for adjacency-based kernel)
+ for (i in 1:N) {
+ k[i, i] <- 1
+ for (j in 1:J) {
+ # distance between areas i and j
+ d[i, j] <- sqrt((x[i] - x[j])*(x[i] - x[j]) + (y[i] - y[j])*(y[i] - y[j]))
+ # (only needed to help compute nearest neighbour weights;
+ # alternatively, read matrix w from file)
+ w[i, j] <- step(30.1 - d[i, j]) # nearest neighbour weights:
+ # areas are 30 sq m, so any pair of areas with centroids > 30m apart are not
+ # nearest neighbours (0.1 added to account for numeric imprecision in d)
+ }
+ for (j in (i+1):J) {
+ k[i, j] <- w[i, j] * exp(theta2) / (sum(w[i,]) - 1)
+ k[j, i] <- w[j, i] * exp(theta2) / (sum(w[j,]) - 1)
+ }
+ }
+
+ # alternatively, compute distance-based kernel
+ # for (i in 1:N) {
+ # k[i, i] <- 1
+ # for (j in 1:J) {
+ # distance between areas i and j
+ # d[i, j] <- sqrt((x[i] - x[j])*(x[i] - x[j]) + (y[i] - y[j])*(y[i] - y[j]))
+ # }
+ # for (j in (i+1):J) {
+ # k[i, j] <- exp(-pow(d[i, j]/exp(theta2), 2))
+ # k[j, i] <- exp(-pow(d[j, i]/exp(theta2), 2))
+ # }
+ # }
+
+ # summary quantities for posterior inference
+ for (i in 1:N) {
+ # smoothed density of hickory trees (per sq metre) in area i
+ density[i] <- sum(lambda[i, ])
+ # observed density of hickory trees (per sq metre) in area i
+ obs.density[i] <- Y[i]/A[i]
+ }
+ # large values indicate strong spatial dependence;
+ # spatial.effect -> 0 indicates spatial independence
+ spatial.effect <- exp(theta2)
+ }
diff --git a/doc/GeoBUGS/Examples/Huddersfield.html b/doc/GeoBUGS/Examples/Huddersfield.html
new file mode 100755
index 0000000..96f1fb6
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Huddersfield.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Huddersfield</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="huddersfield0.bmp" alt="[huddersfield0]">
</font><font face="Courier New" color="#000100" size="6">Poisson-gamma spatial moving<br> average (convolution)model: <br> Ecological regression of air<br>   [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Best et al (2000b) applied the Poisson-gamma convolution model to a small-area ecological regression analysis of traffic-related air pollution and respiratory illness in children living in the Huddersfield region of northern England. They carried out two analyses, one using a partition of the study region into 427 administrative enumeration districts, and the other partitioning the region into 605 regular 750m
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> grid cells. Here we consider the latter partition of the study region. The following data were available:<br><br>Y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = number of cases of self-reported frequent cough amongst children aged 7-9 in each of the i=1,..., 605 areas (750 m
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> grid cells)<br>pop
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = (estimated) population of 7-9 year old children in each area, based on pro-rated 1991 enumeration district census counts. (Note that this leads to <1 child per area in some areas, due to the pro-rata split; counts are also divided by 100, to give rates per 100 children).<br>NO2
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Arial" color="#000000" size="3">average annual nitrogen dioxide concentration in each area, measured in
</font><font face="Symbol" color="#000000" size="3">m
</font><font face="Arial" color="#000000" size="3">g m
</font><font face="Arial" color="#000000" size="2"><sup>-3
</sup></font><font face="Arial" color="#000000" size="3"> above the baseline concentration for the study region of approximately 20
</font><font face="Symbol" color="#000000" size="3">m
</font><font face="Arial" color="#000000" size="3">g m
</font><font face="Arial" color="#000000" size="2"><sup>-3
</sup></font><font face="Arial" color="#000000" size="3"><sup><br>
</sup></font><font face="Arial" color="#000100" size="3"><br>Best et al (2000b) fitted an indentity-link spatial moving average Poisson regression model:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">~ Poisson(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"> m
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">= pop
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> *
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"> l
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> NO2
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">+
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3">where
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">can be thought of as latent unobserved risk factors associated with locations or sub-regions of the study region indexed by j. These locations or sub-regions are typically defined by the user, and are chosen to represent a partition of the region that is appropriate for capturing unmeasured spatial variation in the disease rate. Best et al (2000b) define the latent
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">parameters on a 12 x 8 grid of approx 3km
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> quadrats covering the Huddersfield study region. k
</font><font face="Arial" color="#000100" size="3"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> are then the elements of a 605 x 96 Gaussian kernel matrix, with <br> k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">= 1 / (2
</font><font face="Symbol" color="#000100" size="3">p r
</font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">) exp(
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> / 2
</font><font face="Symbol" color="#000100" size="3">r
</font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">)<br>where d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> represents the Euclidean distance between the centroid of area i of the study region and the location of the j
</font><font face="Arial" color="#000100" size="3"><sup>th
</sup></font><font face="Arial" color="#000100" size="3"> latent factor. Note that if the latent factors are defined on sub-regions rather than points, it is preferable to integrate the above kernel over the latent sub-region (i.e. over all possible distances between the centroid of area i and all locations within the latent sub-region) - the Splus / R function given below impelments this integration when computing the kernel matrix.
</font><font face="Symbol" color="#000100" size="3">r
</font><font face="Arial" color="#000100" size="3">> 0 is a distance scale governing how rapidly the kernel weights (i.e. the influence of the j
</font><font face="Arial" color="#000100" size="2"><sup>th
</sup></font><font face="Arial" color="#000100" size="3"> latent factor on the disease risk in the i
</font><font face="Arial" color="#000100" size="2"><sup>th
</sup></font><font face="Arial" color="#000100" size="3"> area) decline with increasing distance. Best et al (2000b) fix
</font><font face="Symbol" color="#000100" size="3">r
</font><font face="Arial" color="#000100" size="3">= 1 km. By fixing
</font><font face="Symbol" color="#000100" size="3">r
</font><font face="Arial" color="#000100" size="3">, the kernel matrix can be pre-computed outside of WinBUGS (see link in the data file
</font><font face="Arial" color="#0000FF" size="3"><u>
</u></font><font face="Arial" color="#000100" size="3">for Splus / R code for doing this), thus simplifying the implementation. It is possible to treat
</font><font face="Symbol" color="#000100" size="3">r
</font><font face="Arial" color="#000100" size="3"> as uncertain (see
</font><font face="Arial" color="#000000" size="3"><a href="../GeoBUGS/Examples/Forest.html">
</font><font face="Arial" color="#0000FF" size="3"><u>Forest
</u></font><font face="Arial" color="#000100" size="3"></a>), but this entails calculating the elements k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> at each MCMC interation within the BUGS code: this leads to big increases in computation time for all but very small study regions and latent grids. (Note that since the overall scale parameter of the Gaussian kernel is common to all elements k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> it can be factored out of the externel calculation of the kernel, and included as an uncertain parameter (here called
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">) in the BUGS model.<br><br>Independent gamma prior distributions are assumed for the uncertainty quantities
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> as this enables the MCMC sampler to exploit conjugacy with the Poisson likelihood. <br><br>See Best et al (2000b) for full details and interpretation of the model, and
</font><font face="Arial" color="#000000" size="3"><a href="../GeoBUGS/Manuals/Manual.html#Appendix 2">
</font><font face="Arial" color="#0000FF" size="3"><u>Appendix 2
</u></font><font face="Arial" color="#000000" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> for further technical information about the Poisson-gamma model. <br><br>The code for this model is given below.
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Model
</strong></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Likelihood
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1 : I) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># convolution likelihood: <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Y[i] ~ Poisson( sum_ j { mu[i, j] } )<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># where mu[i, j] = pop[i] * lambda[i, j] and<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># pop[i] = (standardised) population (in 100's) in area i<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># lambda[i, j] = disease rate in area i attributed to jth 'source', where<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># the sources include both observed and latent covariates.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y[i] ~ dpois.conv(mu[i, ]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : J) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># rescale kernel matrix<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> k1[i, j] <- ker[i, j] / prec<br>
</font><font face="Arial" color="#000100" size="1"> #
</font><font face="Arial" color="#000100" size="3"> jth 'source' (jth latent spatial grid cell)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3">lambda[i, j] <- beta2 * gamma[j] * k1[i, j]
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># (J+1)th 'source' (overall intercept; represents background rate)
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3">lambda[i,J+1] <- beta0<br> # (J+2)th 'source' (effect of observed NO2 covariate in area i)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> lambda[i,J+2] <- beta1 * NO2[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Note: if additional covariates have been measured, these <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># should be included in the same way as NO2, giving terms<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># lambda[i, J+3], lambda[i, J+4],.....etc.
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : J+2) {
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> mu[i, j] <- lambda[i, j] * pop[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># Priors
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># See Table 22.1 in Best et al. (2000b) for further details.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Priors for latent spatial grid cell (gamma) parameters:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># Assume gamma_j ~ gamma(a, t) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># Prior shape parameter for gamma distn on gamma[j]'s will change in proportion to<br> # the size of the latent grid cells, to ensure aggregation consistency. The prior inverse<br> # scale parameter for gamma distn on gamma[j]'s stays constant across different<br> # partitions, but [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># 'prior points' over the study region.
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br> # Note: area of latent grid cells is read in from data file<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alphaG <- tauG * area<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tauG <- 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : J) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma[j] ~ dgamma(alphaG, tauG)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Priors for beta coefficients:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3">#<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># Assume priors on each beta are of the form beta ~ gamma(a, t).<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3">#<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># Here, parameter of the prior are chosen by setting the prior mean to give an equal <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># number of cases allocated to each of the 3 'sources' (baseline, NO2 and latent), i.e.<br> # prior mean = a / t = a * 3 * Xbar / Ybar,<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># where Ybar is the overall disease rate in number of cases per unit population,<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># and Xbar is the
</font><font face="Arial" color="#808080" size="3"><strong>population-weighted mean
</strong></font><font face="Arial" color="#808080" size="3"> of covariate X. <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># We also take shape parameter a = 0.575, since this gives the ratio of the 90th : 10th<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># percentile of the prior distn = 100, which is suitably diffuse.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> YBAR <- sum(Y[])/sum(pop[]) # mean number of cases per unit population<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> NO2BAR <- inprod(NO2[], pop[]) / sum(pop[]) # population-weighted mean NO2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br> # Shape parameter for Intercept (beta0)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha0<- 0.575<br> # Inverse scale parameter for Intercept (beta0)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau0 <- 3 * alpha0 / YBAR<br> # Shape parameter for effect of NO2 (beta1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha1<- 0.575<br> # Inverse scale parameter for effect of NO2 (beta1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau1 <- 3 * alpha1 * NO2BAR / YBAR<br> # Shape parameter for Latent coefficient (beta2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha2 <- 0.575<br> # Inverse scale parameter for Latent coefficient (beta2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau2 <- 3 * alpha2 / YBAR<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta0 ~ dgamma(alpha0, tau0)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta1 ~ dgamma(alpha1, tau1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta2 ~ dgamma(alpha2, tau2)<br><br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Summary quantities for posterior inference
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000000" size="3">for(i in 1:I) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Overall disease rate in area i <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> RATE[i] <- sum(mu[i, ])/pop[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Rate associated with latent spatial factor in area i <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> LATENT[i] <- beta2 * inprod(k1[i,], gamma[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Expected rate (number of cases per unit population) attributed to each source <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># (see Table 22.2 in Best et al (2000b) )<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Background (overall baseline) rate per 100 population<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">rate.base <- beta0<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Number of cases per 100 population attributed<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># to NO2 = beta1 * population-weighted mean value<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># of NO2 across the study region. <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> rate.no2 <- beta1 * inprod(pop[], NO2[]) / sum(pop[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Number of cases per 100 population attributed to <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># latent sources = beta2 * population-weighted mean<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># value of the latent spatial factor (sum_j k_ij gamma_j)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> rate.latent <- inprod(pop[], LATENT[]) / sum(pop[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Percentage of cases attributed to each source:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Total <- rate.base + rate.no2 + rate.latent
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"># % cases attributed to baseline risk
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3">PC.base <- rate.base / Total * 100<br> # % cases attributed to NO2 exposure<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> PC.no2 <- rate.no2 / Total * 100<br> # % cases attributed to latent spatial factors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> PC.latent <- rate.latent / Total * 100<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Huddersfielddata.html">Data</a>
</u></strong></font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000100" size="3">(Click to open)
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Huddersfieldinits.html">Inits for to chain 1</a>
</u></strong></font><font face="Arial" color="#000000" size="2"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Huddersfieldinits1.html">Inits for to chain 2</a>
</u></strong></font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000100" size="3">(Click to open)
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3">R / Splus functions
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#0000FF" size="3"><u><a href="../GeoBUGS/Examples/HuddersfieldRcode.html">click here to open R Code</a>
</u></font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Results
</strong></font><font face="Arial" color="#000100" size="2"><br><br>A 2000 iteration burn-in followed by a further 10000 updates gave the following results<br>
</font><font face="Arial" color="#000000" size="2"> <center><br><img src="huddersfield1.bmp" alt="[huddersfield1]"><br></center>
</font><font face="Arial" color="#000100" size="3"><br>These differ slightly from those in Best et al (2000b) Table 22.2 since the data in this example have been randomly perturbed for confidentiality. However, the picture is broadly similar, with 1.84 (95% interval 0.046 to 4.2) cases per 100 population attributed to NO2 exposure, 7.75 (95% interval 4.2 to 10.0) cases per 100 population attributed to latent spatially varying risk factors and the remaining 0.39 (95% iterval 0.0019 to 3.4) [...]
</font><font face="Arial" color="#000100" size="3"><strong><em>Huddersfield_750m_grid.<br><center><br>
</em></strong></font><font face="Arial" color="#000100" size="2"><strong><em><br><img src="huddersfield2.bmp" alt="[huddersfield2]"><br><br><img src="huddersfield3.bmp" alt="[huddersfield3]"><br></center>
</em></strong></font>
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</head>
<body>
<p>
<font face="Arial" color="#000100" size="1"># create.kernel: Generates kernel matrix k_ij for use in WinBUGS pois.conv model<br>#<br># Written by Robert Wolpert; last modified by Nicky Best August 2004.<br>#<br>create.kernel <- function(rho=stop("Need radius rho in km"), sig=10,<br>nx, ny, Xx, Xy, outfile="", band=0, seed= 17,<br>sw, ne) {<br>#<br># rho = radius of Gaussian kernel (ASSUMED TO BE GIVEN IN KILOMETRES)<br># sig = number of significant figures for kerne [...]
</font><font face="Arial" color="#FF0000" size="1"> # ********** VERY IMPORTANT *********************<br> # REMEMBER TO EDIT .Dim statement in output<br> # file to switch dimensions of ker<br> # before reading into WinBUGS<br> # ***********************************************
</font><font face="Arial" color="#000100" size="1"><br> prec = prec, # Inverse scale factor for kernel<br> J = NS, I = NX, # Numbers of areas in study region (I) and <br> # number of latent grid cells (J)<br> area= prod(dxy), # Area in km^2 of each latent grid cell B_j<br> dx = dxy[1], dy = dxy[2], rho = rho); # Dimensions in km of B_j and radius of Gaussian<br> # kernel (not needed by WinBUGS, so delete before<br> # reading output file into WinBUGS, or include as<br> # dummy variables in [...]
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<p>
<font face="Arial" color="#0000FF" size="2"><strong>#Data file containing:
</strong></font><font face="Arial" color="#0000FF" size="2"><br><br>
</font><font face="Arial" color="#FF0000" size="2">#Y
</font><font face="Arial" color="#0000FF" size="2"> = observed case count in each area (750m grid cell)<br><br>
</font><font face="Arial" color="#FF0000" size="2">#pop
</font><font face="Arial" color="#0000FF" size="2"> = population in each area (750m grid cell) (divided by 100, to give population units as '100 children')<br><br>
</font><font face="Arial" color="#FF0000" size="2">#NO2
</font><font face="Arial" color="#0000FF" size="2"> = average annual NO2 concentration in each area (750m grid cell) - measured in
</font><font face="Symbol" color="#0000FF" size="2">m
</font><font face="Arial" color="#0000FF" size="2">g m
</font><font face="Arial" color="#0000FF" size="1"><sup>-3
</sup></font><font face="Arial" color="#0000FF" size="2"> above the<br># baseline concentration for the study region of approximately 20
</font><font face="Symbol" color="#0000FF" size="2">m
</font><font face="Arial" color="#0000FF" size="2">g m
</font><font face="Arial" color="#0000FF" size="1"><sup>-3
</sup></font><font face="Arial" color="#0000FF" size="2"><br><br>
</font><font face="Arial" color="#FF0000" size="2">#ker
</font><font face="Arial" color="#0000FF" size="2"> = 605 x 96 dimension matrix of kernel weights k[i, j] where j indexes latent grid cells and i indexes areas <br># in the study region. There are 96 latent grid cell chosen for this analysis, each of dimension approx <br># 2.8km x 3.0km, which cover the entire study region (defined to have south-west corner at co-ordinate at<br># (399000,402000) metres, and north-east corner at co-ordinate(428250,422250) meters) plus a 2km buffer<br># zon [...]
</font><font face="Arial" color="#0000FF" size="2"><strong><em>create.kernel
</em></strong></font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Courier New" color="#000100" size="2"><br>
</font><font face="Arial" color="#FF0000" size="2">#prec
</font><font face="Arial" color="#0000FF" size="2"> = scaling factor for kernel weights (kernel weights to be used in calculations = ker / prec)<br><br>
</font><font face="Arial" color="#FF0000" size="2">#I,
</font><font face="Arial" color="#0000FF" size="2">
</font><font face="Arial" color="#FF0000" size="2">J
</font><font face="Arial" color="#0000FF" size="2"> = number of areas in study region (605) and number of latent grid cells (96)<br><br>
</font><font face="Arial" color="#FF0000" size="2">#area
</font><font face="Arial" color="#0000FF" size="2"> = area (in squared km) of each latent grid cell (needed for specifying priors)
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><br><br>list(ker = structure(.Data = c(0.0001, 0.0001, 0.503325, 1461.495861, 4916.432528, 72.683263, 0.000349, 0.0001, 0.0001, 0.0001, 0.269442, <br> 782.372273, 2631.879155, 38.909019, 0.000187, 0.0001, 0.0001, 0.0001, 0.000602, 1.746658, 5.875709, <br> 0.086865, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,<br> 0.0001, 0.0001, 0.0001, 0 [...]
</font>
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\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Huddersfielddata.txt b/doc/GeoBUGS/Examples/Huddersfielddata.txt
new file mode 100755
index 0000000..271aa33
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Huddersfielddata.txt
@@ -0,0 +1,4927 @@
+#Data file containing:
+
+#Y = observed case count in each area (750m grid cell)
+
+#pop = population in each area (750m grid cell) (divided by 100, to give population units as '100 children')
+
+#NO2 = average annual NO2 concentration in each area (750m grid cell) - measured in mg m-3 above the
+# baseline concentration for the study region of approximately 20mg m-3
+
+#ker = 605 x 96 dimension matrix of kernel weights k[i, j] where j indexes latent grid cells and i indexes areas
+# in the study region. There are 96 latent grid cell chosen for this analysis, each of dimension approx
+# 2.8km x 3.0km, which cover the entire study region (defined to have south-west corner at co-ordinate at
+# (399000,402000) metres, and north-east corner at co-ordinate(428250,422250) meters) plus a 2km buffer
+# zone surrounding the study region. The distance scale of the Gaussian kernel has been fixed at 1km.
+
+# This kernel matrix was generated using the Splus / R function create.kernel
+
+
+#prec = scaling factor for kernel weights (kernel weights to be used in calculations = ker / prec)
+
+#I, J = number of areas in study region (605) and number of latent grid cells (96)
+
+#area = area (in squared km) of each latent grid cell (needed for specifying priors)
+
+
+list(ker = structure(.Data = c(0.0001, 0.0001, 0.503325, 1461.495861, 4916.432528, 72.683263, 0.000349, 0.0001, 0.0001, 0.0001, 0.269442,
+ 782.372273, 2631.879155, 38.909019, 0.000187, 0.0001, 0.0001, 0.0001, 0.000602, 1.746658, 5.875709,
+ 0.086865, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.018913,
+ 430.962047, 5614.657197, 405.460865, 0.016305, 0.0001, 0.0001, 0.0001, 0.010125, 230.703873, 3005.654843,
+ 217.052506, 0.008728, 0.0001, 0.0001, 0.0001, 0.0001, 0.51505, 6.710169, 0.484573, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 4.392524, 1799.197305, 1799.197305,
+ 4.392524, 0.0001, 0.0001, 0.0001, 0.0001, 7.678452, 3145.128203, 3145.128203, 7.678452, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.095366, 39.062485, 39.062485, 0.095366, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.000532,
+ 0.000532, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.281437, 817.204139, 2749.052609, 40.641281, 0.000195, 0.0001,
+ 0.0001, 0.0001, 0.491973, 1428.532478, 4805.544601, 71.043925, 0.000341, 0.0001, 0.0001, 0.0001, 0.00611,
+ 17.74237, 59.684853, 0.882365, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.000241, 0.000812, 0.0001, 0.0001,
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+ 0.0001, 0.0001, 0.010575, 240.975002, 3139.469102, 226.715864, 0.009117, 0.0001, 0.0001, 0.0001, 0.018487,
+ 421.241891, 5488.021126, 396.315877, 0.015937, 0.0001, 0.0001, 0.0001, 0.00023, 5.231823, 68.161209,
+ 4.922242, 0.000198, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.000928, 0.0001, 0.0001, 0.0001, 0.0001,
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+ 0.000231, 44.095638, 2779.143604, 783.692071, 0.248117, 0.0001, 0.0001, 0.0001, 0.000405, 77.082393,
+ 4858.145856, 1369.950938, 0.433726, 0.0001, 0.0001, 0.0001, 0.0001, 0.957363, 60.33816, 17.014787, 0.005387,
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+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.003405, 84.665145, 1172.408508,
+ 89.990101, 0.003949, 0.0001, 0.0001, 0.0001, 0.02066, 513.777313, 7114.579324, 546.090983, 0.023966, 0.0001,
+ 0.0001, 0.0001, 0.001208, 30.033989, 415.898465, 31.922956, 0.001401, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.00286, 0.039605, 0.00304, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 15.177147, 1026.61073, 305.178058, 0.1051, 0.0001,
+ 0.0001, 0.0001, 0.000442, 92.100163, 6229.828106, 1851.925749, 0.637786, 0.0001, 0.0001, 0.0001, 0.0001,
+ 5.383919, 364.178376, 108.258414, 0.037283, 0.0001, 0.0001, 0.0001, 0.0001, 0.000513, 0.03468, 0.010309,
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+ 0.0001, 0.0001, 0.0001, 0.0001, 1.640351, 671.895202, 671.895202, 1.640351, 0.0001, 0.0001, 0.0001, 0.0001,
+ 9.954217, 4077.2919, 4077.2919, 9.954217, 0.0001, 0.0001, 0.0001, 0.0001, 0.581896, 238.347113, 238.347113,
+ 0.581896, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.022697, 0.022697, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
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+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
+ 0.1051, 305.178058, 1026.61073, 15.177147, 0.0001, 0.0001, 0.0001, 0.0001, 0.637786, 1851.925749,
+ 6229.828106, 92.100163, 0.000442, 0.0001, 0.0001, 0.0001, 0.037283, 108.258414, 364.178376, 5.383919,
+ 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.010309, 0.03468, 0.000513, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001,
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+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 4, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 6,
+ 1, 1, 2, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 2, 0, 0, 0, 3, 0, 7, 0, 0,
+ 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 6, 3, 0, 0, 4, 1, 0, 12, 7, 2, 9, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 10, 12, 8, 3, 5,
+ 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 2, 17, 8, 6, 17,
+ 4, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 1, 0, 4, 7, 5, 8, 4, 2, 0,
+ 0, 0, 0, 0, 0, 3, 3, 4, 0, 0, 0, 2, 0, 8, 2, 0, 19, 13, 6, 11, 0, 0, 0,
+ 0, 0, 0, 1, 0, 1, 2, 1, 2, 0, 11, 1, 3, 3, 12, 8, 18, 6, 5, 10, 4, 1, 0,
+ 0, 0, 1, 0, 1, 0, 4, 1, 0, 1, 3, 0, 0, 3, 10, 6, 0, 4, 14, 12, 3, 0, 0,
+ 0, 0, 0, 2, 1, 0, 4, 5, 2, 2, 0, 0, 0, 3, 15, 1, 2, 4, 2, 2, 18, 0, 0,
+ 0, 0, 0, 0, 2, 2, 3, 0, 0, 0, 0, 0, 0, 0, 1, 9, 14, 15, 5, 14, 3, 0, 0,
+ 0, 0, 0, 0, 2, 1, 1, 1, 0, 0, 0, 0, 2, 0, 0, 11, 14, 15, 11, 0, 6, 3,
+ 18, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 1, 11, 17, 1, 0, 0,
+ 0, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 3, 3, 4, 9, 3, 0,
+ 0, 0, 0, 0, 0, 1, 5, 0, 0, 0, 1, 1, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 1, 0, 3, 0, 1, 0, 1, 2, 0, 7, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,
+ 0, 0, 0, 2, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0,
+ 3, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 4, 0, 0, 0, 1, 0, 0, 0,
+ 3, 0, 0, 2, 0, 0, 0, 0, 0, 0, 2, 8, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0), pop = c(0.0003, 0.0003, 0.0003, 0.0021, 0.0022,
+ 0.0002, 0.0004, 0.0016, 0.0022, 0.0023, 0.0023, 0.0005, 0.0008, 0.0022,
+ 0.0023, 0.0023, 0.0023, 0.0023, 0.0006, 0.0012, 0.003, 0.0023, 0.0023,
+ 0.0023, 0.0023, 0.0023, 0.0021, 0.0006, 0.0033, 0.0039, 0.0037, 0.0036,
+ 0.0026, 0.0023, 0.0023, 0.0023, 0.002, 0.0001, 0.0004, 0.0022, 0.0034,
+ 0.004, 0.0098, 0.0118, 0.0121, 0.0323, 0.0095, 0.0109, 0.0067, 0.0057,
+ 0.0056, 0.0002, 0.0029, 0.004, 0.004, 0.004, 0.0062, 0.0448, 0.1813,
+ 0.1047, 0.1253, 0.0268, 0.0153, 0.0094, 0.0094, 0.0076, 0.0001, 0.0008,
+ 0.0036, 0.004, 0.004, 0.004, 0.0128, 0.0431, 0.1713, 0.1716, 0.0915,
+ 0.023, 0.0146, 0.0094, 0.0094, 0.0086, 0.0017, 0.0004, 0.0011, 0.0015,
+ 0.0029, 0.004, 0.004, 0.004, 0.0075, 0.0116, 0.1123, 0.1201, 0.065,
+ 0.0215, 0.0105, 0.0094, 0.0094, 0.0094, 0.0048, 0.0001, 0.0012, 0.0016,
+ 0.0016, 0.0021, 0.004, 0.0041, 0.0126, 0.0221, 0.0294, 0.0865, 0.0411,
+ 0.0427, 0.0257, 0.144, 0.0594, 0.0489, 0.0215, 0.0001, 0.0012, 0.0016,
+ 0.0016, 0.0016, 0.0065, 0.0161, 0.0202, 0.0203, 0.028, 0.0355, 0.0399,
+ 0.0858, 0.125, 0.2157, 0.101, 0.0811, 0.0632, 0.0222, 0.0004, 0.0016,
+ 0.0016, 0.0016, 0.0107, 0.0274, 0.0248, 0.0214, 0.0236, 0.0292, 0.034,
+ 0.0758, 0.2566, 0.2234, 0.0892, 0.0811, 0.0949, 0.0678, 0.0146, 0.0014,
+ 0.0016, 0.0016, 0.0016, 0.0033, 0.0273, 0.0274, 0.0526, 0.1627, 0.0719,
+ 0.0346, 0.0681, 0.1937, 0.2448, 0.0872, 0.3124, 0.3126, 0.1467, 0.0916,
+ 0.0003, 0.0003, 0.0015, 0.0016, 0.0016, 0.0016, 0.0016, 0.0016, 0.0264,
+ 0.0299, 0.0719, 1.0173, 0.2676, 0.0628, 0.0761, 0.1459, 0.4466, 0.2588,
+ 0.8493, 0.5275, 0.1589, 0.4971, 0.0599, 0.034, 0.0002, 0.0015, 0.0016,
+ 0.0016, 0.0016, 0.0016, 0.0016, 0.0123, 0.0375, 0.04, 0.0845, 0.3435,
+ 0.0954, 0.0144, 0.0137, 0.0482, 0.2332, 0.772, 1.0056, 0.8994, 0.3139,
+ 0.6728, 0.2328, 0.036, 0.0014, 0.0016, 0.0016, 0.0055, 0.0143, 0.0394,
+ 0.0449, 0.0327, 0.0396, 0.0306, 0.0599, 0.0154, 0.0134, 0.0375, 0.0492,
+ 0.1121, 0.4639, 0.6155, 0.4167, 0.611, 0.8646, 0.4435, 0.021, 0.0008,
+ 0.0016, 0.0016, 0.0193, 0.0598, 0.0651, 0.0467, 0.0314, 0.0507, 0.0367,
+ 0.0198, 0.0201, 0.0182, 0.1353, 0.1583, 0.2295, 0.6359, 0.4487, 0.7636,
+ 0.8927, 0.4637, 0.1862, 0.0388, 0.0004, 0.0045, 0.0331, 0.0402, 0.0761,
+ 0.1993, 0.51, 0.072, 0.0456, 0.0201, 0.0898, 0.1441, 0.6648, 0.3867,
+ 0.1914, 1.0244, 0.9719, 0.801, 1.0472, 0.5464, 0.2403, 0.0358, 0.0052,
+ 0.0139, 0.0143, 0.0143, 0.0344, 0.2333, 0.1942, 0.1353, 0.0858, 0.0581,
+ 0.66, 0.4534, 0.2322, 0.2485, 0.6957, 1.0477, 1.9077, 0.6736, 0.4194,
+ 1.3988, 0.3005, 0.1446, 0.0321, 0.0232, 0.036, 0.0304, 0.0421, 0.12,
+ 0.2391, 0.2584, 0.1525, 0.1075, 0.1558, 0.1658, 0.0792, 0.0827, 0.3722,
+ 0.7238, 0.3757, 0.2511, 0.3442, 1.5597, 0.886, 0.4912, 0.3166, 0.0059,
+ 0.0578, 0.0586, 0.0795, 0.1102, 0.1945, 0.1935, 0.561, 0.3091, 0.138,
+ 0.1255, 0.0326, 0.025, 0.044, 0.2137, 0.9053, 0.4888, 0.1836, 0.2648,
+ 0.3366, 0.7553, 1.2363, 0.2161, 0.0603, 0.0378, 0.0283, 0.03, 0.0833,
+ 0.228, 0.2608, 0.3488, 0.1253, 0.0586, 0.0499, 0.0227, 0.012, 0.0195,
+ 0.0695, 0.3589, 0.6487, 1.2489, 0.7752, 0.297, 0.7111, 0.7676, 0.1377,
+ 0.0777, 0.0175, 0.0191, 0.0262, 0.0294, 0.0499, 0.0487, 0.062, 0.0421,
+ 0.0382, 0.0285, 0.0215, 0.0159, 0.0104, 0.0113, 0.0578, 0.5598, 0.9029,
+ 0.917, 1.2967, 0.0782, 0.1646, 0.6243, 0.8911, 0.1523, 0.0565, 0.0008,
+ 0.0221, 0.0451, 0.0498, 0.0267, 0.0268, 0.0274, 0.0327, 0.0287, 0.0207,
+ 0.0187, 0.012, 0.0104, 0.034, 0.2421, 0.5582, 0.736, 0.2731, 0.1447,
+ 0.0497, 0.0558, 0.2628, 0.0756, 0.0084, 0.0058, 0.0321, 0.0362, 0.0236,
+ 0.0259, 0.0355, 0.039, 0.0384, 0.021, 0.0199, 0.0183, 0.0105, 0.0142,
+ 0.0807, 0.2693, 0.2344, 0.1792, 0.5337, 0.2159, 0.0387, 0.0366, 0.0031,
+ 0.0054, 0.0236, 0.0267, 0.0382, 0.2554, 0.0924, 0.0447, 0.0442, 0.0772,
+ 0.1233, 0.1019, 0.4633, 0.0541, 0.0477, 0.0509, 0.1179, 0.0543, 0.0371,
+ 0.0247, 0.0002, 0.0089, 0.0351, 0.0398, 0.1285, 0.2525, 0.1117, 0.2653,
+ 0.0885, 0.3689, 0.5072, 0.0559, 0.5226, 0.0292, 0.035, 0.0495, 0.0058,
+ 0.0057, 0.0022, 0.0196, 0.0301, 0.0371, 0.06, 0.0632, 0.0588, 0.0713,
+ 0.0508, 0.1481, 0.082, 0.0508, 0.0462, 0.0168, 0.0004, 0.0006, 0.0167,
+ 0.0186, 0.0651, 0.0484, 0.0398, 0.0352, 0.023, 0.0201, 0.0353, 0.0247,
+ 0.0488, 0.0449, 0.0008, 0.002, 0.0166, 0.0166, 0.0582, 0.0907, 0.068,
+ 0.0497, 0.0204, 0.0189, 0.023, 0.0244, 0.0259, 0.0358, 0.0008, 0.0074,
+ 0.0308, 0.194, 0.136, 0.212, 0.1652, 0.0482, 0.0246, 0.0248, 0.0187,
+ 0.0202, 0.0097, 0.0509, 0.1883, 0.3614, 0.3375, 0.6066, 0.0413, 0.0239,
+ 0.0232, 0.0158, 0.0202, 0.0019, 0.0408, 0.0192, 0.0329, 0.0647, 0.1118,
+ 0.0764, 0.0225, 0.038, 0.0159, 0.0186, 0.0024, 0.0278, 0.0192, 0.0198,
+ 0.0397, 0.1737, 0.0908, 0.0225, 0.0869, 0.0794, 0.0145, 0.0103, 0.017,
+ 0.0306, 0.0469, 0.3564, 0.381, 0.0225, 0.0206, 0.0158, 0.0071, 0.0028,
+ 0.0322, 0.0281, 0.0434, 0.0501, 0.0216, 0.0166, 0.0076, 0.0003, 0.016,
+ 0.0421, 0.0302, 0.0115, 0.0008, 0.0004, 0.0008), NO2 = c(2, 2, 2, 2, 2,
+ 2, 2, 2, 2, 2.143, 2.194, 2, 2, 2, 2.139, 2.5, 2.917, 2.5, 2, 2, 3.032,
+ 2.722, 3.083, 3.278, 3.306, 2.444, 2, 2, 2, 2.694, 3.528, 3.694, 4.417,
+ 3.333, 2.167, 2.139, 2.424, 2.333, 2, 2, 2, 2.057, 2.583, 2.667, 3.028,
+ 4.75, 3.139, 2.5, 2.333, 3.028, 3.13, 3, 1.278, 1.861, 2.056, 2.417,
+ 3.083, 4.25, 6.333, 5.333, 3.028, 2.972, 2.917, 3.083, 3.611, 8.107, 14,
+ 2, 1.686, 1.972, 2.472, 3.25, 3.472, 3.5, 5.778, 8.111, 4.444, 3.528,
+ 3.194, 3.028, 3.361, 11.514, 10.444, 1, 1.222, 1.222, 2, 2, 2.556,
+ 2.528, 2.167, 2.056, 2.917, 4.556, 6.25, 4.222, 4.028, 3.222, 3, 12.667,
+ 4.929, 1, 1, 1, 1.222, 2.056, 2.111, 2.472, 2.028, 2, 2, 2.5, 3.472,
+ 5.944, 5.667, 4.472, 3.667, 3.222, 12, 4.4, 1, 1, 1.667, 2.194, 2.306,
+ 2, 1.889, 2.194, 2.778, 2.75, 3.417, 4.222, 7.306, 7.389, 3.972, 3.028,
+ 9.714, 17.846, 1, 1.194, 1.861, 2.111, 2.611, 2, 2.194, 2.889, 3.722,
+ 3.694, 3.889, 4.25, 7.361, 12.278, 4.944, 3.75, 3.222, 13.114, 21.455,
+ 1, 1.167, 2.25, 2.639, 2.917, 2.278, 3.222, 3.472, 4.639, 4.722, 3.889,
+ 3.806, 5.167, 10.361, 4.722, 5.111, 3.333, 4.5, 17.68, 19, 1, 1.682, 2,
+ 2.194, 2.583, 3.139, 3.194, 2.778, 3.167, 4.25, 6.5, 7.056, 4.139, 4,
+ 5.5, 10.444, 8.75, 8.694, 5.111, 5.083, 11.5, 21.538, 5.667, 1, 1,
+ 1.639, 2.972, 3.417, 3.389, 3.583, 3.444, 3.222, 3.333, 4.694, 7.139,
+ 7.028, 4.528, 4, 4.083, 4.722, 9.139, 9.778, 7.639, 6.75, 5.722, 12,
+ 13.25, 1.36, 2, 3.028, 3.833, 4.417, 4.528, 3.5, 3.556, 3.222, 4.528,
+ 5.556, 7.472, 6.222, 5.083, 4.278, 4.556, 6.722, 14.722, 9.528, 6.444,
+ 5.778, 6.472, 13.625, 2, 2.171, 2.639, 3.111, 3.722, 5.361, 4.083,
+ 4.139, 3.167, 4.194, 4.694, 5.028, 6.333, 6.722, 5.5, 5.139, 6.194,
+ 13.083, 8.583, 9.444, 7.333, 10.361, 7.905, 2, 2, 2.667, 3.417, 5.111,
+ 5.806, 4.583, 3.639, 4.056, 4.222, 5.333, 6.167, 6.528, 7.806, 8.389,
+ 10.333, 15, 11.139, 11.528, 9.778, 7.139, 5.417, 10.4, 2.393, 3, 3.167,
+ 3.556, 5.722, 5.278, 4.667, 4.833, 4.722, 6.917, 8.111, 8.361, 11.417,
+ 12.389, 18.389, 19.611, 13.056, 13.694, 9.25, 7.056, 5.056, 5.25, 2.6,
+ 3.222, 3.889, 4.75, 4.944, 8.083, 8.417, 6.694, 5.611, 8.333, 12.167,
+ 11.139, 7.75, 6.583, 8.806, 19.139, 22.111, 19.417, 13.444, 11.194,
+ 8.028, 8.222, 19.333, 2.6, 3.5, 3.611, 4.083, 4.528, 4.444, 7.361,
+ 8.472, 9.028, 10.417, 6.611, 5.556, 4.972, 5.917, 7.611, 12.139, 21.944,
+ 18.722, 16.139, 12.833, 9.472, 11, 21.591, 2.333, 3.417, 3.917, 4.194,
+ 4.5, 5.111, 8.611, 7.944, 6.417, 5.25, 4.333, 4.972, 5.639, 5.389,
+ 6.556, 8.806, 15.472, 8.278, 16.306, 11, 7.083, 7.528, 16, 21.429, 2.5,
+ 3.056, 3.861, 4.861, 5.583, 6.111, 7.5, 4.639, 4.111, 4.111, 4, 4.139,
+ 5.5, 6.806, 8.5, 8.444, 12.028, 9.056, 13, 17.444, 11.833, 8.778, 8.444,
+ 12.125, 3, 3.103, 3.889, 3.75, 3.639, 4.861, 5.167, 4.75, 4.306, 4.917,
+ 4.444, 5.028, 4.944, 6.278, 7.639, 7.389, 11.639, 10.972, 10.889, 10.25,
+ 13.194, 13.8, 10.208, 9.909, 4, 3.5, 2.97, 3, 4.056, 4.75, 4.694, 5.056,
+ 5.528, 5.056, 5.833, 6.194, 6.694, 8.861, 11.389, 12.056, 9.056, 7.444,
+ 7.028, 7.917, 11.303, 14.6, 3, 3, 3.139, 5.528, 4.611, 5.306, 6.556,
+ 6.944, 8.056, 9.333, 10.472, 11.111, 8.917, 7.167, 7.667, 6.606, 6.567,
+ 7.457, 9.448, 15.667, 3, 3.111, 3.917, 5.639, 6.028, 6.278, 6.694,
+ 6.806, 8.472, 7.083, 6.75, 9.111, 6.5, 7.3, 6.528, 6.667, 8.429, 9.8,
+ 3.214, 4.25, 5.028, 4.972, 5.222, 7.083, 6.417, 6.444, 6.056, 6.111,
+ 6.306, 7.083, 5.966, 6.5, 6.333, 3.933, 4.444, 4.611, 4.722, 5.083,
+ 6.25, 5.861, 4.556, 4.861, 5.417, 5.222, 5.943, 7, 5, 4.581, 4.111,
+ 5.667, 4.694, 5.472, 5.417, 6.028, 4.889, 4.333, 4.5, 4.75, 4.833, 5,
+ 4.5, 4.343, 7.667, 5.778, 5, 6.083, 6.083, 5.444, 4.167, 4.028, 4.857,
+ 5.364, 5.2, 6.222, 6.417, 5.25, 6.861, 6.583, 5.5, 4.639, 4.861, 5.364,
+ 8.2, 5.625, 5.222, 6.028, 6.972, 7.194, 6.694, 5.889, 5.306, 5.25,
+ 5.778, 7.917, 6.444, 5.5, 5.139, 7.194, 9.25, 7.139, 6.444, 5.639,
+ 5.972, 6.171, 6.909, 5.848, 5.25, 5.556, 7.583, 8.972, 8.25, 6.194,
+ 6.306, 6.808, 6, 5.552, 5.387, 5.879, 8.056, 9.861, 6.944, 6.96, 6,
+ 6.273, 6.771, 8.706, 8.879, 8.818, 6.6, 7.25))
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Huddersfieldinits.html b/doc/GeoBUGS/Examples/Huddersfieldinits.html
new file mode 100755
index 0000000..d8d488f
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Huddersfieldinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Huddersfieldinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(beta0 = 0.3, beta1 = 0.4, beta2 = 0.8, <br>gamma = c(0.435, 0.4452, 0.4013, 0.2145, 0.4547, 0.519, 0.4103, 0.312, 0.2794, 0.9507, 0.0248, 0.2708, 0.0772, 0.1258,<br> 0.4658, 0.7443, 0.4568, 0.7619, 0.9945, 0.9549, 0.1669, 0.0522, 0.9516, 0.4272, 0.9826, 0.0503, 0.0687,<br> 0.7318, 0.6423, 0.7253, 0.8606, 0.3799, 0.4604, 0.4013, 0.8105, 0.1944, 0.5127, 0.6675, 0.9646, 0.7237,<br> 0.1236, 0.3 [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Huddersfieldinits.txt b/doc/GeoBUGS/Examples/Huddersfieldinits.txt
new file mode 100755
index 0000000..26817fa
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Huddersfieldinits.txt
@@ -0,0 +1,10 @@
+list(beta0 = 0.3, beta1 = 0.4, beta2 = 0.8,
+ gamma = c(0.435, 0.4452, 0.4013, 0.2145, 0.4547, 0.519, 0.4103, 0.312, 0.2794, 0.9507, 0.0248, 0.2708, 0.0772, 0.1258,
+ 0.4658, 0.7443, 0.4568, 0.7619, 0.9945, 0.9549, 0.1669, 0.0522, 0.9516, 0.4272, 0.9826, 0.0503, 0.0687,
+ 0.7318, 0.6423, 0.7253, 0.8606, 0.3799, 0.4604, 0.4013, 0.8105, 0.1944, 0.5127, 0.6675, 0.9646, 0.7237,
+ 0.1236, 0.3486, 0.3207, 0.4205, 0.6715, 0.5283, 0.9392, 0.8191, 0.856, 0.8074, 0.914, 0.4292, 0.587, 0.4402,
+ 0.4528, 0.7178, 0.7896, 0.3419, 0.7756, 0.236, 0.7347, 0.2341, 0.8215, 0.4804, 0.7596, 0.0879, 0.571,
+ 0.1607, 0.9535, 0.7979, 0.6197, 0.023, 0.9796, 0.3223, 0.2413, 0.8539, 0.9368, 0.0523, 0.5056, 0.3569,
+ 0.5191, 0.2819, 0.2342, 0.6008, 0.2186, 0.863, 0.9514, 0.1193, 0.4628, 0.2861, 0.666, 0.0684, 0.4337,
+ 0.6453, 0.9405, 0.7658)
+)
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Huddersfieldinits1.html b/doc/GeoBUGS/Examples/Huddersfieldinits1.html
new file mode 100755
index 0000000..626f082
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Huddersfieldinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Huddersfieldinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(beta0 = 3, beta1 = 4, beta2 = 8, <br>gamma = c(1.435, 1.4452, 1.4013, 1.2145, 1.4547, 1.519, 1.4103, 1.312, 1.2794, 1.9507, 1.0248, 1.2708, 1.0772, 1.1258,<br> 1.4658, 1.7443, 1.4568, 1.7619, 1.9945, 1.9549, 1.1669, 1.0522, 1.9516, 1.4272, 1.9826, 1.0503, 1.0687,<br> 1.7318, 1.6423, 1.7253, 1.8606, 1.3799, 1.4604, 1.4013, 1.8105, 1.1944, 1.5127, 1.6675, 1.9646, 1.7237,<br> 1.1236, 1.3486, 1 [...]
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diff --git a/doc/GeoBUGS/Examples/Huddersfieldinits1.txt b/doc/GeoBUGS/Examples/Huddersfieldinits1.txt
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+++ b/doc/GeoBUGS/Examples/Huddersfieldinits1.txt
@@ -0,0 +1,10 @@
+list(beta0 = 3, beta1 = 4, beta2 = 8,
+ gamma = c(1.435, 1.4452, 1.4013, 1.2145, 1.4547, 1.519, 1.4103, 1.312, 1.2794, 1.9507, 1.0248, 1.2708, 1.0772, 1.1258,
+ 1.4658, 1.7443, 1.4568, 1.7619, 1.9945, 1.9549, 1.1669, 1.0522, 1.9516, 1.4272, 1.9826, 1.0503, 1.0687,
+ 1.7318, 1.6423, 1.7253, 1.8606, 1.3799, 1.4604, 1.4013, 1.8105, 1.1944, 1.5127, 1.6675, 1.9646, 1.7237,
+ 1.1236, 1.3486, 1.3207, 1.4205, 1.6715, 1.5283, 1.9392, 1.8191, 1.856, 1.8074, 1.914, 1.4292, 1.587, 1.4402,
+ 1.4528, 1.7178, 1.7896, 1.3419, 1.7756, 1.236, 1.7347, 1.2341, 1.8215, 1.4804, 1.7596, 1.0879, 1.571,
+ 1.1607, 1.9535, 1.7979, 1.6197, 1.023, 1.9796, 1.3223, 1.2413, 1.8539, 1.9368, 1.0523, 1.5056, 1.3569,
+ 1.5191, 1.2819, 1.2342, 1.6008, 1.2186, 1.863, 1.9514, 1.1193, 1.4628, 1.2861, 1.666, 1.0684, 1.4337,
+ 1.6453, 1.9405, 1.7658)
+)
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
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<title>Huddersfieldmodel</title>
</head>
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<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Likelihood
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1 : I) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># convolution likelihood: <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Y[i] ~ Poisson( sum_ j { mu[i, j] } )<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># where mu[i, j] = pop[i] * lambda[i, j] and<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># pop[i] = (standardised) population (in 100's) in area i<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># lambda[i, j] = disease rate in area i attributed to jth 'source', where<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># the sources include both observed and latent covariates.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y[i] ~ dpois.conv(mu[i, ]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : J) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># rescale kernel matrix<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> k1[i, j] <- ker[i, j] / prec<br>
</font><font face="Arial" color="#000100" size="1"> #
</font><font face="Arial" color="#000100" size="3"> jth 'source' (jth latent spatial grid cell)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3">lambda[i, j] <- beta2 * gamma[j] * k1[i, j]
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># (J+1)th 'source' (overall intercept; represents background rate)
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3">lambda[i,J+1] <- beta0<br> # (J+2)th 'source' (effect of observed NO2 covariate in area i)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> lambda[i,J+2] <- beta1 * NO2[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Note: if additional covariates have been measured, these <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># should be included in the same way as NO2, giving terms<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># lambda[i, J+3], lambda[i, J+4],.....etc.
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : J+2) {
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> mu[i, j] <- lambda[i, j] * pop[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># Priors
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># See Table 22.1 in Best et al. (2000b) for further details.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Priors for latent spatial grid cell (gamma) parameters:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># Assume gamma_j ~ gamma(a, t) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># Prior shape parameter for gamma distn on gamma[j]'s will change in proportion to<br> # the size of the latent grid cells, to ensure aggregation consistency. The prior inverse<br> # scale parameter for gamma distn on gamma[j]'s stays constant across different<br> # partitions, but [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># 'prior points' over the study region.
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br> # Note: area of latent grid cells is read in from data file<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alphaG <- tauG * area<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tauG <- 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1 : J) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma[j] ~ dgamma(alphaG, tauG)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># Priors for beta coefficients:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3">#<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># Assume priors on each beta are of the form beta ~ gamma(a, t).<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3">#<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># Here, parameter of the prior are chosen by setting the prior mean to give an equal <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># number of cases allocated to each of the 3 'sources' (baseline, NO2 and latent), i.e.<br> # prior mean = a / t = a * 3 * Xbar / Ybar,<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># where Ybar is the overall disease rate in number of cases per unit population,<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># and Xbar is the
</font><font face="Arial" color="#808080" size="3"><strong>population-weighted mean
</strong></font><font face="Arial" color="#808080" size="3"> of covariate X. <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># We also take shape parameter a = 0.575, since this gives the ratio of the 90th : 10th<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#808080" size="3"># percentile of the prior distn = 100, which is suitably diffuse.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> YBAR <- sum(Y[])/sum(pop[]) # mean number of cases per unit population<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> NO2BAR <- inprod(NO2[], pop[]) / sum(pop[]) # population-weighted mean NO2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br> # Shape parameter for Intercept (beta0)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha0<- 0.575<br> # Inverse scale parameter for Intercept (beta0)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau0 <- 3 * alpha0 / YBAR<br> # Shape parameter for effect of NO2 (beta1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha1<- 0.575<br> # Inverse scale parameter for effect of NO2 (beta1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau1 <- 3 * alpha1 * NO2BAR / YBAR<br> # Shape parameter for Latent coefficient (beta2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha2 <- 0.575<br> # Inverse scale parameter for Latent coefficient (beta2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau2 <- 3 * alpha2 / YBAR<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta0 ~ dgamma(alpha0, tau0)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta1 ~ dgamma(alpha1, tau1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta2 ~ dgamma(alpha2, tau2)<br><br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Summary quantities for posterior inference
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000000" size="3">for(i in 1:I) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Overall disease rate in area i <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> RATE[i] <- sum(mu[i, ])/pop[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Rate associated with latent spatial factor in area i <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> LATENT[i] <- beta2 * inprod(k1[i,], gamma[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Expected rate (number of cases per unit population) attributed to each source <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># (see Table 22.2 in Best et al (2000b) )<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Background (overall baseline) rate per 100 population<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">rate.base <- beta0<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Number of cases per 100 population attributed<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># to NO2 = beta1 * population-weighted mean value<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># of NO2 across the study region. <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> rate.no2 <- beta1 * inprod(pop[], NO2[]) / sum(pop[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Number of cases per 100 population attributed to <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># latent sources = beta2 * population-weighted mean<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># value of the latent spatial factor (sum_j k_ij gamma_j)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> rate.latent <- inprod(pop[], LATENT[]) / sum(pop[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Percentage of cases attributed to each source:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Total <- rate.base + rate.no2 + rate.latent
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"># % cases attributed to baseline risk
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3">PC.base <- rate.base / Total * 100<br> # % cases attributed to NO2 exposure<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> PC.no2 <- rate.no2 / Total * 100<br> # % cases attributed to latent spatial factors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> PC.latent <- rate.latent / Total * 100<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font>
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diff --git a/doc/GeoBUGS/Examples/Huddersfieldmodel.txt b/doc/GeoBUGS/Examples/Huddersfieldmodel.txt
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+ model {
+
+ # Likelihood
+ for (i in 1 : I) {
+ # convolution likelihood:
+ # Y[i] ~ Poisson( sum_ j { mu[i, j] } )
+ # where mu[i, j] = pop[i] * lambda[i, j] and
+ # pop[i] = (standardised) population (in 100's) in area i
+ # lambda[i, j] = disease rate in area i attributed to jth 'source', where
+ # the sources include both observed and latent covariates.
+ Y[i] ~ dpois.conv(mu[i, ])
+
+ for (j in 1 : J) {
+ # rescale kernel matrix
+ k1[i, j] <- ker[i, j] / prec
+ # jth 'source' (jth latent spatial grid cell)
+ lambda[i, j] <- beta2 * gamma[j] * k1[i, j]
+ }
+ # (J+1)th 'source' (overall intercept; represents background rate)
+ lambda[i,J+1] <- beta0
+ # (J+2)th 'source' (effect of observed NO2 covariate in area i)
+ lambda[i,J+2] <- beta1 * NO2[i]
+ # Note: if additional covariates have been measured, these
+ # should be included in the same way as NO2, giving terms
+ # lambda[i, J+3], lambda[i, J+4],.....etc.
+ for (j in 1 : J+2) {
+ mu[i, j] <- lambda[i, j] * pop[i]
+ }
+ }
+
+ # Priors
+ # See Table 22.1 in Best et al. (2000b) for further details.
+
+ # Priors for latent spatial grid cell (gamma) parameters:
+ #
+ # Assume gamma_j ~ gamma(a, t)
+ #
+ # Prior shape parameter for gamma distn on gamma[j]'s will change in proportion to
+ # the size of the latent grid cells, to ensure aggregation consistency. The prior inverse
+ # scale parameter for gamma distn on gamma[j]'s stays constant across different
+ # partitions, but depends on the units used to measure the area of the latent grid cells:
+ # here we are assuming # 'area' is in sq kilometres, and we take tauG = 1 (per km^2)
+ # which corresponds to assuming # that our prior guess at the value of the gamma[j]'s
+ # is based on 'observing' about 1 * (area of study region = 30*20km^2) = 600
+ # 'prior points' over the study region.
+
+ # Note: area of latent grid cells is read in from data file
+ alphaG <- tauG * area
+ tauG <- 1
+
+ for (j in 1 : J) {
+ gamma[j] ~ dgamma(alphaG, tauG)
+ }
+
+ # Priors for beta coefficients:
+ #
+ # Assume priors on each beta are of the form beta ~ gamma(a, t).
+ #
+ # Here, parameter of the prior are chosen by setting the prior mean to give an equal
+ # number of cases allocated to each of the 3 'sources' (baseline, NO2 and latent), i.e.
+ # prior mean = a / t = a * 3 * Xbar / Ybar,
+ # where Ybar is the overall disease rate in number of cases per unit population,
+ # and Xbar is the population-weighted mean of covariate X.
+ #
+ # We also take shape parameter a = 0.575, since this gives the ratio of the 90th : 10th
+ # percentile of the prior distn = 100, which is suitably diffuse.
+
+ YBAR <- sum(Y[])/sum(pop[]) # mean number of cases per unit population
+ NO2BAR <- inprod(NO2[], pop[]) / sum(pop[]) # population-weighted mean NO2
+
+ # Shape parameter for Intercept (beta0)
+ alpha0<- 0.575
+ # Inverse scale parameter for Intercept (beta0)
+ tau0 <- 3 * alpha0 / YBAR
+ # Shape parameter for effect of NO2 (beta1)
+ alpha1<- 0.575
+ # Inverse scale parameter for effect of NO2 (beta1)
+ tau1 <- 3 * alpha1 * NO2BAR / YBAR
+ # Shape parameter for Latent coefficient (beta2)
+ alpha2 <- 0.575
+ # Inverse scale parameter for Latent coefficient (beta2)
+ tau2 <- 3 * alpha2 / YBAR
+
+ beta0 ~ dgamma(alpha0, tau0)
+ beta1 ~ dgamma(alpha1, tau1)
+ beta2 ~ dgamma(alpha2, tau2)
+
+
+ # Summary quantities for posterior inference
+ for(i in 1:I) {
+ # Overall disease rate in area i
+ RATE[i] <- sum(mu[i, ])/pop[i]
+ # Rate associated with latent spatial factor in area i
+ LATENT[i] <- beta2 * inprod(k1[i,], gamma[])
+ }
+
+ # Expected rate (number of cases per unit population) attributed to each source
+ # (see Table 22.2 in Best et al (2000b) )
+
+ # Background (overall baseline) rate per 100 population
+ rate.base <- beta0
+
+ # Number of cases per 100 population attributed
+ # to NO2 = beta1 * population-weighted mean value
+ # of NO2 across the study region.
+ rate.no2 <- beta1 * inprod(pop[], NO2[]) / sum(pop[])
+
+ # Number of cases per 100 population attributed to
+ # latent sources = beta2 * population-weighted mean
+ # value of the latent spatial factor (sum_j k_ij gamma_j)
+ rate.latent <- inprod(pop[], LATENT[]) / sum(pop[])
+
+ # Percentage of cases attributed to each source:
+ Total <- rate.base + rate.no2 + rate.latent
+ # % cases attributed to baseline risk
+ PC.base <- rate.base / Total * 100
+ # % cases attributed to NO2 exposure
+ PC.no2 <- rate.no2 / Total * 100
+ # % cases attributed to latent spatial factors
+ PC.latent <- rate.latent / Total * 100
+
+ }
diff --git a/doc/GeoBUGS/Examples/LHA.html b/doc/GeoBUGS/Examples/LHA.html
new file mode 100755
index 0000000..280b075
--- /dev/null
+++ b/doc/GeoBUGS/Examples/LHA.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LHA</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="lha0.bmp" alt="[lha0]">
</font><font face="Courier New" color="#000100" size="6">Convolution priors:Lung cancer in a London Health Authority
</font><font face="Arial" color="#000100" size="3"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="3">This example has been modified from a London Health Authority annual report. The theme of the report was inequality in health and the aim was to investigate links between poverty and ill health. To investigate this issue, the Health Authority carried out a series of disease mapping studies at census ward level. There are 44 wards in the Health Authority in this example. The data are simulated observed and expected counts of lung [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">~ Poisson(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> log
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">= log E
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3">depriv
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">+
</font><font face="Symbol" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">h
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub><br><br>
</sub></font><font face="Arial" color="#000100" size="3">where depriv
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is the deprivation covariate, b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> are spatial random effects assigned a CAR prior, and we introduce a second set of random effects h
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> for which we assume an exchangeable Normal prior. The random effect for each area is thus the sum of a spatially structured component b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">and an unstructured component
</font><font face="Symbol" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">h
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> . This is termed a convolution prior (Besag, York and Mollie 1991; Mollie 1996). Besag, York and Mollie argue that this model is more flexible than assuming only CAR random effects, since it allows the data to decide how much of the residual disease risk is due to spatially structured variation, and how much is unstructured over-dispersion. <br><br>The code for this model is given below.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Model
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br> model {<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Likelihood<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O[i] ~ dpois(mu[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> log(mu[i]) <- log(E[i]) + alpha + beta * depriv[i] + b[i] + h[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Area-specific relative risk (for maps)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> RR[i] <- exp(alpha + beta * depriv[i] + b[i] + h[i]) <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Exchangeable prior on unstructured random effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> h[i] ~ dnorm(0, tau.h) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # CAR prior distribution for spatial random effects: <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> b[1 : N] ~ car.normal(adj[], weights[], num[], tau.b)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(k in 1:sumNumNeigh) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> weights[k] <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Other priors:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha ~ dflat() <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta ~ dnorm(0.0, 1.0E-5)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau.b ~ dgamma(0.5, 0.0005) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma.b <- sqrt(1 / tau.b) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau.h ~ dgamma(0.5, 0.0005) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma.h <- sqrt(1 / tau.h) <br><br> }
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/LHAdata.html">Data</a>
</u></strong></font><font face="Arial" color="#0000FF" size="3"><u>
</u></font><font face="Arial" color="#000100" size="3">(click to open)
</font><font face="Arial" color="#0000FF" size="3"><u><br>
</u></font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/LHAinits.html">Inits for chain 1</a> <a href="../GeoBUGS/Examples/LHAinits1.html">Inits for chain 2</a>
</u></strong></font><font face="Arial" color="#0000FF" size="3"><u>
</u></font><font face="Arial" color="#000100" size="3">(click to open<br><br><center><br><img src="lha1.bmp" alt="[lha1]"><br><br><br><img src="lha2.bmp" alt="[lha2]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/LHAdata.html b/doc/GeoBUGS/Examples/LHAdata.html
new file mode 100755
index 0000000..379ce22
--- /dev/null
+++ b/doc/GeoBUGS/Examples/LHAdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LHAdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 44,<br>O = c(4, 8, 3, 6, 2, 7, 7, 2, 10, 13, 5, 7, 9, 3, 3, 1, 2, 3, 19, 7, 5, 4, <br> 9, 2, 4, 6, 14, 13, 6, 7, 9, 3, 4, 10, 10, 8, 23, 24, 18, 10, 6, 4, 17, 7), <br>E = c(7.20902956, 7.81436792, 3.46693788, 7.04393728, 7.37412184, <br> 4.45749156, 6.3285374, 4.45749156, 6.3285374, 6.76878348, 9.30019844, <br> 6.6036912, 3.17289144, 1.68706092, 4.43859892, 6.6036912, 7.26406032, <br>&n [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/LHAdata.txt b/doc/GeoBUGS/Examples/LHAdata.txt
new file mode 100755
index 0000000..85ddcfa
--- /dev/null
+++ b/doc/GeoBUGS/Examples/LHAdata.txt
@@ -0,0 +1,71 @@
+list(N = 44,
+O = c(4, 8, 3, 6, 2, 7, 7, 2, 10, 13, 5, 7, 9, 3, 3, 1, 2, 3, 19, 7, 5, 4,
+ 9, 2, 4, 6, 14, 13, 6, 7, 9, 3, 4, 10, 10, 8, 23, 24, 18, 10, 6, 4, 17, 7),
+E = c(7.20902956, 7.81436792, 3.46693788, 7.04393728, 7.37412184,
+ 4.45749156, 6.3285374, 4.45749156, 6.3285374, 6.76878348, 9.30019844,
+ 6.6036912, 3.17289144, 1.68706092, 4.43859892, 6.6036912, 7.26406032,
+ 6.21847588, 7.31909108, 6.21847588, 7.04393728, 5.2934088044,
+ 10.370546722, 6.58993351, 6.1573917364, 7.6701873288, 13.9359896624,
+ 12.7473252464, 6.2658023336, 10.96487893, 8.5341702608, 6.1034615916,
+ 6.6977937996, 8.9661617268, 8.8043712924, 8.3723798264, 15.3166165772,
+ 15.7486080432, 17.6933951016, 8.642580858, 4.969277628, 6.3736626232,
+ 11.2890101064, 6.3736626232),
+depriv = c(1.233, 8.162, 0.919, -0.78, -1.182, 3.647, 6.47, 0.948, 4.479,
+ 11.739, -0.125, 0.063, 4.392, -1.021,-0.609, 1.896, -0.053, 1.043, -0.899,
+ 8.441, 5.81, 3.575, 5.78, -0.375, 4.828, 1.668, 4.97, 10.21, -0.234, 7.804,
+ 5.544, -1.699, 7.029, 2.581, 0.958, 2.811, 6.376, 8.627, 1.139, 3.169, 3.332,
+ 2.754, 7.55, 3.961),
+num = c(5, 4, 6, 7, 4, 5, 6, 6, 3, 6,
+5, 3, 4, 5, 6, 6, 5, 3, 5, 3,
+2, 4, 4, 6, 6, 3, 3, 6, 4, 4,
+8, 9, 5, 7, 3, 3, 2, 4, 5, 5,
+5, 3, 8, 6
+),
+adj = c(
+17, 12, 9, 8, 4,
+14, 13, 10, 7,
+32, 17, 15, 11, 8, 6,
+33, 32, 17, 16, 14, 12, 1,
+21, 19, 15, 6,
+19, 15, 11, 5, 3,
+43, 16, 14, 13, 10, 2,
+18, 17, 15, 9, 3, 1,
+18, 8, 1,
+43, 38, 20, 13, 7, 2,
+32, 24, 19, 6, 3,
+14, 4, 1,
+20, 10, 7, 2,
+16, 12, 7, 4, 2,
+21, 18, 8, 6, 5, 3,
+43, 33, 23, 14, 7, 4,
+32, 8, 4, 3, 1,
+15, 9, 8,
+27, 24, 11, 6, 5,
+38, 13, 10,
+15, 5,
+44, 39, 26, 25,
+43, 33, 31, 16,
+41, 40, 32, 27, 19, 11,
+44, 39, 34, 31, 28, 22,
+44, 39, 22,
+40, 24, 19,
+39, 35, 34, 31, 29, 25,
+36, 35, 34, 28,
+43, 38, 36, 34,
+44, 43, 34, 33, 32, 28, 25, 23,
+44, 41, 33, 31, 24, 17, 11, 4, 3,
+32, 31, 23, 16, 4,
+43, 36, 31, 30, 29, 28, 25,
+39, 29, 28,
+34, 30, 29,
+42, 40,
+43, 30, 20, 10,
+35, 28, 26, 25, 22,
+42, 41, 37, 27, 24,
+44, 42, 40, 32, 24,
+41, 40, 37,
+38, 34, 31, 30, 23, 16, 10, 7,
+41, 32, 31, 26, 25, 22
+),
+sumNumNeigh = 212
+)
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/LHAinits.html b/doc/GeoBUGS/Examples/LHAinits.html
new file mode 100755
index 0000000..9f0edde
--- /dev/null
+++ b/doc/GeoBUGS/Examples/LHAinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LHAinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="1">list(tau.b = 0.5, tau.h = 0.2, alpha=0, beta=0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/LHAinits.txt b/doc/GeoBUGS/Examples/LHAinits.txt
new file mode 100755
index 0000000..a274c77
--- /dev/null
+++ b/doc/GeoBUGS/Examples/LHAinits.txt
@@ -0,0 +1 @@
+list(tau.b = 0.5, tau.h = 0.2, alpha=0, beta=0)
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/LHAinits1.html b/doc/GeoBUGS/Examples/LHAinits1.html
new file mode 100755
index 0000000..2bbf814
--- /dev/null
+++ b/doc/GeoBUGS/Examples/LHAinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LHAinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="1">list(tau.b = 1.0, tau.h = 1.0, alpha=1.0, beta=1.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/LHAinits1.txt b/doc/GeoBUGS/Examples/LHAinits1.txt
new file mode 100755
index 0000000..b1c89bf
--- /dev/null
+++ b/doc/GeoBUGS/Examples/LHAinits1.txt
@@ -0,0 +1 @@
+list(tau.b = 1.0, tau.h = 1.0, alpha=1.0, beta=1.0)
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/LHAmodel.html b/doc/GeoBUGS/Examples/LHAmodel.html
new file mode 100755
index 0000000..357a09a
--- /dev/null
+++ b/doc/GeoBUGS/Examples/LHAmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LHAmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model {<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Likelihood<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O[i] ~ dpois(mu[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> log(mu[i]) <- log(E[i]) + alpha + beta * depriv[i] + b[i] + h[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Area-specific relative risk (for maps)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> RR[i] <- exp(alpha + beta * depriv[i] + b[i] + h[i]) <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Exchangeable prior on unstructured random effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> h[i] ~ dnorm(0, tau.h) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # CAR prior distribution for spatial random effects: <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> b[1 : N] ~ car.normal(adj[], weights[], num[], tau.b)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(k in 1:sumNumNeigh) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> weights[k] <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # Other priors:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha ~ dflat() <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta ~ dnorm(0.0, 1.0E-5)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau.b ~ dgamma(0.5, 0.0005) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma.b <- sqrt(1 / tau.b) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau.h ~ dgamma(0.5, 0.0005) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma.h <- sqrt(1 / tau.h) <br><br> }
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/GeoBUGS/Examples/LHAmodel.txt b/doc/GeoBUGS/Examples/LHAmodel.txt
new file mode 100755
index 0000000..1d7df95
--- /dev/null
+++ b/doc/GeoBUGS/Examples/LHAmodel.txt
@@ -0,0 +1,28 @@
+ model {
+
+ for (i in 1 : N) {
+ # Likelihood
+ O[i] ~ dpois(mu[i])
+ log(mu[i]) <- log(E[i]) + alpha + beta * depriv[i] + b[i] + h[i]
+ # Area-specific relative risk (for maps)
+ RR[i] <- exp(alpha + beta * depriv[i] + b[i] + h[i])
+
+ # Exchangeable prior on unstructured random effects
+ h[i] ~ dnorm(0, tau.h)
+ }
+
+ # CAR prior distribution for spatial random effects:
+ b[1 : N] ~ car.normal(adj[], weights[], num[], tau.b)
+ for(k in 1:sumNumNeigh) {
+ weights[k] <- 1
+ }
+
+ # Other priors:
+ alpha ~ dflat()
+ beta ~ dnorm(0.0, 1.0E-5)
+ tau.b ~ dgamma(0.5, 0.0005)
+ sigma.b <- sqrt(1 / tau.b)
+ tau.h ~ dgamma(0.5, 0.0005)
+ sigma.h <- sqrt(1 / tau.h)
+
+ }
diff --git a/doc/GeoBUGS/Examples/MVCAR.html b/doc/GeoBUGS/Examples/MVCAR.html
new file mode 100755
index 0000000..f6f0142
--- /dev/null
+++ b/doc/GeoBUGS/Examples/MVCAR.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
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<font face="Arial" color="#000100" size="2"><img src="mvcar0.bmp" alt="[mvcar0]">
</font><font face="Courier New" color="#000100" size="6">Intrinsic multivariate CAR<br> prior for mapping multiple <br> diseases: Oral cavity cancer <br> &n [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>This example illustrates the use of the multivariate CAR prior distribution for joint mapping of two diseases. The data represent observed and age and sex standardised expected counts of incidenct cases of oral cavity and lung cancer in each of 126 electoral wards in the West Yorkshire region of England between 1986 and 1991. Some of the counts have been randomly peturbed by a small amount for confidentiality. <br><br>Since both outco [...]
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"> for cancer k (k=1, 2) in area i (i=1,126) are assumed to follow independent Poisson distributions, conditional on an unknown mean
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Poisson(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> log
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">= log E
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> + S
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"><sub><br>
</sub></font><font face="Arial" color="#000100" size="3"><br>where E
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"> is the age and sex standardised expected count for cancer k in area i,
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> is an intercept term representing the baseline (log) relative risk of cancer k across the study region, and S
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"> is the area- and cancer-specific log relative risk of death. For cancer k, we assume that these log relative risks are spatially correlated across areas, and within area i, we assume that the log relative risks for cancer 1 (oral cavity) and cancer 2 (lung) are also correlated due to dependence on shared area-level unmeasured risk factors. We represent these correlation assumptions using an intrinsic bivariate CAR prior for the 2 x [...]
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"> values. Technical details of this prior distribution are given in <a href="../GeoBUGS/Manuals/Manual.html#MV">
</font><font face="Arial" color="#0000FF" size="3"><u>appendix 1</a>
</u></font><font face="Arial" color="#000100" size="3">. The
</font><font face="Arial" color="#000100" size="3"><strong><em><a href="../GeoBUGS/Manuals/Manual.html#mv.car">
</em></strong></font><font face="Arial" color="#0000FF" size="3"><strong><em><u>mv.car
</u></em></strong></font><font face="Arial" color="#000100" size="3"><strong><em></a>
</em></strong></font><font face="Arial" color="#000100" size="3"> distribution may be used to fit this model. The OpenBUGS code is given below:<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Model
</strong></font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#000100" size="3"> model {<br> # Likelihood <br> for (i in 1 : Nareas) {<br> for (k in 1 : Ndiseases) {<br> &nb [...]
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"> # MV CAR prior for the spatial random effects
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"># MVCAR prior
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"> S[1:Ndiseases, 1 : Nareas] ~ mv.car(adj[], weights[], num[], omega[ , ])<br> for (i in 1:sumNumNeigh) {<br> weights[i] <- 1 <br> }<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"># Other priors<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"> for (k in 1 : Ndiseases) {<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3"> alpha[k] ~ dflat()<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="3"># Precision matrix of MVCAR
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"> omega[1 : Ndiseases, 1 : Ndiseases] ~ dwish(R[ , ], Ndiseases)<br> # Covariance matrix of MVCAR <br> sigma2[1 : Ndiseases, 1 : Ndiseases] <- inverse(omega[ , ])<br> # condit [...]
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000100" size="3">mean1 <- mean(S[1,])<br> mean2 <- mean(S[2,])<br><br> }<br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/MVCARdata.html">Data</a>
</u></strong></font><font face="Arial" color="#000100" size="3"> (click to open)
</font><font face="Arial" color="#000100" size="2"><strong><br><br>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/MVCARinits.html">Inits for chain 1</a>
</u></strong></font><font face="Arial" color="#000000" size="2"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/MVCARinits1.html">Inits for chain 2</a>
</u></strong></font><font face="Arial" color="#000100" size="3"> (click to open)
</font><font face="Arial" color="#000100" size="2"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Results
</strong></font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> alpha[1] -0.008088 0.03675 3.728E-4 -0.08058 -0.00809 0.06387 1001 20000<br> alpha[2] -0.0228 0.008293 6.589E-5 -0.03894 -0.02275 -0.006552 100 [...]
</font><font face="Arial" color="#000100" size="3">The posterior correlation between risk of oral cavity and lung cancers is 0.84 (95% CI: 0.48, 0.97) suggesting strong shared geographical pattern of risk between the two diseases. <br>A 1000 iteration burn-in followed by a further 10000 updates gave the following results<br>
</font><font face="Arial" color="#000100" size="2"><br><img src="mvcar1.bmp" alt="[mvcar1]"><br><br><br><br><img src="mvcar2.bmp" alt="[mvcar2]">
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="3">Multivariate convolution prior <br>
</font><font face="Arial" color="#000100" size="3"><br>Note that it is also possible to fit a multivariate equivalent of the BYM convolution model, by including an additional unstructured random effect for each area and disease, and assuming independent bivariate normal priors for each pair of unstructured effects within an area:<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Likelihood <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (i in 1 : Nareas) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (k in 1 : Ndiseases) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Y[i, k] ~ dpois(mu[i, k])<br> # Dimension of S reversed as before<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">log(mu[i, k]) <- log(E[i, k]) + alpha[k] + S[k, i] + U[i, k]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br> # area specific relative risk for disease 1 (oral) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> RR1[i] <- exp(alpha[1] + S[1,i])<br> # area specific relative risk for disease 2 (lung)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">RR2[i] <- exp(alpha[2] + S[2,i])
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># MV CAR prior for the spatial random effects
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"># MVCAR prior
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">S[1 : Ndiseases, 1:Nareas] ~ mv.car(adj[], weights[], num[], omega[ , ])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (i in 1 : sumNumNeigh) { <br> weights[i] <- 1 <br> }<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Bivariate normal prior for unstructured random effects within each area
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : Nareas) {<br> # Unstructured multivariate normal<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> U[i, 1 : Ndiseases] ~ dmnorm(zero[], tau[ , ]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Other priors <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (k in 1 : Ndiseases) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> alpha[k] ~ dflat()<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="3"># Precision matrix of MVCAR
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> omega[1:Ndiseases, 1:Ndiseases] ~ dwish(R[ , ], Ndiseases)<br> # Covariance matrix of MVCAR <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma2[1 : Ndiseases, 1:Ndiseases] <- inverse(omega[ , ])<br> # conditional SD of S[1,] (oral cancer)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma[1] <- sqrt(sigma2[1, 1])<br> # conditional SD of S[2,] (lung cancer)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma[2] <- sqrt(sigma2[2, 2])<br> # within-area conditional correlation between spatial component of variation in oral<br> # and lung cancers.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">corr <- sigma2[1, 2] / (sigma[1] * sigma[2])<br><br> # Precision matrix of MV Normal<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau[1:Ndiseases, 1:Ndiseases] ~ dwish(Q[ , ], Ndiseases)<br> # Covariance matrix of MV Normal<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma2.U[1:2, 1:2] <- inverse(tau[ , ])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma.U[1] <- sqrt(sigma2.U[1, 1])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma.U[2] <- sqrt(sigma2.U[2, 2])<br> # within-area correlation between unstructured component of variation in oral and <br> # lung cancers<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">corr.U <- sigma2.U[1, 2] / (sigma.U[1] * sigma.U[2])<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># within-area conditional correlation between total random effect <br> # (i.e. spatial + unstructured components) for oral cancer and for lung cancer<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">corr.sum <- (sigma2[1, 2] + sigma2.U[1, 2]) / <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">(sqrt(sigma2[1, 1] + sigma2.U[1, 1]) * sqrt(sigma2[2, 2] + sigma2.U[2, 2]))<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mean1 <- mean(S[1,])<br> mean2 <- mean(S[2,])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Data
</strong></font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#0000FF" size="3"><u><a href="../GeoBUGS/Examples/MVCARConData.html">click here to open data</a>
</u></font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Inits
</strong></font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#0000FF" size="3"><u><a href="../GeoBUGS/Examples/MVCARConInits.html">click here to open initial values</a>
</u></font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Results
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>A 10000 iteration burn-in followed by a further 50000 updates gave the following results<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><strong> node mean sd MC error 2.5% median 97.5% start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> alpha[1] -0.01151 0.03821 2.997E-4 -0.08717 -0.01135 0.06302 1001 50000<br> alpha[2] -0.02305 0.01207 1.121E-4 -0.04691 -0.02299 4.938E-4 1001& [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Again, the posterior correlation between the spatially structured risk components (S) for oral cavity and lung cancers is high (0.82; 95% CI: 0.29, 0.98), although correlation between the unstructured risk components (U) is less strong (0.38; 95% CI: -0.64, 0.92). Since the spatial component of risk dominates, the correlation between the total random effect (U + S) for oral cancer and lung cancer is also high (0.75; 95% CI: 0.36, 0.94), a [...]
</font><font face="Arial" color="#0000FF" size="3"><u><br>
</u></font>
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<font face="Arial" color="#000100" size="2">list(Nareas=126, Ndiseases=2, <br>R = structure(.Data = c(0.02, 0, 0, 0.02), .Dim=c(2,2)),<br>Y = structure(.Data = c(7, 103, 3, 160, 6, 97, 5, 156, 3, 88, 8, 168, 1, 88, 12, 157, 8, 110,<br> 5, 134, 4, 74, 11, 162, 8, 136, 7, 81, 4, 108, 4, 100, 7, 137,<br> 7, 130, 5, 176, 8, 182, 7, 161, 4, 86, 6, 169, 10, 154, 7, 121,<br> 4, 247, 10, 179, 10, 219, 10, 88, 4, 108, 6, 211, 3, 107, 3, 120,<br>&n [...]
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+list(Nareas=126, Ndiseases=2,
+ R = structure(.Data = c(0.02, 0, 0, 0.02), .Dim=c(2,2)),
+ Y = structure(.Data = c(7, 103, 3, 160, 6, 97, 5, 156, 3, 88, 8, 168, 1, 88, 12, 157, 8, 110,
+ 5, 134, 4, 74, 11, 162, 8, 136, 7, 81, 4, 108, 4, 100, 7, 137,
+ 7, 130, 5, 176, 8, 182, 7, 161, 4, 86, 6, 169, 10, 154, 7, 121,
+ 4, 247, 10, 179, 10, 219, 10, 88, 4, 108, 6, 211, 3, 107, 3, 120,
+ 4, 70, 6, 216, 6, 221, 4, 142, 8, 136, 11, 246, 11, 209, 4, 130,
+ 8, 90, 9, 117, 3, 121, 6, 157, 14, 300, 5, 160, 6, 107, 10, 233,
+ 10, 270, 7, 141, 7, 110, 14, 158, 12, 203, 5, 74, 12, 149, 3, 98,
+ 3, 110, 9, 151, 7, 157, 8, 111, 2, 84, 8, 149, 9, 166, 3, 205,
+ 9, 114, 3, 68, 7, 115, 5, 179, 2, 101, 1, 73, 6, 109, 4, 118,
+ 9, 73, 7, 108, 7, 98, 9, 137, 3, 79, 4, 126, 8, 134, 4, 108, 5,
+ 119, 3, 144, 2, 89, 2, 103, 6, 99, 4, 74, 3, 75, 3, 90, 3, 69,
+ 6, 137, 3, 129, 5, 122, 8, 114, 7, 115, 4, 73, 5, 94, 2, 110,
+ 3, 69, 7, 94, 6, 133, 4, 120, 7, 112, 5, 118, 9, 129, 9, 128,
+ 7, 91, 8, 141, 4, 93, 9, 107, 13, 85, 5, 81, 7, 98, 7, 85, 3,
+ 89, 4, 82, 5, 98, 4, 127, 4, 105, 5, 119, 6, 133, 7, 82, 5, 73,
+ 5, 77, 3, 109, 4, 80.), .Dim=c(126,2)),
+E = structure(.Data = c(5.7993, 124.2824, 9.8345, 199.3086,
+ 6.5001, 138.3337, 9.0741, 191.0307, 6.4746, 136.3728,
+ 9.9171, 208.4544, 5.515, 113.2827, 9.8557, 205.0383, 5.7956, 118.5219, 8.299,
+ 168.9939, 4.8596, 99.1749, 8.8737, 182.1041, 5.3387, 115.9417, 6.2182, 128.2199,
+ 5.368, 111.3884, 5.4669, 115.3283, 8.3298, 172.3197, 8.5829, 176.3519, 8.0016,
+ 172.5571, 9.8149, 217.5105, 6.8331, 137.3765, 5.4115, 111.0865, 5.6492, 119.7825,
+ 8.7562, 178.6785, 6.3436, 132.6835, 7.8424, 165.7296, 7.9467, 163.6806, 8.2651,
+ 179.5329, 4.9209, 99.8676, 4.8173, 97.8898, 8.2088, 172.8071, 5.1494, 111.4239,
+ 6.1063, 125.3408, 4.2812, 89.5027, 7.439, 154.4872, 6.4687, 138.0246, 8.648,
+ 173.9356, 5.4981, 112.8979, 8.1535, 172.1137, 8.1074, 167.9885, 5.0473, 103.0942,
+ 5.337, 110.1, 4.9104, 95.0673, 4.899, 100.6339, 8.2719, 166.6911, 9.0572, 192.7174,
+ 8.3271, 170.1211, 5.2504, 109.0334, 9.2167, 189.3181, 8.2078, 173.5003, 6.3403,
+ 130.4997, 5.2363, 106.8044, 5.7656, 119.1885, 6.349, 134.6238, 3.1955, 63.4971,
+ 4.8059, 96.6801, 4.3527, 92.6587, 5.6589, 113.8283, 7.3528, 158.2496, 6.4591,
+ 134.9901, 5.0808, 103.3924, 3.6248, 73.217, 8.1897, 167.9081, 8.29, 167.5654,
+ 7.3986, 153.8624, 6.3236, 127.4593, 4.261, 86.9421, 5.5404, 111.7691, 9.0518,
+ 186.5931, 5.6972, 117.9196, 4.1577, 90.4632, 3.7059, 75.4029, 4.5956, 99.7396,
+ 4.0921, 85.8003, 5.0072, 99.5433, 5.7554, 118.2132, 5.4192, 113.6951, 4.4614,
+ 95.4255, 5.3266, 113.212, 5.9185, 120.4505, 5.0662, 99.3974, 5.5931, 113.8424,
+ 4.7091, 100.6834, 5.7394, 118.5351, 5.4592, 110.8379, 5.6211, 113.0633, 4.2743,
+ 91.6488, 4.2199, 87.8078, 5.0116, 106.9507, 3.9801, 84.0584, 5.2632, 107.4919,
+ 5.1299, 103.2763, 5.5062, 114.7298, 5.684, 119.65, 5.033, 102.6666, 3.6625,
+ 74.6299, 4.2702, 92.1799, 5.9149, 121.8377, 4.048, 84.8317, 5.8719, 121.1919,
+ 6.6767, 141.6445, 5.3587, 110.0901, 5.4904, 111.204, 4.7363, 96.3014, 5.3231,
+ 108.2957, 6.5753, 137.6387, 5.457, 111.0015, 5.8437, 120.9779, 5.2844, 106.7001,
+ 5.0919, 101.9814, 6.5409, 135.9033, 5.3966, 106.1728, 5.1725, 102.7724, 6.066,
+ 129.0506, 5.9403, 123.6225, 5.4443, 117.149, 5.5746, 115.9296, 5.4766, 113.8003,
+ 5.3397, 108.0343, 5.8259, 124.6071, 5.7783, 125.2003, 6.0794, 127.5812, 5.6695,
+ 116.8155, 5.5123, 114.1313, 5.1238, 104.6006, 5.46, 112.2663), .Dim=c(126,2)),
+num = c(3, 2, 3, 6, 6, 5, 7, 5, 4, 9,
+6, 5, 4, 6, 7, 6, 7, 8, 6, 5,
+4, 8, 6, 8, 6, 5, 6, 7, 4, 4,
+5, 4, 6, 4, 5, 7, 7, 10, 6, 5,
+6, 4, 6, 3, 6, 8, 6, 5, 6, 6,
+7, 5, 6, 5, 9, 8, 7, 6, 5, 5,
+6, 5, 6, 6, 7, 8, 7, 6, 6, 6,
+1, 3, 6, 5, 4, 4, 6, 6, 6, 5,
+3, 5, 8, 8, 5, 7, 4, 6, 5, 9,
+6, 5, 5, 6, 7, 4, 6, 5, 6, 5,
+6, 6, 5, 7, 7, 6, 5, 5, 5, 7,
+6, 6, 6, 6, 9, 7, 4, 4, 4, 4,
+6, 5, 3, 5, 2, 4
+),
+adj = c(
+9, 7, 3,
+10, 4,
+7, 5, 1,
+20, 17, 12, 10, 6, 2,
+16, 14, 8, 7, 6, 3,
+18, 12, 8, 5, 4,
+22, 16, 13, 9, 5, 3, 1,
+18, 15, 14, 6, 5,
+13, 11, 7, 1,
+79, 77, 75, 45, 37, 21, 17, 4, 2,
+57, 55, 34, 22, 13, 9,
+20, 19, 18, 6, 4,
+22, 11, 9, 7,
+25, 23, 16, 15, 8, 5,
+30, 29, 24, 23, 18, 14, 8,
+25, 23, 22, 14, 7, 5,
+35, 27, 26, 21, 20, 10, 4,
+31, 28, 24, 19, 15, 12, 8, 6,
+32, 28, 27, 20, 18, 12,
+27, 19, 17, 12, 4,
+37, 26, 17, 10,
+55, 41, 33, 25, 16, 13, 11, 7,
+38, 29, 25, 16, 15, 14,
+51, 47, 44, 38, 31, 30, 18, 15,
+38, 33, 23, 22, 16, 14,
+39, 37, 35, 21, 17,
+36, 35, 32, 20, 19, 17,
+46, 40, 36, 32, 31, 19, 18,
+38, 30, 23, 15,
+38, 29, 24, 15,
+47, 40, 28, 24, 18,
+36, 28, 27, 19,
+43, 42, 41, 38, 25, 22,
+88, 71, 57, 11,
+39, 36, 27, 26, 17,
+50, 46, 39, 35, 32, 28, 27,
+63, 50, 45, 39, 26, 21, 10,
+53, 51, 44, 43, 33, 30, 29, 25, 24, 23,
+50, 46, 37, 36, 35, 26,
+49, 47, 46, 31, 28,
+58, 55, 48, 42, 33, 22,
+48, 43, 41, 33,
+53, 52, 48, 42, 38, 33,
+51, 38, 24,
+84, 79, 77, 63, 37, 10,
+59, 54, 50, 49, 40, 39, 36, 28,
+56, 51, 49, 40, 31, 24,
+58, 52, 43, 42, 41,
+64, 59, 56, 47, 46, 40,
+63, 54, 46, 39, 37, 36,
+60, 56, 53, 47, 44, 38, 24,
+61, 58, 53, 48, 43,
+61, 60, 52, 51, 43, 38,
+65, 63, 59, 50, 46,
+73, 72, 67, 62, 58, 57, 41, 22, 11,
+70, 68, 66, 64, 60, 51, 49, 47,
+88, 87, 78, 62, 55, 34, 11,
+67, 61, 55, 52, 48, 41,
+65, 64, 54, 49, 46,
+68, 61, 56, 53, 51,
+68, 67, 60, 58, 53, 52,
+78, 73, 72, 57, 55,
+84, 65, 54, 50, 45, 37,
+69, 66, 65, 59, 56, 49,
+84, 82, 69, 64, 63, 59, 54,
+86, 85, 80, 76, 70, 69, 64, 56,
+83, 74, 73, 68, 61, 58, 55,
+74, 70, 67, 61, 60, 56,
+95, 85, 82, 66, 65, 64,
+90, 76, 74, 68, 66, 56,
+34,
+73, 62, 55,
+83, 78, 72, 67, 62, 55,
+90, 83, 70, 68, 67,
+92, 81, 77, 10,
+90, 86, 70, 66,
+92, 91, 79, 75, 45, 10,
+89, 87, 83, 73, 62, 57,
+94, 91, 84, 77, 45, 10,
+98, 93, 86, 85, 66,
+103, 92, 75,
+102, 95, 84, 69, 65,
+99, 97, 90, 89, 78, 74, 73, 67,
+102, 101, 94, 82, 79, 65, 63, 45,
+95, 93, 80, 69, 66,
+106, 100, 98, 90, 80, 76, 66,
+89, 88, 78, 57,
+116, 99, 89, 87, 57, 34,
+99, 88, 87, 83, 78,
+106, 104, 97, 96, 86, 83, 76, 74, 70,
+110, 103, 94, 92, 79, 77,
+103, 91, 81, 77, 75,
+105, 98, 95, 85, 80,
+112, 110, 101, 91, 84, 79,
+109, 105, 102, 93, 85, 82, 69,
+107, 104, 97, 90,
+111, 107, 99, 96, 90, 83,
+105, 100, 93, 86, 80,
+116, 111, 97, 89, 88, 83,
+115, 106, 105, 98, 86,
+112, 110, 108, 102, 94, 84,
+109, 108, 101, 95, 84, 82,
+118, 110, 92, 91, 81,
+121, 120, 114, 107, 106, 96, 90,
+115, 113, 109, 100, 98, 95, 93,
+120, 115, 104, 100, 90, 86,
+114, 111, 104, 97, 96,
+113, 112, 109, 102, 101,
+113, 108, 105, 102, 95,
+119, 118, 112, 103, 101, 94, 91,
+117, 116, 114, 107, 99, 97,
+119, 113, 110, 108, 101, 94,
+123, 115, 112, 109, 108, 105,
+122, 121, 117, 111, 107, 104,
+126, 124, 123, 121, 120, 113, 106, 105, 100,
+126, 124, 122, 117, 111, 99, 88,
+122, 116, 114, 111,
+125, 119, 110, 103,
+125, 118, 112, 110,
+121, 115, 106, 104,
+124, 122, 120, 115, 114, 104,
+124, 121, 117, 116, 114,
+126, 115, 113,
+126, 122, 121, 116, 115,
+119, 118,
+124, 123, 116, 115
+),
+sumNumNeigh = 710
+)
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/MVCARinits.html b/doc/GeoBUGS/Examples/MVCARinits.html
new file mode 100755
index 0000000..086c1bd
--- /dev/null
+++ b/doc/GeoBUGS/Examples/MVCARinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>MVCARinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha = c(-0.02, -0.07), omega = structure(.Data=c(1000, 0, 0, 10), .Dim=c(2,2))))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/MVCARinits.txt b/doc/GeoBUGS/Examples/MVCARinits.txt
new file mode 100755
index 0000000..4c290da
--- /dev/null
+++ b/doc/GeoBUGS/Examples/MVCARinits.txt
@@ -0,0 +1 @@
+list(alpha = c(-0.02, -0.07), omega = structure(.Data=c(1000, 0, 0, 10), .Dim=c(2,2))))
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/MVCARinits1.html b/doc/GeoBUGS/Examples/MVCARinits1.html
new file mode 100755
index 0000000..eadd2ca
--- /dev/null
+++ b/doc/GeoBUGS/Examples/MVCARinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>MVCARinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(alpha = c(-0.09253,-0.02152), omega = structure(.Data = c(35.81,-20.98,-20.98,23.12),.Dim = c(2,2)))<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/MVCARinits1.txt b/doc/GeoBUGS/Examples/MVCARinits1.txt
new file mode 100755
index 0000000..4260b59
--- /dev/null
+++ b/doc/GeoBUGS/Examples/MVCARinits1.txt
@@ -0,0 +1 @@
+list(alpha = c(-0.09253,-0.02152), omega = structure(.Data = c(35.81,-20.98,-20.98,23.12),.Dim = c(2,2)))
diff --git a/doc/GeoBUGS/Examples/MVCARmodel.html b/doc/GeoBUGS/Examples/MVCARmodel.html
new file mode 100755
index 0000000..e63fd59
--- /dev/null
+++ b/doc/GeoBUGS/Examples/MVCARmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>MVCARmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model {<br> # Likelihood <br> for (i in 1 : Nareas) {<br> for (k in 1 : Ndiseases) {<br> &nbs [...]
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"> # MV CAR prior for the spatial random effects
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"># MVCAR prior
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"> S[1:Ndiseases, 1 : Nareas] ~ mv.car(adj[], weights[], num[], omega[ , ])<br> for (i in 1:sumNumNeigh) {<br> weights[i] <- 1 <br> }<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"># Other priors<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"> for (k in 1 : Ndiseases) {<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3"> alpha[k] ~ dflat()<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="3"># Precision matrix of MVCAR
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"> omega[1 : Ndiseases, 1 : Ndiseases] ~ dwish(R[ , ], Ndiseases)<br> # Covariance matrix of MVCAR <br> sigma2[1 : Ndiseases, 1 : Ndiseases] <- inverse(omega[ , ])<br> # condit [...]
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000100" size="3">mean1 <- mean(S[1,])<br> mean2 <- mean(S[2,])<br><br> }<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/MVCARmodel.txt b/doc/GeoBUGS/Examples/MVCARmodel.txt
new file mode 100755
index 0000000..f549496
--- /dev/null
+++ b/doc/GeoBUGS/Examples/MVCARmodel.txt
@@ -0,0 +1,44 @@
+ model {
+ # Likelihood
+ for (i in 1 : Nareas) {
+ for (k in 1 : Ndiseases) {
+ Y[i, k] ~ dpois(mu[i, k])
+ # Note dimension of S is reversed:
+ log(mu[i, k]) <- log(E[i, k]) + alpha[k] + S[k, i]
+ # rows=k, cols=i because mv.car assumes rows represent variables
+ # (diseases) and columns represent observations (areas).
+ }
+ # The GeoBUGS map tool can only map vectors, so need to create separate vector
+ # of quantities to be mapped, rather than an array (i.e. RR[i,k] won't work!)
+ # area specific relative risk for disease 1 (oral)
+ RR1[i] <- exp(alpha[1] + S[1, i])
+ # area specific relative risk for disease 2 (lung)
+ RR2[i] <- exp(alpha[2] + S[2, i])
+ }
+
+ # MV CAR prior for the spatial random effects
+ # MVCAR prior
+ S[1:Ndiseases, 1 : Nareas] ~ mv.car(adj[], weights[], num[], omega[ , ])
+ for (i in 1:sumNumNeigh) {
+ weights[i] <- 1
+ }
+
+ # Other priors
+ for (k in 1 : Ndiseases) {
+ alpha[k] ~ dflat()
+ }
+ # Precision matrix of MVCAR
+ omega[1 : Ndiseases, 1 : Ndiseases] ~ dwish(R[ , ], Ndiseases)
+ # Covariance matrix of MVCAR
+ sigma2[1 : Ndiseases, 1 : Ndiseases] <- inverse(omega[ , ])
+ # conditional SD of S[1, ] (oral cancer)
+ sigma[1] <- sqrt(sigma2[1, 1])
+ # conditional SD of S[2,] (lung cancer)
+ sigma[2] <- sqrt(sigma2[2, 2])
+ # within-area conditional correlation
+ corr <- sigma2[1, 2] / (sigma[1] * sigma[2])
+ # between oral and lung cancers.
+ mean1 <- mean(S[1,])
+ mean2 <- mean(S[2,])
+
+ }
diff --git a/doc/GeoBUGS/Examples/Pollution.html b/doc/GeoBUGS/Examples/Pollution.html
new file mode 100755
index 0000000..f3a00a1
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Pollution.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pollution</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="pollution0.bmp" alt="[pollution0]">
</font><font face="Courier New" color="#000100" size="6">Random walk priors for<br> temporal smoothing of daily<br> air pollution estimates
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Shaddick and Wakefield (2002) consider spatiotemporal modelling of daily ambient air pollution at a number of monitoring sites in London. Here we take a subset of their data on a single pollutant measured at one site for 366 days, and model temporal autocorrelation using a random walk prior. <br><br>Conditional on the underlying mean concentration
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"> on day t, the likelihood for the observed pollution concetration Y
</font><font face="Arial" color="#000100" size="3"><sub>t
</sub></font><font face="Arial" color="#000100" size="3">is assumed to be independent Normal i.e.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Normal(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>err
</sub></font><font face="Arial" color="#000100" size="3">) where 1/
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="2"><sub>err
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">is the measurement error variance<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"> m
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3"><br><br>where
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="3"> is the overall mean pollution concentration at the site, and
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3"><sub>t
</sub></font><font face="Arial" color="#000100" size="3">is a (zero mean) random error term representing daily fluctuations about this mean. To reflect the prior belief that these daily fluctuations are correlated, a <a href="../GeoBUGS/Manuals/Manual.html#rw">
</font><font face="Arial" color="#0000FF" size="3"><u>random walk
</u></font><font face="Arial" color="#000100" size="3"></a> prior is assumed for
</font><font face="Symbol" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3"><strong>q
</strong></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">{q
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">, ......,
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>366
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">} (see equation 7 in Shaddick and Wakefield):<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"> |
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal
</font><font face="Symbol" color="#000100" size="3">( q
</font><font face="Arial" color="#000100" size="2"><sub>t+1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> ) for t = 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> ~ Normal
</font><font face="Symbol" color="#000100" size="3">( (q
</font><font face="Arial" color="#000100" size="2"><sub>t-1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">+ q
</font><font face="Arial" color="#000100" size="2"><sub>t+1
</sub></font><font face="Arial" color="#000100" size="3">)/2,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> / 2 ) for t = 2, ...., T-1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> ~ Normal
</font><font face="Symbol" color="#000100" size="3">( q
</font><font face="Arial" color="#000100" size="2"><sub>t-1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> ) for t = T<br><br>where
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">denotes all elements of
</font><font face="Symbol" color="#000100" size="3"><strong>q
</strong></font><font face="Symbol" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">except the
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3">. This prior may be specified in WinBUGS 1.4 using the
</font><font face="Arial" color="#000100" size="3"><strong><em>car.normal
</em></strong></font><font face="Arial" color="#000100" size="3">distribution, with adjacency vector
</font><font face="Arial" color="#000100" size="3"><strong><em>adj[]
</em></strong></font><font face="Arial" color="#000100" size="3"> listing neighbouring time points (i.e. (t-1) and (t+1) are neighbours of time point t), corresponding weight vector
</font><font face="Arial" color="#000100" size="3"><strong><em>weight[]
</em></strong></font><font face="Arial" color="#000100" size="3"> set to a sequence of 1's, and vector giving the number of neighbours,
</font><font face="Arial" color="#000100" size="3"><strong><em>num[]
</em></strong></font><font face="Arial" color="#000100" size="3">, set to 2 for all time points except
</font><font face="Arial" color="#000100" size="3"><strong><em>num[1]
</em></strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong><em>num[T]
</em></strong></font><font face="Arial" color="#000100" size="3">which are set to 1. <br><br>The RW(1) reflects prior beliefs about smoothness of first differences, i.e. sudden jumps between consecutive values of
</font><font face="Symbol" color="#000100" size="3"><strong>q
</strong></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">are unlikely. Alternatively, we may assume a second order random walk prior RW(2) for
</font><font face="Symbol" color="#000100" size="3"><strong>q
</strong></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">, which represents prior beliefs that the rate of change (gradient) of
</font><font face="Symbol" color="#000100" size="3"><strong>q
</strong></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">is smooth:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"> |
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Normal
</font><font face="Symbol" color="#000100" size="3">(
</font><font face="Arial" color="#000100" size="3">2
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t+1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">- q
</font><font face="Arial" color="#000100" size="2"><sub>t+2
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> ) for t = 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> ~ Normal
</font><font face="Symbol" color="#000100" size="3">(
</font><font face="Arial" color="#000100" size="3">(2
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t-1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">+
</font><font face="Arial" color="#000100" size="3">4
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t+1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">- q
</font><font face="Arial" color="#000100" size="2"><sub>t+2
</sub></font><font face="Arial" color="#000100" size="3">) / 5,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> / 5 ) for t = 2 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> ~ Normal
</font><font face="Symbol" color="#000100" size="3">( (-q
</font><font face="Arial" color="#000100" size="2"><sub>t-2
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">+
</font><font face="Arial" color="#000100" size="3">4
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t-1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">+
</font><font face="Arial" color="#000100" size="3">4
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t+1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">- q
</font><font face="Arial" color="#000100" size="2"><sub>t+2
</sub></font><font face="Arial" color="#000100" size="3">) / 6,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> / 6 ) for t = 3, ...., T - 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> ~ Normal
</font><font face="Symbol" color="#000100" size="3">( (-q
</font><font face="Arial" color="#000100" size="2"><sub>t-2
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">+ 4q
</font><font face="Arial" color="#000100" size="2"><sub>t-1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">+
</font><font face="Arial" color="#000100" size="3">2
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t+1
</sub></font><font face="Arial" color="#000100" size="3">) / 5,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> / 5 ) for t = T -1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> ~ Normal
</font><font face="Symbol" color="#000100" size="3">( -q
</font><font face="Arial" color="#000100" size="2"><sub>t-2
</sub></font><font face="Symbol" color="#000100" size="3">+
</font><font face="Arial" color="#000100" size="3">2
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t-1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> ) for t = T<br><br>Again this may be specified using the
</font><font face="Arial" color="#000100" size="3"><strong><em>car.normal
</em></strong></font><font face="Arial" color="#000100" size="3">distribution in OpenBUGS via appropriate specification of the
</font><font face="Arial" color="#000100" size="3"><strong><em>adj[]
</em></strong></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><strong><em>weight[]
</em></strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong><em>num[]
</em></strong></font><font face="Arial" color="#000100" size="3"> vectors.<br><br>The model code for fitting these two models is given below.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Model
</strong></font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">#likelihood
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for(t in 1:T) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y[t] ~ dnorm(mu[t], tau.err)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[t] <- beta + theta[t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3"># prior for temporal effects <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># RW prior for theta[t] - specified using car.normal with <br> #neighbours (t-1) and (t+1) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for theta[2],....,theta[T-1], and neighbours (t+1) for <br> #theta[1] and (t-1) for theta[T]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[1:T] ~ car.normal(adj[], weights[], num[], tau) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta ~ dflat()<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Specify weight matrix and adjacency matrix corresponding to RW(1) prior
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># (Note - this could be given in the data file instead)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(t in 1:1) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> weights[t] <- 1;<br> adj[t] <- t+1;<br> num[t] <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(t in 2:(T-1)) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> weights[2+(t-2)*2] <- 1;<br> adj[2+(t-2)*2] <- t-1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> weights[3+(t-2)*2] <- 1;<br> adj[3+(t-2)*2] <- t+1;<br> num[t] <- 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(t in T:T) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> weights[(T-2)*2 + 2] <- 1;<br> adj[(T-2)*2 + 2] <- t-1;<br> num[t] <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"># Alternatively, a weight matrix and adjacency matrix <br> #corresponding to RW(2) prior can<br> # be specified or given in the data file <br> #(note, no need to change the prior distribution<br> # on theta, just the weights/adjac [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for(t in 1:1) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[t] <- 2; adj[t] <- t+1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[t+1] <- -1; adj[t+1] <- t+2; num[t] <- 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for(t in 2:2) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[t+1] <- 2; adj[t+1] <- t-1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[t+2] <- 4; adj[t+2] <- t+1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[t+3] <- -1; adj[t+3] <- t+2; num[t] <- 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">#for(t in 3:(T-2)) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[6+(t-3)*4] <- -1; adj[6+(t-3)*4] <- t-2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[7+(t-3)*4] <- 4; adj[7+(t-3)*4] <- t-1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[8+(t-3)*4] <- 4; adj[8+(t-3)*4] <- t+1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[9+(t-3)*4] <- -1; adj[9+(t-3)*4] <- t+2; num[t] <- 4<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for(t in (T-1):(T-1)) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[(T-4)*4 + 6] <- 2; adj[(T-4)*4 + 6] <- t+1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[(T-4)*4 + 7] <- 4; adj[(T-4)*4 + 7] <- t-1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[(T-4)*4 + 8] <- -1; adj[(T-4)*4 + 8] <- t-2; num[t] <- 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for(t in T:T) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[(T-4)*4 + 9] <- 2; adj[(T-4)*4 + 9] <- t-1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[(T-4)*4 + 10] <- -1; adj[(T-4)*4 + 10] <- t-2; num[t] <- 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># other priors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau.err ~ dgamma(0.01, 0.01) # measurement error precision<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma.err <- 1 / sqrt(tau.err)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma2.err <- 1/tau.err<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau ~ dgamma(0.01, 0.01) # random walk precision<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma <- 1 / sqrt(tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma2 <- 1/tau<br> # include this variable to use in time series (model fit) plot<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(t in 1:T) { day[t] <- t } <br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Note that pollution concentrations were not measured every day. However it is necessary to include days with no measurements as missing values (NA) in the data set, otherwise the temporal neighbourhood structure cannot be specified correctly.<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Pollutiondata.html">Data</a>
</u></strong></font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000100" size="3">(Click to open)
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Pollutioninits.html">Inits for chain 1</a> <a href="../GeoBUGS/Examples/Pollutioninits1.html">Inits for chain 2</a>
</u></strong></font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000100" size="3">(Click to open)
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3"><br>Plus click on
</font><font face="Arial" color="#000100" size="3"><em>gen inits
</em></font><font face="Arial" color="#000100" size="3"> to generate initial values for the missing data<br>
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Results
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>RW(1) prior:<br><center><br><img src="pollution1.bmp" alt="[pollution1]">
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1"></center>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Plot of posterior median (red line) and posterior 95% intervals (dashed blue lines) for mu[t] (the true mean daily pollutant concentration), with observed concentrations shown as black dots. (This plot was produced by selecting the
</font><font face="Arial" color="#000100" size="3"><em>model fit
</em></font><font face="Arial" color="#000100" size="3"> option from the
</font><font face="Arial" color="#000100" size="3"><em>Compare
</em></font><font face="Arial" color="#000100" size="3"> menu (available from the
</font><font face="Arial" color="#000100" size="3"><em>Inference
</em></font><font face="Arial" color="#000100" size="3"> menu), with
</font><font face="Arial" color="#000100" size="3"><em>mu
</em></font><font face="Arial" color="#000100" size="3"> specified as the
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><em>day
</em></font><font face="Arial" color="#000100" size="3"> as the
</font><font face="Arial" color="#000100" size="3"><em>axis
</em></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><em>y
</em></font><font face="Arial" color="#000100" size="3"> as
</font><font face="Arial" color="#000100" size="3"><em>other
</em></font><font face="Arial" color="#000100" size="3">). Note that the dashed blue line shows the posterior 95% interval for the estimated mean daily concentration, and is not a predictive interval - hence we would not necessarily expect all of the observed data points to lie within the interval.<br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#FF8040" size="6"><strong><img src="pollution2.bmp" alt="[pollution2]">
</strong></font><font face="Arial" color="#000100" size="3"><br><br>Equivalent plot assuming an RW(2) prior. Note the greater amount of smoothing imposed by this prior:<br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="2"><u>
</u></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><img src="pollution3.bmp" alt="[pollution3]">
</font>
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<title>Pollutiondata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><br>list(T=366, y = c(2.89037175789616, 2.56494935746154, 3.17805383034795, <br>3.68887945411394, 3.13549421592915, 2.484906649788, 3.13549421592915, <br>3.04452243772342, 3.43398720448515, 3.52636052461616, 3.63758615972639, <br>4.21950770517611, 1.94591014905531, 3.09104245335832, 3.98898404656427, <br>4.02535169073515, 4.07753744390572, 3.13549421592915, 2.07944154167984, <br>2.94443897916644, NA, 2.89037175789616, 3.09104245335832, 3.0445224 [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Pollutiondata.txt b/doc/GeoBUGS/Examples/Pollutiondata.txt
new file mode 100755
index 0000000..c2538b0
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Pollutiondata.txt
@@ -0,0 +1,87 @@
+
+list(T=366, y = c(2.89037175789616, 2.56494935746154, 3.17805383034795,
+3.68887945411394, 3.13549421592915, 2.484906649788, 3.13549421592915,
+3.04452243772342, 3.43398720448515, 3.52636052461616, 3.63758615972639,
+4.21950770517611, 1.94591014905531, 3.09104245335832, 3.98898404656427,
+4.02535169073515, 4.07753744390572, 3.13549421592915, 2.07944154167984,
+2.94443897916644, NA, 2.89037175789616, 3.09104245335832, 3.04452243772342,
+3.52636052461616, 3.78418963391826, 3.3322045101752, 3.46573590279973,
+2.94443897916644, 2.89037175789616, 3.09104245335832, 3.36729582998647,
+3.40119738166216, 3.13549421592915, 3.29583686600433, 2.56494935746154,
+3.09104245335832, 2.83321334405622, 3.55534806148941, 3.36729582998647,
+3.3322045101752, NA, NA, NA, NA, 3.43398720448515, 3.17805383034795,
+2.89037175789616, 2.77258872223978, 2.484906649788, 2.99573227355399,
+3.04452243772342, 3.04452243772342, 2.77258872223978, 2.77258872223978,
+2.77258872223978, 2.83321334405622, 2.70805020110221, 3.04452243772342,
+3.13549421592915, 2.56494935746154, 2.56494935746154, 2.94443897916644,
+3.36729582998647, 2.56494935746154, 3.04452243772342, 3.2188758248682,
+3.58351893845611, 4.02535169073515, 4.06044301054642, 3.73766961828337,
+3.78418963391826, 2.83321334405622, 3.09104245335832, 3.09104245335832,
+3.17805383034795, 3.40119738166216, 2.63905732961526, 2.56494935746154,
+2.89037175789616, 2.89037175789616, 3.13549421592915, 2.484906649788,
+2.89037175789616, 3.13549421592915, 2.89037175789616, 2.63905732961526,
+2.39789527279837, 2.83321334405622, 2.70805020110221, 3.09104245335832,
+3.40119738166216, 3.68887945411394, 3.04452243772342, 2.94443897916644,
+3.13549421592915, 2.94443897916644, 3.25809653802148, 3.55534806148941,
+4.02535169073515, 3.71357206670431, 3.36729582998647, 3.3322045101752,
+3.36729582998647, 3.29583686600433, 3.13549421592915, 3.29583686600433,
+2.89037175789616, NA, NA, NA, NA, 2.77258872223978, 2.99573227355399,
+3.40119738166216, 3.3322045101752, 2.63905732961526, 2.89037175789616,
+2.83321334405622, 2.77258872223978, 3.2188758248682, 3.09104245335832,
+NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 3.63758615972639,
+3.71357206670431, 2.89037175789616, 2.77258872223978, NA, NA,
+2.83321334405622, 2.77258872223978, 2.77258872223978, 2.94443897916644,
+2.94443897916644, 2.83321334405622, 2.99573227355399, 3.36729582998647,
+3.36729582998647, 3.09104245335832, 3.09104245335832, 3.13549421592915,
+3.17805383034795, 3.36729582998647, 3.66356164612965, 2.83321334405622,
+2.39789527279837, 2.77258872223978, 2.83321334405622, 3.66356164612965,
+3.2188758248682, 2.39789527279837, 2.56494935746154, 2.70805020110221,
+2.70805020110221, 3.09104245335832, 2.83321334405622, 2.99573227355399,
+2.56494935746154, 2.56494935746154, 2.39789527279837, 2.484906649788,
+2.99573227355399, 3.04452243772342, 2.39789527279837, 2.70805020110221,
+2.07944154167984, 2.77258872223978, 2.99573227355399, 2.94443897916644,
+2.77258872223978, 2.19722457733622, NA, 3.04452243772342, 3.46573590279973,
+3.17805383034795, 3.04452243772342, 3.36729582998647, 3.2188758248682,
+2.99573227355399, 3.55534806148941, 3.2188758248682, 2.70805020110221,
+2.63905732961526, 2.83321334405622, 2.63905732961526, 2.70805020110221,
+2.99573227355399, 3.13549421592915, 2.89037175789616, 2.99573227355399,
+3.2188758248682, 3.43398720448515, 3.13549421592915, 2.63905732961526,
+2.70805020110221, 2.19722457733622, NA, NA, NA, NA, 3.04452243772342,
+2.63905732961526, 2.89037175789616, 3.04452243772342, 3.13549421592915,
+3.55534806148941, 3.49650756146648, 3.76120011569356, 3.55534806148941,
+3.89182029811063, 4.12713438504509, 3.52636052461616, 2.70805020110221,
+2.94443897916644, 3.46573590279973, 3.49650756146648, 3.61091791264422,
+3.85014760171006, 3.97029191355212, 4.02535169073515, 3.52636052461616,
+2.30258509299405, 2.07944154167984, 1.94591014905531, 1.94591014905531,
+2.19722457733622, 2.77258872223978, 2.484906649788, 2.83321334405622,
+2.63905732961526, 2.83321334405622, 2.83321334405622, 2.56494935746154,
+2.56494935746154, 2.83321334405622, 2.83321334405622, 2.56494935746154,
+2.63905732961526, 2.89037175789616, 3.04452243772342, 3.66356164612965,
+3.55534806148941, 2.07944154167984, 2.39789527279837, 2.56494935746154,
+2.70805020110221, 2.94443897916644, 3.36729582998647, 3.76120011569356,
+3.04452243772342, 2.89037175789616, 3.04452243772342, 3.3322045101752,
+3.13549421592915, 2.94443897916644, 3.25809653802148, 3.3322045101752,
+3.40119738166216, 3.29583686600433, 3.78418963391826, 3.36729582998647,
+2.39789527279837, 3.17805383034795, 3.36729582998647, 2.99573227355399,
+2.83321334405622, 3.40119738166216, 2.07944154167984, 2.30258509299405,
+2.30258509299405, 2.19722457733622, 2.19722457733622, 2.19722457733622,
+2.484906649788, 2.89037175789616, 2.56494935746154, 2.89037175789616,
+2.70805020110221, 3.3322045101752, 3.61091791264422, 2.99573227355399,
+2.99573227355399, 3.29583686600433, 2.77258872223978, 2.94443897916644,
+3.58351893845611, 3.71357206670431, 3.2188758248682, 2.99573227355399,
+3.87120101090789, 4.23410650459726, 4.04305126783455, 4.29045944114839,
+4.52178857704904, 3.52636052461616, 3.3322045101752, 2.89037175789616,
+2.77258872223978, 3.25809653802148, 2.484906649788, 1.94591014905531,
+2.39789527279837, 3.43398720448515, 3.66356164612965, 3.52636052461616,
+3.13549421592915, 2.30258509299405, 2.63905732961526, 2.94443897916644,
+2.89037175789616, 2.89037175789616, 2.77258872223978, 2.63905732961526,
+3.13549421592915, 2.56494935746154, 2.94443897916644, 3.63758615972639,
+3.8286413964891, 3.25809653802148, 2.63905732961526, 2.39789527279837,
+2.484906649788, 3.29583686600433, 2.56494935746154, 2.77258872223978,
+2.77258872223978, 3.04452243772342, 2.77258872223978, 2.89037175789616,
+2.89037175789616, 2.63905732961526, NA, 2.56494935746154, 2.70805020110221,
+3.09104245335832, 2.89037175789616, 2.63905732961526, 3.13549421592915,
+3.46573590279973, 3.13549421592915, 3.25809653802148, 3.17805383034795,
+2.63905732961526, 3.43398720448515, 2.70805020110221, 2.484906649788,
+2.70805020110221, 2.19722457733622, 2.39789527279837, 2.484906649788,
+2.63905732961526, 2.39789527279837, 2.19722457733622))
diff --git a/doc/GeoBUGS/Examples/Pollutioninits.html b/doc/GeoBUGS/Examples/Pollutioninits.html
new file mode 100755
index 0000000..d3ec1ba
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Pollutioninits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pollutioninits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(beta = 2, tau.err=1, tau=0.1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Pollutioninits.txt b/doc/GeoBUGS/Examples/Pollutioninits.txt
new file mode 100755
index 0000000..f257b99
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Pollutioninits.txt
@@ -0,0 +1 @@
+list(beta = 2, tau.err=1, tau=0.1)
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Pollutioninits1.html b/doc/GeoBUGS/Examples/Pollutioninits1.html
new file mode 100755
index 0000000..72423f5
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Pollutioninits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pollutioninits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(beta = 0.2, tau.err=0.1, tau=1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Pollutioninits1.txt b/doc/GeoBUGS/Examples/Pollutioninits1.txt
new file mode 100755
index 0000000..b539748
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Pollutioninits1.txt
@@ -0,0 +1 @@
+list(beta = 0.2, tau.err=0.1, tau=1)
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Pollutionmodel.html b/doc/GeoBUGS/Examples/Pollutionmodel.html
new file mode 100755
index 0000000..3354779
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Pollutionmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Pollutionmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">#likelihood
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for(t in 1:T) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y[t] ~ dnorm(mu[t], tau.err)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[t] <- beta + theta[t]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3"># prior for temporal effects <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># RW prior for theta[t] - specified using car.normal with <br> #neighbours (t-1) and (t+1) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for theta[2],....,theta[T-1], and neighbours (t+1) for <br> #theta[1] and (t-1) for theta[T]<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[1:T] ~ car.normal(adj[], weights[], num[], tau) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> beta ~ dflat()<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Specify weight matrix and adjacency matrix corresponding to RW(1) prior
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># (Note - this could be given in the data file instead)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(t in 1:1) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> weights[t] <- 1;<br> adj[t] <- t+1;<br> num[t] <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(t in 2:(T-1)) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> weights[2+(t-2)*2] <- 1;<br> adj[2+(t-2)*2] <- t-1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> weights[3+(t-2)*2] <- 1;<br> adj[3+(t-2)*2] <- t+1;<br> num[t] <- 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(t in T:T) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> weights[(T-2)*2 + 2] <- 1;<br> adj[(T-2)*2 + 2] <- t-1;<br> num[t] <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"># Alternatively, a weight matrix and adjacency matrix <br> #corresponding to RW(2) prior can<br> # be specified or given in the data file <br> #(note, no need to change the prior distribution<br> # on theta, just the weights/adjac [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for(t in 1:1) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[t] <- 2; adj[t] <- t+1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[t+1] <- -1; adj[t+1] <- t+2; num[t] <- 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for(t in 2:2) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[t+1] <- 2; adj[t+1] <- t-1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[t+2] <- 4; adj[t+2] <- t+1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[t+3] <- -1; adj[t+3] <- t+2; num[t] <- 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">#for(t in 3:(T-2)) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[6+(t-3)*4] <- -1; adj[6+(t-3)*4] <- t-2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[7+(t-3)*4] <- 4; adj[7+(t-3)*4] <- t-1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[8+(t-3)*4] <- 4; adj[8+(t-3)*4] <- t+1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[9+(t-3)*4] <- -1; adj[9+(t-3)*4] <- t+2; num[t] <- 4<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for(t in (T-1):(T-1)) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[(T-4)*4 + 6] <- 2; adj[(T-4)*4 + 6] <- t+1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[(T-4)*4 + 7] <- 4; adj[(T-4)*4 + 7] <- t-1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[(T-4)*4 + 8] <- -1; adj[(T-4)*4 + 8] <- t-2; num[t] <- 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># for(t in T:T) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[(T-4)*4 + 9] <- 2; adj[(T-4)*4 + 9] <- t-1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># weights[(T-4)*4 + 10] <- -1; adj[(T-4)*4 + 10] <- t-2; num[t] <- 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># other priors<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau.err ~ dgamma(0.01, 0.01) # measurement error precision<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma.err <- 1 / sqrt(tau.err)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma2.err <- 1/tau.err<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau ~ dgamma(0.01, 0.01) # random walk precision<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma <- 1 / sqrt(tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma2 <- 1/tau<br> # include this variable to use in time series (model fit) plot<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(t in 1:T) { day[t] <- t } <br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/GeoBUGS/Examples/Pollutionmodel.txt b/doc/GeoBUGS/Examples/Pollutionmodel.txt
new file mode 100755
index 0000000..37de35c
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Pollutionmodel.txt
@@ -0,0 +1,80 @@
+ model {
+
+ #likelihood
+ for(t in 1:T) {
+ y[t] ~ dnorm(mu[t], tau.err)
+ mu[t] <- beta + theta[t]
+ }
+
+ # prior for temporal effects
+ # RW prior for theta[t] - specified using car.normal with
+ #neighbours (t-1) and (t+1)
+ # for theta[2],....,theta[T-1], and neighbours (t+1) for
+ #theta[1] and (t-1) for theta[T]
+
+ theta[1:T] ~ car.normal(adj[], weights[], num[], tau)
+ beta ~ dflat()
+
+ # Specify weight matrix and adjacency matrix corresponding to RW(1) prior
+ # (Note - this could be given in the data file instead)
+
+ for(t in 1:1) {
+ weights[t] <- 1;
+ adj[t] <- t+1;
+ num[t] <- 1
+ }
+ for(t in 2:(T-1)) {
+ weights[2+(t-2)*2] <- 1;
+ adj[2+(t-2)*2] <- t-1
+ weights[3+(t-2)*2] <- 1;
+ adj[3+(t-2)*2] <- t+1;
+ num[t] <- 2
+ }
+ for(t in T:T) {
+ weights[(T-2)*2 + 2] <- 1;
+ adj[(T-2)*2 + 2] <- t-1;
+ num[t] <- 1
+ }
+
+ # Alternatively, a weight matrix and adjacency matrix
+ #corresponding to RW(2) prior can
+ # be specified or given in the data file
+ #(note, no need to change the prior distribution
+ # on theta, just the weights/adjacencies)
+ # for(t in 1:1) {
+ # weights[t] <- 2; adj[t] <- t+1
+ # weights[t+1] <- -1; adj[t+1] <- t+2; num[t] <- 2
+ # }
+ # for(t in 2:2) {
+ # weights[t+1] <- 2; adj[t+1] <- t-1
+ # weights[t+2] <- 4; adj[t+2] <- t+1
+ # weights[t+3] <- -1; adj[t+3] <- t+2; num[t] <- 3
+ # }
+ #for(t in 3:(T-2)) {
+ # weights[6+(t-3)*4] <- -1; adj[6+(t-3)*4] <- t-2
+ # weights[7+(t-3)*4] <- 4; adj[7+(t-3)*4] <- t-1
+ # weights[8+(t-3)*4] <- 4; adj[8+(t-3)*4] <- t+1
+ # weights[9+(t-3)*4] <- -1; adj[9+(t-3)*4] <- t+2; num[t] <- 4
+ # }
+ # for(t in (T-1):(T-1)) {
+ # weights[(T-4)*4 + 6] <- 2; adj[(T-4)*4 + 6] <- t+1
+ # weights[(T-4)*4 + 7] <- 4; adj[(T-4)*4 + 7] <- t-1
+ # weights[(T-4)*4 + 8] <- -1; adj[(T-4)*4 + 8] <- t-2; num[t] <- 3
+ # }
+ # for(t in T:T) {
+ # weights[(T-4)*4 + 9] <- 2; adj[(T-4)*4 + 9] <- t-1
+ # weights[(T-4)*4 + 10] <- -1; adj[(T-4)*4 + 10] <- t-2; num[t] <- 2
+ # }
+
+ # other priors
+ tau.err ~ dgamma(0.01, 0.01) # measurement error precision
+ sigma.err <- 1 / sqrt(tau.err)
+ sigma2.err <- 1/tau.err
+
+ tau ~ dgamma(0.01, 0.01) # random walk precision
+ sigma <- 1 / sqrt(tau)
+ sigma2 <- 1/tau
+ # include this variable to use in time series (model fit) plot
+ for(t in 1:T) { day[t] <- t }
+
+ }
diff --git a/doc/GeoBUGS/Examples/Scotland.html b/doc/GeoBUGS/Examples/Scotland.html
new file mode 100755
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--- /dev/null
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@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Scotland</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"><strong><img src="scotland0.bmp" alt="[scotland0]">
</strong></font><font face="Courier New" color="#000100" size="6">Conditional Autoregressive<br> (CAR) models for disease<br> mapping: Lip cancer in<br> Scotland
</font><font face="Arial" color="#000100" size="3"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="3">The rates of lip cancer in 56 counties in Scotland have been analysed by Clayton and Kaldor (1987) and Breslow and Clayton (1993). The form of the data includes the observed and expected cases (expected numbers based on the population and its age and sex distribution in the county), a covariate measuring the percentage of the population engaged in agriculture, fishing, or forestry, and the "position'' of each county expresse [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">O
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">~ Poisson(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">log
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">= og E
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> / 10 +
</font><font face="Symbol" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub><br>
</sub></font><font face="Arial" color="#000100" size="3"><br>where
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"> is an intercept term representing the baseline (log) relative risk of disease across the study region, x
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">is the covariate "percentage of the population engaged in agriculture, fishing, or forestry" in district i, with associated regression coefficient
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> and b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is an area-specific random effect capturing the residual or unexplained (log) relative risk of disease in area i. We often think of b
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> as representing the effect of latent (unobserved) risk factors. <br><br>To allow for spatial dependence between the random effects b
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> in nearby areas, we may assume a CAR prior for these terms. Technical details, including parameterisation and a discussion of suitable hyperpriors for the parameters of this model, are given in
</font><font face="Arial" color="#0000FF" size="3"><a href="../GeoBUGS/Manuals/Manual.html#Appendix">
</font><font face="Arial" color="#0000FF" size="3"><u>appendix 1
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">. The
</font><font face="Arial" color="#000100" size="3"><strong><em><a href="../GeoBUGS/Manuals/Manual.html#car.normal">
</em></strong></font><font face="Arial" color="#0000FF" size="3"><strong><em><u>car.normal
</u></em></strong></font><font face="Arial" color="#000100" size="3"><strong><em></a>
</em></strong></font><font face="Arial" color="#000100" size="3"> distribution may be used to fit this model. The code for the lip cancer data is given below:<br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Model
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Likelihood<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">O[i] ~ dpois(mu[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">log(mu[i]) <- log(E[i]) + alpha0 + alpha1 * X[i]/10 + b[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Area-specific relative risk (for maps)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">RR[i] <- exp(alpha0 + alpha1 * X[i]/10 + b[i]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># CAR prior distribution for random effects: <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">b[1:N] ~ car.normal(adj[], weights[], num[], tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(k in 1:sumNumNeigh) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> weights[k] <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Other priors:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha0 ~ dflat() <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha1 ~ dnorm(0.0, 1.0E-5)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau ~ dgamma(0.5, 0.0005) # prior on precision<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma <- sqrt(1 / tau) # standard deviation<br> b.mean <- sum(b[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Scotlanddata.html">Data</a>
</u></strong></font><font face="Arial" color="#000000" size="3">(click to open)
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>Note that the data for the adjacency matrix (variables
</font><font face="Arial" color="#000000" size="3"><strong><em>adj
</em></strong></font><font face="Arial" color="#000000" size="3">,
</font><font face="Arial" color="#000000" size="3"><strong><em>num
</em></strong></font><font face="Arial" color="#000000" size="3"> and
</font><font face="Arial" color="#000000" size="3"><strong><em>SumNumNeigh
</em></strong></font><font face="Arial" color="#000000" size="3">) have been generated using the <a href="../GeoBUGS/Manuals/Manual.html#Adj">
</font><font face="Arial" color="#0000FF" size="3"><strong><em><u>adj matrix
</u></em></strong></font><font face="Arial" color="#000000" size="3"></a> option of the
</font><font face="Arial" color="#000000" size="3"><strong><em>Adjacency Tool
</em></strong></font><font face="Arial" color="#000000" size="3"> menu in
</font><font face="Arial" color="#000000" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000000" size="3">. By default, this treats islands as having no neighbours, and so the three areas representing the Orkneys, Shetland and the Outer Hebrides islands in Scotland have zero neighbours. You can <a href="../GeoBUGS/Manuals/Manual.html#Edit">
</font><font face="Arial" color="#0000FF" size="3"><u>edit
</u></font><font face="Arial" color="#000000" size="3"></a> the adjacency map of Scotland to include these areas as neighbours if you wish. The
</font><font face="Arial" color="#000000" size="3"><strong><em>car.normal
</em></strong></font><font face="Arial" color="#000000" size="3"> distribution sets the value of b
</font><font face="Arial" color="#000000" size="3"><sub>i
</sub></font><font face="Arial" color="#000000" size="3"> equal to zero for areas i that are islands. Hence the posterior relative risks for the Orkneys, Shetland and the Outer Hebrides in the present example will just depend on the overall baseline rate
</font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"> and the covariate x
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">. Alternatively, you could specify a
</font><font face="Arial" color="#000100" size="3"><em>convolution
</em></font><font face="Arial" color="#000100" size="3"> prior for the area-specific random effects (Besag, York and Mollie 1991) which partitions the overall random effect for each area into the sum of a spatial component plus a non-spatial component. In this model, the islands will just have a non-spatial term for the random effect. See
</font><font face="Arial" color="#000000" size="3"><a href="../GeoBUGS/Examples/LHA.html">
</font><font face="Arial" color="#0000FF" size="3"><u>example on lung cancer in a London Health Authority
</u></font><font face="Arial" color="#000100" size="3"></a> for details of this model.
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Scotlandinits.html">Inits for chain 1</a> <a href="../GeoBUGS/Examples/Scotlandinits1.html">Inits for chain 2</a>
</u></strong></font><font face="Arial" color="#000000" size="3">(click to open)
</font><font face="Arial" color="#000100" size="3"><br><br>Note that the initial values for elements 6, 8 and 11 of the vector
</font><font face="Arial" color="#000100" size="3"><strong>b
</strong></font><font face="Arial" color="#000100" size="3"> are set to NA since these correspond to the three islands (
</font><font face="Arial" color="#000000" size="3">Orkneys, Shetland and the Outer Hebrides). The values of
</font><font face="Arial" color="#000000" size="3"><strong>b
</strong></font><font face="Arial" color="#000000" size="3"> are set to zero by the
</font><font face="Arial" color="#000000" size="3"><strong><em>car.normal
</em></strong></font><font face="Arial" color="#000000" size="3">prior for these 3 areas, and so they are not stochastic nodes.<br><br> <br> <center><img src="scotland2.bmp" alt="[scotland2]"><br><br><br><img src="scotland3.bmp" alt="[scotland3]">
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br><br>
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/GeoBUGS/Examples/Scotland1.html b/doc/GeoBUGS/Examples/Scotland1.html
new file mode 100755
index 0000000..f04089e
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Scotland1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Scotland1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="scotland10.bmp" alt="[scotland10]">
</font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">CAR model: Lip cancer<br> revisited
</font><font face="Arial" color="#000100" size="3"><strong><br><br>
</strong></font><font face="Arial" color="#000000" size="3">This example illustrates the use of the proper CAR distribution (<a href="../GeoBUGS/Manuals/Manual.html#car.proper">
</font><font face="Arial" color="#0000FF" size="3"><strong><em><u>car.proper
</u></em></strong></font><font face="Arial" color="#000000" size="3"></a>) rather than the intrinsic CAR distribution for the area-specific random effects in the Lip cancer example (9.1). We use the definition of the
</font><font face="Arial" color="#000100" size="3"><strong>C
</strong></font><font face="Arial" color="#000000" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong>M
</strong></font><font face="Arial" color="#000000" size="3"> matrices proposed by Cressie and colleagues (see section on <a href="../GeoBUGS/Manuals/Manual.html#Proper">
</font><font face="Arial" color="#0000FF" size="3"><u>proper CAR models
</u></font><font face="Arial" color="#000000" size="3"></a> in Appendix 1).
</font><font face="Arial" color="#000100" size="3"><strong><br><br>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong>Model
</strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"> model {<br><br>
</font><font face="Arial" color="#000000" size="3"># Set up 'data' to define spatial dependence structure<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3"># =====================================
</font><font face="Arial" color="#000100" size="3"><br> for(i in 1 : N) { <br> m[i] <- 1/E[i] # scaling factor for variance in each cell<br> } <br><br> # The vector
</font><font face="Courier New" color="#000100" size="3">C[]
</font><font face="Arial" color="#000100" size="3">required as input into the car.proper distribution is a vector<br> # respresention of the weight matrix with elements Cij. The first J1 elements of the
</font><font face="Courier New" color="#000100" size="3">C[]<br>
</font><font face="Arial" color="#000100" size="3"> # vector contain the weights for the J1 neighbours of area i=1; the (J1+1) to J2<br> # elements of the
</font><font face="Courier New" color="#000100" size="3">C[]
</font><font face="Arial" color="#000100" size="3"> vector contain the weights for the J2 neighbours of area i=2;<br> # etc. To set up this vector, we need to define a variable
</font><font face="Courier New" color="#000100" size="3">cumsum
</font><font face="Arial" color="#000100" size="3">, which gives the<br> # values of J1, J2, etc.; we then set up an index matrix
</font><font face="Courier New" color="#000100" size="3">pick[,]
</font><font face="Arial" color="#000100" size="3"> with N columns<br> # corresponding to the i=1,...,N areas, and with the same number of rows as there are<br> # elements in the
</font><font face="Courier New" color="#000100" size="3">C[]
</font><font face="Arial" color="#000100" size="3"> vector (i.e.
</font><font face="Courier New" color="#000100" size="3">sumNumNeigh
</font><font face="Arial" color="#000100" size="3">). The elements
</font><font face="Courier New" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Courier New" color="#000100" size="3">#C[ (cumsum[i]+1):cumsum[i+1] ]
</font><font face="Arial" color="#000100" size="3">correspond to <br> # the set of weights Cij associated with area i, and so we set up ith column of the<br> # matrix
</font><font face="Courier New" color="#000100" size="3">pick[,]
</font><font face="Arial" color="#000100" size="3">to have a 1 in all the rows k for which
</font><font face="Courier New" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"> #
</font><font face="Courier New" color="#000100" size="3">cumsum[i] < k <= cumsum[i+1]
</font><font face="Arial" color="#000100" size="3">, and 0's elsewhere. <br> # For example, let
</font><font face="Courier New" color="#000100" size="3">N
</font><font face="Arial" color="#000100" size="3">=4 and
</font><font face="Courier New" color="#000100" size="3">cumsum
</font><font face="Arial" color="#000100" size="3">=c(0,3,5,6,8), so area i=1 has 3 neighbours, area<br> # i=2 has 2 neighbours, area i=3 has 1 neighbour and area i=4 has 2 neighbours. The<br> # the matrix
</font><font face="Courier New" color="#000100" size="3">pick[,]
</font><font face="Arial" color="#000100" size="3"> is:<br> #
</font><font face="Courier New" color="#000100" size="3">pick
</font><font face="Arial" color="#000100" size="3">
</font><font face="Courier New" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><br> # 1, 0, 0, 0, <br> # 1, 0, 0, 0, <br> # 1, 0, 0, 0, <br> # 0, 1, 0, 0, <br> # 0, 1, 0, 0, <br> # 0, 0, 1, 0, <br> [...]
</font><font face="Courier New" color="#000100" size="3">inprod(,)
</font><font face="Arial" color="#000100" size="3">) function in WinBUGS and the kth<br> # row of
</font><font face="Courier New" color="#000100" size="3">pick
</font><font face="Arial" color="#000100" size="3"> to select which area corresponds to the kth element in the vector
</font><font face="Courier New" color="#000100" size="3">C[]
</font><font face="Arial" color="#000100" size="3">;<br> # likewise, we can use
</font><font face="Courier New" color="#000100" size="3">inprod(,)
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # and the ith column of
</font><font face="Courier New" color="#000100" size="3">pick
</font><font face="Arial" color="#000100" size="3"> to select the elements of
</font><font face="Courier New" color="#000100" size="3">C[]
</font><font face="Arial" color="#000100" size="3"> which correspond to area i.<br> #<br> # Note: this way of setting up the C vector is somewhat convoluted!!!! In future<br> # versions, we hope the GeoBUGS adjacency matrix tool will be able to dump out the<br> # relevant vectors [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> cumsum[1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for(i in 2:(N+1)) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> cumsum[i] <- sum(num[1:(i-1)])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(k in 1 : sumNumNeigh) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> pick[k,i] <- step(k - cumsum[i] - epsilon) * step(cumsum[i+1] - k) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # pick[k,i] = 1 if cumsum[i] < k <= cumsum[i=1]; otherwise, pick[k,i] = 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> C[k] <- sqrt(E[adj[k]] / inprod(E[], pick[k,])) # weight for each pair of neighbours<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> epsilon <- 0.0001<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Model<br> # =====<br><br> # Likelihood<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O[i] ~ dpois(mu[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> log(mu[i]) <- log(E[i]) + S[i]<br>
</font><font face="Arial" color="#000100" size="3"># Area-specific relative risk
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> RR[i] <- exp(S[i])
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[i] <- alpha
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Proper CAR prior distribution for spatial random effects: <br> S[1:N] ~ car.proper(theta[], C[], adj[], num[], m[], prec, gamma)<br><br> # Other priors:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha ~ dnorm(0, 0.0001) <br>
</font><font face="Arial" color="#000100" size="3"># prior on precision
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> prec ~ dgamma(0.5, 0.0005)
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> v <- 1/prec # variance<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma <- sqrt(1 / prec) # standard deviation<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma.min <- min.bound(C
</font><font face="Arial" color="#000100" size="3">[], adj[], num[], m[]
</font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma.max <- max.bound(C
</font><font face="Arial" color="#000100" size="3">[], adj[], num[], m[]
</font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma ~ dunif(gamma.min, gamma.max)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Scotland1data.html">Data</a>
</u></strong></font><font face="Arial" color="#000100" size="3"> (Click to open)
</font><font face="Arial" color="#0000FF" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Scotland1inits.html">Inits for chain 1</a> <a href="../GeoBUGS/Examples/Scotland1inits1.html">Inits for chain 2</a>
</u></strong></font><font face="Arial" color="#0000FF" size="3"><u>
</u></font><font face="Arial" color="#000100" size="3">(Click to open)<br><br><center>
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3"><img src="scotland11.bmp" alt="[scotland11]"><br><br><br><img src="scotland12.bmp" alt="[scotland12]">
</font>
</center>
</p>
</body>
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diff --git a/doc/GeoBUGS/Examples/Scotland1data.html b/doc/GeoBUGS/Examples/Scotland1data.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Scotland1data</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 56, <br>O = c( 9, 39, 11, 9, 15, 8, 26, 7, 6, 20,<br>13, 5, 3, 8, 17, 9, 2, 7, 9, 7,<br>16, 31, 11, 7, 19, 15, 7, 10, 16, 11,<br>5, 3, 7, 8, 11, 9, 11, 8, 6, 4,<br>10, 8, 2, 6, 19, 3, 2, 3, 28, 6,<br>1, 1, 1, 1,
</font><font face="Arial" color="#FF0000" size="1">
</font><font face="Arial" color="#000000" size="1">0,
</font><font face="Arial" color="#FF0000" size="1">
</font><font face="Arial" color="#000100" size="1">0),<br>E = c( 1.4, 8.7, 3.0, 2.5, 4.3, 2.4, 8.1, 2.3, 2.0, 6.6,<br>4.4, 1.8, 1.1, 3.3, 7.8, 4.6, 1.1, 4.2, 5.5, 4.4,<br>10.5,22.7, 8.8, 5.6,15.5,12.5, 6.0, 9.0,14.4,10.2,<br>4.8, 2.9, 7.0, 8.5,12.3,10.1,12.7, 9.4, 7.2, 5.3,<br>18.8,15.8, 4.3,14.6,50.7, 8.2, 5.6, 9.3,88.7,19.6,<br>3.4, 3.6, 5.7, 7.0, 4.2, 1.8), <br>
</font><font face="Arial" color="#000100" size="1">num = c(3, 2, 1, 3, 3, 0, 5, 0, 5, 4, <br>0, 2, 3, 3, 2, 6, 6, 6, 5, 3, <br>3, 2, 4, 8, 3, 3, 4, 4, 11, 6, <br>7, 3, 4, 9, 4, 2, 4, 6, 3, 4, <br>5, 5, 4, 5, 4, 6, 6, 4, 9, 2, <br>4, 4, 4, 5, 6, 5<br>),<br>adj = c(<br>19, 9, 5, <br>10, 7, <br>12, <br>28, 20, 18, <br>19, 12, 1, <br><br>17, 16, 13, 10, 2, <br><br>29, 23, 19, 17, 1, <br>22, 16, 7, 2, <br><br>5, 3, <br>19, 17, 7, <br>35, 32, 31, <br>29, 25, <br>29, 22, 21, 17, 10, 7, <br>29, 1 [...]
</font><font face="Arial" color="#000100" size="1">)
</font>
</p>
</body>
</html>
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diff --git a/doc/GeoBUGS/Examples/Scotland1data.txt b/doc/GeoBUGS/Examples/Scotland1data.txt
new file mode 100755
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--- /dev/null
+++ b/doc/GeoBUGS/Examples/Scotland1data.txt
@@ -0,0 +1,79 @@
+list(N = 56,
+O = c( 9, 39, 11, 9, 15, 8, 26, 7, 6, 20,
+ 13, 5, 3, 8, 17, 9, 2, 7, 9, 7,
+ 16, 31, 11, 7, 19, 15, 7, 10, 16, 11,
+ 5, 3, 7, 8, 11, 9, 11, 8, 6, 4,
+ 10, 8, 2, 6, 19, 3, 2, 3, 28, 6,
+ 1, 1, 1, 1, 0, 0),
+E = c( 1.4, 8.7, 3.0, 2.5, 4.3, 2.4, 8.1, 2.3, 2.0, 6.6,
+ 4.4, 1.8, 1.1, 3.3, 7.8, 4.6, 1.1, 4.2, 5.5, 4.4,
+ 10.5,22.7, 8.8, 5.6,15.5,12.5, 6.0, 9.0,14.4,10.2,
+ 4.8, 2.9, 7.0, 8.5,12.3,10.1,12.7, 9.4, 7.2, 5.3,
+ 18.8,15.8, 4.3,14.6,50.7, 8.2, 5.6, 9.3,88.7,19.6,
+ 3.4, 3.6, 5.7, 7.0, 4.2, 1.8),
+num = c(3, 2, 1, 3, 3, 0, 5, 0, 5, 4,
+0, 2, 3, 3, 2, 6, 6, 6, 5, 3,
+3, 2, 4, 8, 3, 3, 4, 4, 11, 6,
+7, 3, 4, 9, 4, 2, 4, 6, 3, 4,
+5, 5, 4, 5, 4, 6, 6, 4, 9, 2,
+4, 4, 4, 5, 6, 5
+),
+adj = c(
+19, 9, 5,
+10, 7,
+12,
+28, 20, 18,
+19, 12, 1,
+
+17, 16, 13, 10, 2,
+
+29, 23, 19, 17, 1,
+22, 16, 7, 2,
+
+5, 3,
+19, 17, 7,
+35, 32, 31,
+29, 25,
+29, 22, 21, 17, 10, 7,
+29, 19, 16, 13, 9, 7,
+56, 55, 33, 28, 20, 4,
+17, 13, 9, 5, 1,
+56, 18, 4,
+50, 29, 16,
+16, 10,
+39, 34, 29, 9,
+56, 55, 48, 47, 44, 31, 30, 27,
+29, 26, 15,
+43, 29, 25,
+56, 32, 31, 24,
+45, 33, 18, 4,
+50, 43, 34, 26, 25, 23, 21, 17, 16, 15, 9,
+55, 45, 44, 42, 38, 24,
+47, 46, 35, 32, 27, 24, 14,
+31, 27, 14,
+55, 45, 28, 18,
+54, 52, 51, 43, 42, 40, 39, 29, 23,
+46, 37, 31, 14,
+41, 37,
+46, 41, 36, 35,
+54, 51, 49, 44, 42, 30,
+40, 34, 23,
+52, 49, 39, 34,
+53, 49, 46, 37, 36,
+51, 43, 38, 34, 30,
+42, 34, 29, 26,
+49, 48, 38, 30, 24,
+55, 33, 30, 28,
+53, 47, 41, 37, 35, 31,
+53, 49, 48, 46, 31, 24,
+49, 47, 44, 24,
+54, 53, 52, 48, 47, 44, 41, 40, 38,
+29, 21,
+54, 42, 38, 34,
+54, 49, 40, 34,
+49, 47, 46, 41,
+52, 51, 49, 38, 34,
+56, 45, 33, 30, 24, 18,
+55, 27, 24, 20, 18
+),
+sumNumNeigh = 234)
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Scotland1inits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="1">list(alpha=3, prec=1, gamma=0.1)
</font>
</p>
</body>
</html>
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+list(alpha=3, prec=1, gamma=0.1)
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Scotland1inits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="1">list(alpha=0.3, prec=0.1, gamma=0.05)
</font>
</p>
</body>
</html>
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+list(alpha=0.3, prec=0.1, gamma=0.05)
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diff --git a/doc/GeoBUGS/Examples/Scotland1model.html b/doc/GeoBUGS/Examples/Scotland1model.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Scotland1model</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="3"> model {<br><br>
</font><font face="Arial" color="#000000" size="3"># Set up 'data' to define spatial dependence structure<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3"># =====================================
</font><font face="Arial" color="#000100" size="3"><br> for(i in 1 : N) { <br> m[i] <- 1/E[i] # scaling factor for variance in each cell<br> } <br><br> # The vector
</font><font face="Courier New" color="#000100" size="3">C[]
</font><font face="Arial" color="#000100" size="3">required as input into the car.proper distribution is a vector<br> # respresention of the weight matrix with elements Cij. The first J1 elements of the
</font><font face="Courier New" color="#000100" size="3">C[]<br>
</font><font face="Arial" color="#000100" size="3"> # vector contain the weights for the J1 neighbours of area i=1; the (J1+1) to J2<br> # elements of the
</font><font face="Courier New" color="#000100" size="3">C[]
</font><font face="Arial" color="#000100" size="3"> vector contain the weights for the J2 neighbours of area i=2;<br> # etc. To set up this vector, we need to define a variable
</font><font face="Courier New" color="#000100" size="3">cumsum
</font><font face="Arial" color="#000100" size="3">, which gives the<br> # values of J1, J2, etc.; we then set up an index matrix
</font><font face="Courier New" color="#000100" size="3">pick[,]
</font><font face="Arial" color="#000100" size="3"> with N columns<br> # corresponding to the i=1,...,N areas, and with the same number of rows as there are<br> # elements in the
</font><font face="Courier New" color="#000100" size="3">C[]
</font><font face="Arial" color="#000100" size="3"> vector (i.e.
</font><font face="Courier New" color="#000100" size="3">sumNumNeigh
</font><font face="Arial" color="#000100" size="3">). The elements
</font><font face="Courier New" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Courier New" color="#000100" size="3">#C[ (cumsum[i]+1):cumsum[i+1] ]
</font><font face="Arial" color="#000100" size="3">correspond to <br> # the set of weights Cij associated with area i, and so we set up ith column of the<br> # matrix
</font><font face="Courier New" color="#000100" size="3">pick[,]
</font><font face="Arial" color="#000100" size="3">to have a 1 in all the rows k for which
</font><font face="Courier New" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"> #
</font><font face="Courier New" color="#000100" size="3">cumsum[i] < k <= cumsum[i+1]
</font><font face="Arial" color="#000100" size="3">, and 0's elsewhere. <br> # For example, let
</font><font face="Courier New" color="#000100" size="3">N
</font><font face="Arial" color="#000100" size="3">=4 and
</font><font face="Courier New" color="#000100" size="3">cumsum
</font><font face="Arial" color="#000100" size="3">=c(0,3,5,6,8), so area i=1 has 3 neighbours, area<br> # i=2 has 2 neighbours, area i=3 has 1 neighbour and area i=4 has 2 neighbours. The<br> # the matrix
</font><font face="Courier New" color="#000100" size="3">pick[,]
</font><font face="Arial" color="#000100" size="3"> is:<br> #
</font><font face="Courier New" color="#000100" size="3">pick
</font><font face="Arial" color="#000100" size="3">
</font><font face="Courier New" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><br> # 1, 0, 0, 0, <br> # 1, 0, 0, 0, <br> # 1, 0, 0, 0, <br> # 0, 1, 0, 0, <br> # 0, 1, 0, 0, <br> # 0, 0, 1, 0, <br> [...]
</font><font face="Courier New" color="#000100" size="3">inprod(,)
</font><font face="Arial" color="#000100" size="3">) function in WinBUGS and the kth<br> # row of
</font><font face="Courier New" color="#000100" size="3">pick
</font><font face="Arial" color="#000100" size="3"> to select which area corresponds to the kth element in the vector
</font><font face="Courier New" color="#000100" size="3">C[]
</font><font face="Arial" color="#000100" size="3">;<br> # likewise, we can use
</font><font face="Courier New" color="#000100" size="3">inprod(,)
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # and the ith column of
</font><font face="Courier New" color="#000100" size="3">pick
</font><font face="Arial" color="#000100" size="3"> to select the elements of
</font><font face="Courier New" color="#000100" size="3">C[]
</font><font face="Arial" color="#000100" size="3"> which correspond to area i.<br> #<br> # Note: this way of setting up the C vector is somewhat convoluted!!!! In future<br> # versions, we hope the GeoBUGS adjacency matrix tool will be able to dump out the<br> # relevant vectors [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> cumsum[1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for(i in 2:(N+1)) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> cumsum[i] <- sum(num[1:(i-1)])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(k in 1 : sumNumNeigh) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for(i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> pick[k,i] <- step(k - cumsum[i] - epsilon) * step(cumsum[i+1] - k) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> # pick[k,i] = 1 if cumsum[i] < k <= cumsum[i=1]; otherwise, pick[k,i] = 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> C[k] <- sqrt(E[adj[k]] / inprod(E[], pick[k,])) # weight for each pair of neighbours<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> epsilon <- 0.0001<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Model<br> # =====<br><br> # Likelihood<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> O[i] ~ dpois(mu[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> log(mu[i]) <- log(E[i]) + S[i]<br>
</font><font face="Arial" color="#000100" size="3"># Area-specific relative risk
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> RR[i] <- exp(S[i])
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta[i] <- alpha
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Proper CAR prior distribution for spatial random effects: <br> S[1:N] ~ car.proper(theta[], C[], adj[], num[], m[], prec, gamma)<br><br> # Other priors:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> alpha ~ dnorm(0, 0.0001) <br>
</font><font face="Arial" color="#000100" size="3"># prior on precision
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> prec ~ dgamma(0.5, 0.0005)
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> v <- 1/prec # variance<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sigma <- sqrt(1 / prec) # standard deviation<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma.min <- min.bound(C
</font><font face="Arial" color="#000100" size="3">[], adj[], num[], m[]
</font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma.max <- max.bound(C
</font><font face="Arial" color="#000100" size="3">[], adj[], num[], m[]
</font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> gamma ~ dunif(gamma.min, gamma.max)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Scotland1model.txt b/doc/GeoBUGS/Examples/Scotland1model.txt
new file mode 100755
index 0000000..7455565
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Scotland1model.txt
@@ -0,0 +1,83 @@
+ model {
+
+ # Set up 'data' to define spatial dependence structure
+ # =====================================
+ for(i in 1 : N) {
+ m[i] <- 1/E[i] # scaling factor for variance in each cell
+ }
+
+ # The vector C[] required as input into the car.proper distribution is a vector
+ # respresention of the weight matrix with elements Cij. The first J1 elements of the C[]
+ # vector contain the weights for the J1 neighbours of area i=1; the (J1+1) to J2
+ # elements of the C[] vector contain the weights for the J2 neighbours of area i=2;
+ # etc. To set up this vector, we need to define a variable cumsum, which gives the
+ # values of J1, J2, etc.; we then set up an index matrix pick[,] with N columns
+ # corresponding to the i=1,...,N areas, and with the same number of rows as there are
+ # elements in the C[] vector (i.e. sumNumNeigh). The elements
+ #C[ (cumsum[i]+1):cumsum[i+1] ] correspond to
+ # the set of weights Cij associated with area i, and so we set up ith column of the
+ # matrix pick[,]to have a 1 in all the rows k for which
+ #cumsum[i] < k <= cumsum[i+1], and 0's elsewhere.
+ # For example, let N=4 and cumsum=c(0,3,5,6,8), so area i=1 has 3 neighbours, area
+ # i=2 has 2 neighbours, area i=3 has 1 neighbour and area i=4 has 2 neighbours. The
+ # the matrix pick[,] is:
+ # pick
+ # 1, 0, 0, 0,
+ # 1, 0, 0, 0,
+ # 1, 0, 0, 0,
+ # 0, 1, 0, 0,
+ # 0, 1, 0, 0,
+ # 0, 0, 1, 0,
+ # 0, 0, 0, 1,
+ # 0, 0, 0, 1,
+ #
+ # We can then use the inner product (inprod(,)) function in WinBUGS and the kth
+ # row of pick to select which area corresponds to the kth element in the vector C[];
+ # likewise, we can use inprod(,)
+ # and the ith column of pick to select the elements of C[] which correspond to area i.
+ #
+ # Note: this way of setting up the C vector is somewhat convoluted!!!! In future
+ # versions, we hope the GeoBUGS adjacency matrix tool will be able to dump out the
+ # relevant vectors required. Alternatively, the C vector could be created using another
+ # package (e.g. Splus) and read into WinBUGS as data.
+ #
+ cumsum[1] <- 0
+ for(i in 2:(N+1)) {
+ cumsum[i] <- sum(num[1:(i-1)])
+ }
+ for(k in 1 : sumNumNeigh) {
+ for(i in 1:N) {
+ pick[k,i] <- step(k - cumsum[i] - epsilon) * step(cumsum[i+1] - k)
+ # pick[k,i] = 1 if cumsum[i] < k <= cumsum[i=1]; otherwise, pick[k,i] = 0
+ }
+ C[k] <- sqrt(E[adj[k]] / inprod(E[], pick[k,])) # weight for each pair of neighbours
+ }
+ epsilon <- 0.0001
+
+ # Model
+ # =====
+
+ # Likelihood
+ for (i in 1 : N) {
+ O[i] ~ dpois(mu[i])
+ log(mu[i]) <- log(E[i]) + S[i]
+ # Area-specific relative risk
+ RR[i] <- exp(S[i])
+ theta[i] <- alpha
+ }
+
+ # Proper CAR prior distribution for spatial random effects:
+ S[1:N] ~ car.proper(theta[], C[], adj[], num[], m[], prec, gamma)
+
+ # Other priors:
+ alpha ~ dnorm(0, 0.0001)
+ # prior on precision
+ prec ~ dgamma(0.5, 0.0005)
+ v <- 1/prec # variance
+ sigma <- sqrt(1 / prec) # standard deviation
+
+ gamma.min <- min.bound(C[], adj[], num[], m[])
+ gamma.max <- max.bound(C[], adj[], num[], m[])
+ gamma ~ dunif(gamma.min, gamma.max)
+
+ }
diff --git a/doc/GeoBUGS/Examples/Scotlanddata.html b/doc/GeoBUGS/Examples/Scotlanddata.html
new file mode 100755
index 0000000..e41f314
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Scotlanddata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Scotlanddata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(N = 56, <br>O = c( 9, 39, 11, 9, 15, 8, 26, 7, 6, 20,<br>13, 5, 3, 8, 17, 9, 2, 7, 9, 7,<br>16, 31, 11, 7, 19, 15, 7, 10, 16, 11,<br>5, 3, 7, 8, 11, 9, 11, 8, 6, 4,<br>10, 8, 2, 6, 19, 3, 2, 3, 28, 6,<br>1, 1, 1, 1,
</font><font face="Arial" color="#FF0000" size="1">
</font><font face="Arial" color="#000000" size="1">0,
</font><font face="Arial" color="#FF0000" size="1">
</font><font face="Arial" color="#000100" size="1">0),<br>E = c( 1.4, 8.7, 3.0, 2.5, 4.3, 2.4, 8.1, 2.3, 2.0, 6.6,<br>4.4, 1.8, 1.1, 3.3, 7.8, 4.6, 1.1, 4.2, 5.5, 4.4,<br>10.5,22.7, 8.8, 5.6,15.5,12.5, 6.0, 9.0,14.4,10.2,<br>4.8, 2.9, 7.0, 8.5,12.3,10.1,12.7, 9.4, 7.2, 5.3,<br>18.8,15.8, 4.3,14.6,50.7, 8.2, 5.6, 9.3,88.7,19.6,<br>3.4, 3.6, 5.7, 7.0, 4.2, 1.8), <br>X = c(16,16,10,24,10,24,10, 7, 7,16, <br>7,16,10,24, 7,16,10, 7, 7,10,<br>7,16,10, 7, 1, 1, 7, 7,10,10,<br>7,24,10, 7, 7, 0,10 [...]
</font><font face="Arial" color="#000100" size="1">num = c(3, 2, 1, 3, 3, 0, 5, 0, 5, 4, <br>0, 2, 3, 3, 2, 6, 6, 6, 5, 3, <br>3, 2, 4, 8, 3, 3, 4, 4, 11, 6, <br>7, 3, 4, 9, 4, 2, 4, 6, 3, 4, <br>5, 5, 4, 5, 4, 6, 6, 4, 9, 2, <br>4, 4, 4, 5, 6, 5<br>),<br>adj = c(<br>19, 9, 5, <br>10, 7, <br>12, <br>28, 20, 18, <br>19, 12, 1, <br><br>17, 16, 13, 10, 2, <br><br>29, 23, 19, 17, 1, <br>22, 16, 7, 2, <br><br>5, 3, <br>19, 17, 7, <br>35, 32, 31, <br>29, 25, <br>29, 22, 21, 17, 10, 7, <br>29, 1 [...]
</font><font face="Arial" color="#000100" size="1">)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Scotlanddata.txt b/doc/GeoBUGS/Examples/Scotlanddata.txt
new file mode 100755
index 0000000..ec92de3
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Scotlanddata.txt
@@ -0,0 +1,85 @@
+list(N = 56,
+O = c( 9, 39, 11, 9, 15, 8, 26, 7, 6, 20,
+ 13, 5, 3, 8, 17, 9, 2, 7, 9, 7,
+ 16, 31, 11, 7, 19, 15, 7, 10, 16, 11,
+ 5, 3, 7, 8, 11, 9, 11, 8, 6, 4,
+ 10, 8, 2, 6, 19, 3, 2, 3, 28, 6,
+ 1, 1, 1, 1, 0, 0),
+E = c( 1.4, 8.7, 3.0, 2.5, 4.3, 2.4, 8.1, 2.3, 2.0, 6.6,
+ 4.4, 1.8, 1.1, 3.3, 7.8, 4.6, 1.1, 4.2, 5.5, 4.4,
+ 10.5,22.7, 8.8, 5.6,15.5,12.5, 6.0, 9.0,14.4,10.2,
+ 4.8, 2.9, 7.0, 8.5,12.3,10.1,12.7, 9.4, 7.2, 5.3,
+ 18.8,15.8, 4.3,14.6,50.7, 8.2, 5.6, 9.3,88.7,19.6,
+ 3.4, 3.6, 5.7, 7.0, 4.2, 1.8),
+X = c(16,16,10,24,10,24,10, 7, 7,16,
+ 7,16,10,24, 7,16,10, 7, 7,10,
+ 7,16,10, 7, 1, 1, 7, 7,10,10,
+ 7,24,10, 7, 7, 0,10, 1,16, 0,
+ 1,16,16, 0, 1, 7, 1, 1, 0, 1,
+ 1, 0, 1, 1,16,10),
+num = c(3, 2, 1, 3, 3, 0, 5, 0, 5, 4,
+0, 2, 3, 3, 2, 6, 6, 6, 5, 3,
+3, 2, 4, 8, 3, 3, 4, 4, 11, 6,
+7, 3, 4, 9, 4, 2, 4, 6, 3, 4,
+5, 5, 4, 5, 4, 6, 6, 4, 9, 2,
+4, 4, 4, 5, 6, 5
+),
+adj = c(
+19, 9, 5,
+10, 7,
+12,
+28, 20, 18,
+19, 12, 1,
+
+17, 16, 13, 10, 2,
+
+29, 23, 19, 17, 1,
+22, 16, 7, 2,
+
+5, 3,
+19, 17, 7,
+35, 32, 31,
+29, 25,
+29, 22, 21, 17, 10, 7,
+29, 19, 16, 13, 9, 7,
+56, 55, 33, 28, 20, 4,
+17, 13, 9, 5, 1,
+56, 18, 4,
+50, 29, 16,
+16, 10,
+39, 34, 29, 9,
+56, 55, 48, 47, 44, 31, 30, 27,
+29, 26, 15,
+43, 29, 25,
+56, 32, 31, 24,
+45, 33, 18, 4,
+50, 43, 34, 26, 25, 23, 21, 17, 16, 15, 9,
+55, 45, 44, 42, 38, 24,
+47, 46, 35, 32, 27, 24, 14,
+31, 27, 14,
+55, 45, 28, 18,
+54, 52, 51, 43, 42, 40, 39, 29, 23,
+46, 37, 31, 14,
+41, 37,
+46, 41, 36, 35,
+54, 51, 49, 44, 42, 30,
+40, 34, 23,
+52, 49, 39, 34,
+53, 49, 46, 37, 36,
+51, 43, 38, 34, 30,
+42, 34, 29, 26,
+49, 48, 38, 30, 24,
+55, 33, 30, 28,
+53, 47, 41, 37, 35, 31,
+53, 49, 48, 46, 31, 24,
+49, 47, 44, 24,
+54, 53, 52, 48, 47, 44, 41, 40, 38,
+29, 21,
+54, 42, 38, 34,
+54, 49, 40, 34,
+49, 47, 46, 41,
+52, 51, 49, 38, 34,
+56, 45, 33, 30, 24, 18,
+55, 27, 24, 20, 18
+),
+sumNumNeigh = 234)
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diff --git a/doc/GeoBUGS/Examples/Scotlandinits.html b/doc/GeoBUGS/Examples/Scotlandinits.html
new file mode 100755
index 0000000..81f1c4a
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Scotlandinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Scotlandinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="1">list(tau = 1, alpha0 = 0, alpha1 = 0
</font><font face="Arial" color="#000000" size="2">)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Scotlandinits.txt b/doc/GeoBUGS/Examples/Scotlandinits.txt
new file mode 100755
index 0000000..fc9b009
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Scotlandinits.txt
@@ -0,0 +1,2 @@
+
+list(tau = 1, alpha0 = 0, alpha1 = 0)
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Scotlandinits1.html b/doc/GeoBUGS/Examples/Scotlandinits1.html
new file mode 100755
index 0000000..1cb93c2
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Scotlandinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Scotlandinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="1">list(tau = 10.0, alpha0 = 1.0, alpha1 = 1.0
</font><font face="Arial" color="#000000" size="2">)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Scotlandinits1.txt b/doc/GeoBUGS/Examples/Scotlandinits1.txt
new file mode 100755
index 0000000..b07ba65
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Scotlandinits1.txt
@@ -0,0 +1,2 @@
+
+list(tau = 10.0, alpha0 = 1.0, alpha1 = 1.0)
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diff --git a/doc/GeoBUGS/Examples/Scotlandmodel.html b/doc/GeoBUGS/Examples/Scotlandmodel.html
new file mode 100755
index 0000000..cd4f544
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Scotlandmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Scotlandmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Likelihood<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (i in 1 : N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">O[i] ~ dpois(mu[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">log(mu[i]) <- log(E[i]) + alpha0 + alpha1 * X[i]/10 + b[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Area-specific relative risk (for maps)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">RR[i] <- exp(alpha0 + alpha1 * X[i]/10 + b[i]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># CAR prior distribution for random effects: <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">b[1:N] ~ car.normal(adj[], weights[], num[], tau)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(k in 1:sumNumNeigh) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> weights[k] <- 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Other priors:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha0 ~ dflat() <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">alpha1 ~ dnorm(0.0, 1.0E-5)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">tau ~ dgamma(0.5, 0.0005) # prior on precision<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">sigma <- sqrt(1 / tau) # standard deviation<br> b.mean <- sum(b[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/GeoBUGS/Examples/Scotlandmodel.txt b/doc/GeoBUGS/Examples/Scotlandmodel.txt
new file mode 100755
index 0000000..98f6559
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Scotlandmodel.txt
@@ -0,0 +1,23 @@
+ model {
+
+ # Likelihood
+ for (i in 1 : N) {
+ O[i] ~ dpois(mu[i])
+ log(mu[i]) <- log(E[i]) + alpha0 + alpha1 * X[i]/10 + b[i]
+ # Area-specific relative risk (for maps)
+ RR[i] <- exp(alpha0 + alpha1 * X[i]/10 + b[i])
+ }
+
+ # CAR prior distribution for random effects:
+ b[1:N] ~ car.normal(adj[], weights[], num[], tau)
+ for(k in 1:sumNumNeigh) {
+ weights[k] <- 1
+ }
+
+ # Other priors:
+ alpha0 ~ dflat()
+ alpha1 ~ dnorm(0.0, 1.0E-5)
+ tau ~ dgamma(0.5, 0.0005) # prior on precision
+ sigma <- sqrt(1 / tau) # standard deviation
+ b.mean <- sum(b[])
+ }
diff --git a/doc/GeoBUGS/Examples/Shared.html b/doc/GeoBUGS/Examples/Shared.html
new file mode 100755
index 0000000..334108a
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Shared.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Shared</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="shared0.bmp" alt="[shared0]">
</font><font face="Arial" color="#000100" size="6"><strong><sup>Shared component model for mapping<br> multiple diseases: Oral cavity cancer and<br> lung cancer cancer in West Yorkshire, UK
</sup></strong></font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3">Knorr-Held and Best (2001) analysed data on mortality from oral cavity and oesophageal cancer in Germany using a shared component model. This model is similar in spirit to conventional factor analysis, and partitions the geographical variation in two diseases into a common (shared) component (
</font><font face="Symbol" color="#000100" size="3"><strong>f
</strong></font><font face="Arial" color="#000100" size="3">), and two disease-specific (residual) components (
</font><font face="Symbol" color="#000100" size="3"><strong>y
</strong></font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3"><strong>y
</strong></font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">). Making the rare disease assumption, the likelihood for each disease is assumed to be independent Poisson, conditional on an unknown mean
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="3"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3">~ Poisson(
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> log
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i1
</sub></font><font face="Arial" color="#000100" size="3">= log E
</font><font face="Arial" color="#000100" size="2"><sub>i1
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Symbol" color="#000100" size="3">*d
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">y
</font><font face="Arial" color="#000100" size="2"><sub>i1
</sub></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> log
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i2
</sub></font><font face="Arial" color="#000100" size="3">= log E
</font><font face="Arial" color="#000100" size="2"><sub>i2
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">/
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="3"> +
</font><font face="Symbol" color="#000100" size="3">y
</font><font face="Arial" color="#000100" size="2"><sub>i2
</sub></font><font face="Arial" color="#000100" size="3"><br><br>where Y
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"> and E
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"> are the observed and age/sex standardised expected counts for cancer k in area i respectively,
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> is an intercept term representing the baseline (log) relative risk of cancer k across the study region, and
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="3"> is a scaling factor to allow the risk gradient associated with the shared component to be different for each disease (this is in some sense similar to the factor loadings in conventional factor analysis - see Knorr-Held and Best (2001) for more details). Each of the three components (
</font><font face="Symbol" color="#000100" size="3"><strong>f
</strong></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3"><strong>y
</strong></font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3"><strong>y
</strong></font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">) is assumed to be spatially structured with zero mean; the components are assumed to be independent of each other. Knorr-Held and Best (2001) used a spatial partition model as a prior for each component. In this example, we fit a similar model, but assume an BYM convolution prior for each component. Here we re-consider the data on incidence of oral cavity cancer and lung cancer in 126 electoral wards in the West Yorkshire region of [...]
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Likelihood
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1 : Nareas) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1 : Ndiseases) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y[i, k] ~ dpois(mu[i, k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> log(mu[i, k]) <- log(E[i, k]) + alpha[k] + eta[i, k] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"> for(i in 1:Nareas) { <br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"># Define log relative risk in terms of disease-specific (psi) and shared (phi) <br> # random effects <br> # changed order of k and i index for psi (needed because car.normal assumes <br> # right hand index is areas)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> eta[i, 1] <- phi[i] * delta + psi[1, i] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> eta[i, 2] <- phi[i] / delta + psi[2, i] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Spatial priors (BYM) for the disease-specific random effects
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (k in 1 : Ndiseases) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : Nareas) {<br> # convolution prior = sum of unstructured and spatial effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> psi[k, i] <- U.sp[k, i] + S.sp[k, i]<br> # unstructured disease-specific random effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> U.sp[k, i] ~ dnorm(0, tau.unstr[k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br> # spatial disease-specific effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> S.sp[k,1 : Nareas] ~ car.normal(adj[], weights[], num[], tau.spatial[k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Spatial priors (BYM) for the shared random effects
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1:Nareas) {<br> # convolution prior = sum of unstructured and spatial effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> phi[i] <- U.sh[i] + S.sh[i]<br> # unstructured shared random effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> U.sh[i] ~ dnorm(0, omega.unstr) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br> # spatial shared random effects <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> S.sh[1:Nareas] ~ car.normal(adj[], weights[], num[], omega.spatial)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1:sumNumNeigh) {<br> weights[k] <- 1 <br> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Other priors
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (k in 1:Ndiseases) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3"> alpha[k] ~ dflat()
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau.unstr[k] ~ dgamma(0.5, 0.0005) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau.spatial[k] ~ dgamma(0.5, 0.0005) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> omega.unstr ~ dgamma(0.5, 0.0005) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> omega.spatial ~ dgamma(0.5, 0.0005)
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># scaling factor for relative strength of shared component for each disease<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> logdelta ~ dnorm(0, 5.9)<br> # (prior assumes 95% probability that delta^2 is between 1/5 and 5; <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> delta <- exp(logdelta)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># lognormal assumption is invariant to which disease is labelled 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># and which is labelled 2)<br> # ratio (relative risk of disease 1 associated with shared component) to <br> # (relative risk of disease 2 associated with shared component)<br> # - see Knorr-Held and Best (2001) for further details<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> RR.ratio <- pow(delta, 2)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Relative risks and other summary quantities <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># The GeoBUGS map tool can only map vectors, so need to create separate vector<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># of quantities to be mapped, rather than an array (i.e. totalRR[i,k] won't work!)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1 : Nareas) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> SMR1[i] <- Y[i,1] / E[i,1] # SMR for disease 1 (oral)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> SMR2[i] <- Y[i,2] / E[i,2] # SMR for disease 2 (lung)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> totalRR1[i] <- exp(eta[i,1]) # overall RR of disease 1 (oral) in area i<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> totalRR2[i] <- exp(eta[i,2]) # overall RR of disease 2 (lung) in area i<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># residulal RR specific to disease 1 (oral cancer)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> specificRR1[i]<- exp(psi[1,i]) <br> # residulal RR specific to disease 2 (lung cancer)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> specificRR2[i]<- exp(psi[2,i]) <br> # shared component of risk common to both diseases <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sharedRR[i] <- exp(phi[i])<br> # Note that this needs to be scaled by delta or 1/delta if the<br> # absolute magnitude of shared RR for each disease is of interest<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> logsharedRR1[i] <- phi[i] * delta<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> logsharedRR2[i] <- phi[i] /delta<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }
</font><font face="Arial" color="#000100" size="3"> <br> # empirical variance of shared effects (scaled for disease 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> var.shared[1] <- sd(logsharedRR1[])*sd(logsharedRR1[])<br> # empirical variance of shared effects (scaled for disease 2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> var.shared[2] <- sd(logsharedRR2[])*sd(logsharedRR2[])<br> # empirical variance of disease 1 specific effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> var.specific[1] <- sd(psi[1,])*sd(psi[1,])<br> # empirical variance of disease 2 specific effects <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> var.specific[2] <- sd(psi[2,])*sd(psi[2,]) <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># fraction of total variation in relative risks for each disease that is explained <br> # by the shared component<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> frac.shared[1] <- var.shared[1] / (var.shared[1] + var.specific[1])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> frac.shared[2] <- var.shared[2] / (var.shared[2] + var.specific[2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Shareddata.html">Data</a>
</u></strong></font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000100" size="3">(Click to open)
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Sharedinits.html">Inits for chain 1</a>
</u></strong></font><font face="Arial" color="#000000" size="2"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong><u><a href="../GeoBUGS/Examples/Sharedinits1.html">Inits for chain 2</a>
</u></strong></font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000100" size="3">(Click to open)
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Results
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>A 2000 iteration burn-in followed by a further 30000 updates gave the following results<br><center><br><img src="shared1.bmp" alt="[shared1]"><br></center>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">These indicate that for oral cancer, about 75% of the total between-area variation in risk is captured by the shared component, while for lung cancer about 64% of the total between-area variation in risk is captured by the shared component, although the 95% CI for frac.shared are very wide. RR.ratio is slightly less than 1 (although again with a wide credible interval), indicating that the shared component has a slightly weaker associatio [...]
</font><font face="Arial" color="#000100" size="3"><strong><em>WestYorkshire
</em></strong></font><font face="Arial" color="#000100" size="3">, and is available in the maps directory of GeoBUGS 1.2.<br>
</font><font face="Arial" color="#000100" size="1"><br><center><br><br><img src="shared2.bmp" alt="[shared2]"><br><br><br><img src="shared3.bmp" alt="[shared3]"><br><br><img src="shared4.bmp" alt="[shared4]"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="2"><u><br>
</u></font>
</center>
</p>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Shareddata</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">list(Nareas=126, Ndiseases=2,<br>Y = structure(.Data = c(7, 103, 3, 160, 6, 97, 5, 156, 3, 88, 8, 168, 1, 88, 12, 157, 8, 110,<br> 5, 134, 4, 74, 11, 162, 8, 136, 7, 81, 4, 108, 4, 100, 7, 137,<br> 7, 130, 5, 176, 8, 182, 7, 161, 4, 86, 6, 169, 10, 154, 7, 121,<br> 4, 247, 10, 179, 10, 219, 10, 88, 4, 108, 6, 211, 3, 107, 3, 120,<br> 4, 70, 6, 216, 6, 221, 4, 142, 8, 136, 11, 24 [...]
</font>
</p>
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--- /dev/null
+++ b/doc/GeoBUGS/Examples/Shareddata.txt
@@ -0,0 +1,190 @@
+list(Nareas=126, Ndiseases=2,
+ Y = structure(.Data = c(7, 103, 3, 160, 6, 97, 5, 156, 3, 88, 8, 168, 1, 88, 12, 157, 8, 110,
+ 5, 134, 4, 74, 11, 162, 8, 136, 7, 81, 4, 108, 4, 100, 7, 137,
+ 7, 130, 5, 176, 8, 182, 7, 161, 4, 86, 6, 169, 10, 154, 7, 121,
+ 4, 247, 10, 179, 10, 219, 10, 88, 4, 108, 6, 211, 3, 107, 3, 120,
+ 4, 70, 6, 216, 6, 221, 4, 142, 8, 136, 11, 246, 11, 209, 4, 130,
+ 8, 90, 9, 117, 3, 121, 6, 157, 14, 300, 5, 160, 6, 107, 10, 233,
+ 10, 270, 7, 141, 7, 110, 14, 158, 12, 203, 5, 74, 12, 149, 3, 98,
+ 3, 110, 9, 151, 7, 157, 8, 111, 2, 84, 8, 149, 9, 166, 3, 205,
+ 9, 114, 3, 68, 7, 115, 5, 179, 2, 101, 1, 73, 6, 109, 4, 118,
+ 9, 73, 7, 108, 7, 98, 9, 137, 3, 79, 4, 126, 8, 134, 4, 108, 5,
+ 119, 3, 144, 2, 89, 2, 103, 6, 99, 4, 74, 3, 75, 3, 90, 3, 69,
+ 6, 137, 3, 129, 5, 122, 8, 114, 7, 115, 4, 73, 5, 94, 2, 110,
+ 3, 69, 7, 94, 6, 133, 4, 120, 7, 112, 5, 118, 9, 129, 9, 128,
+ 7, 91, 8, 141, 4, 93, 9, 107, 13, 85, 5, 81, 7, 98, 7, 85, 3,
+ 89, 4, 82, 5, 98, 4, 127, 4, 105, 5, 119, 6, 133, 7, 82, 5, 73,
+ 5, 77, 3, 109, 4, 80.), .Dim=c(126,2)),
+E = structure(.Data = c(5.7993, 124.2824, 9.8345, 199.3086,
+ 6.5001, 138.3337, 9.0741, 191.0307, 6.4746, 136.3728,
+ 9.9171, 208.4544, 5.515, 113.2827, 9.8557, 205.0383, 5.7956, 118.5219, 8.299,
+ 168.9939, 4.8596, 99.1749, 8.8737, 182.1041, 5.3387, 115.9417, 6.2182, 128.2199,
+ 5.368, 111.3884, 5.4669, 115.3283, 8.3298, 172.3197, 8.5829, 176.3519, 8.0016,
+ 172.5571, 9.8149, 217.5105, 6.8331, 137.3765, 5.4115, 111.0865, 5.6492, 119.7825,
+ 8.7562, 178.6785, 6.3436, 132.6835, 7.8424, 165.7296, 7.9467, 163.6806, 8.2651,
+ 179.5329, 4.9209, 99.8676, 4.8173, 97.8898, 8.2088, 172.8071, 5.1494, 111.4239,
+ 6.1063, 125.3408, 4.2812, 89.5027, 7.439, 154.4872, 6.4687, 138.0246, 8.648,
+ 173.9356, 5.4981, 112.8979, 8.1535, 172.1137, 8.1074, 167.9885, 5.0473, 103.0942,
+ 5.337, 110.1, 4.9104, 95.0673, 4.899, 100.6339, 8.2719, 166.6911, 9.0572, 192.7174,
+ 8.3271, 170.1211, 5.2504, 109.0334, 9.2167, 189.3181, 8.2078, 173.5003, 6.3403,
+ 130.4997, 5.2363, 106.8044, 5.7656, 119.1885, 6.349, 134.6238, 3.1955, 63.4971,
+ 4.8059, 96.6801, 4.3527, 92.6587, 5.6589, 113.8283, 7.3528, 158.2496, 6.4591,
+ 134.9901, 5.0808, 103.3924, 3.6248, 73.217, 8.1897, 167.9081, 8.29, 167.5654,
+ 7.3986, 153.8624, 6.3236, 127.4593, 4.261, 86.9421, 5.5404, 111.7691, 9.0518,
+ 186.5931, 5.6972, 117.9196, 4.1577, 90.4632, 3.7059, 75.4029, 4.5956, 99.7396,
+ 4.0921, 85.8003, 5.0072, 99.5433, 5.7554, 118.2132, 5.4192, 113.6951, 4.4614,
+ 95.4255, 5.3266, 113.212, 5.9185, 120.4505, 5.0662, 99.3974, 5.5931, 113.8424,
+ 4.7091, 100.6834, 5.7394, 118.5351, 5.4592, 110.8379, 5.6211, 113.0633, 4.2743,
+ 91.6488, 4.2199, 87.8078, 5.0116, 106.9507, 3.9801, 84.0584, 5.2632, 107.4919,
+ 5.1299, 103.2763, 5.5062, 114.7298, 5.684, 119.65, 5.033, 102.6666, 3.6625,
+ 74.6299, 4.2702, 92.1799, 5.9149, 121.8377, 4.048, 84.8317, 5.8719, 121.1919,
+ 6.6767, 141.6445, 5.3587, 110.0901, 5.4904, 111.204, 4.7363, 96.3014, 5.3231,
+ 108.2957, 6.5753, 137.6387, 5.457, 111.0015, 5.8437, 120.9779, 5.2844, 106.7001,
+ 5.0919, 101.9814, 6.5409, 135.9033, 5.3966, 106.1728, 5.1725, 102.7724, 6.066,
+ 129.0506, 5.9403, 123.6225, 5.4443, 117.149, 5.5746, 115.9296, 5.4766, 113.8003,
+ 5.3397, 108.0343, 5.8259, 124.6071, 5.7783, 125.2003, 6.0794, 127.5812, 5.6695,
+ 116.8155, 5.5123, 114.1313, 5.1238, 104.6006, 5.46, 112.2663), .Dim=c(126,2)),
+num = c(3, 2, 3, 6, 6, 5, 7, 5, 4, 9,
+6, 5, 4, 6, 7, 6, 7, 8, 6, 5,
+4, 8, 6, 8, 6, 5, 6, 7, 4, 4,
+5, 4, 6, 4, 5, 7, 7, 10, 6, 5,
+6, 4, 6, 3, 6, 8, 6, 5, 6, 6,
+7, 5, 6, 5, 9, 8, 7, 6, 5, 5,
+6, 5, 6, 6, 7, 8, 7, 6, 6, 6,
+1, 3, 6, 5, 4, 4, 6, 6, 6, 5,
+3, 5, 8, 8, 5, 7, 4, 6, 5, 9,
+6, 5, 5, 6, 7, 4, 6, 5, 6, 5,
+6, 6, 5, 7, 7, 6, 5, 5, 5, 7,
+6, 6, 6, 6, 9, 7, 4, 4, 4, 4,
+6, 5, 3, 5, 2, 4
+),
+adj = c(
+9, 7, 3,
+10, 4,
+7, 5, 1,
+20, 17, 12, 10, 6, 2,
+16, 14, 8, 7, 6, 3,
+18, 12, 8, 5, 4,
+22, 16, 13, 9, 5, 3, 1,
+18, 15, 14, 6, 5,
+13, 11, 7, 1,
+79, 77, 75, 45, 37, 21, 17, 4, 2,
+57, 55, 34, 22, 13, 9,
+20, 19, 18, 6, 4,
+22, 11, 9, 7,
+25, 23, 16, 15, 8, 5,
+30, 29, 24, 23, 18, 14, 8,
+25, 23, 22, 14, 7, 5,
+35, 27, 26, 21, 20, 10, 4,
+31, 28, 24, 19, 15, 12, 8, 6,
+32, 28, 27, 20, 18, 12,
+27, 19, 17, 12, 4,
+37, 26, 17, 10,
+55, 41, 33, 25, 16, 13, 11, 7,
+38, 29, 25, 16, 15, 14,
+51, 47, 44, 38, 31, 30, 18, 15,
+38, 33, 23, 22, 16, 14,
+39, 37, 35, 21, 17,
+36, 35, 32, 20, 19, 17,
+46, 40, 36, 32, 31, 19, 18,
+38, 30, 23, 15,
+38, 29, 24, 15,
+47, 40, 28, 24, 18,
+36, 28, 27, 19,
+43, 42, 41, 38, 25, 22,
+88, 71, 57, 11,
+39, 36, 27, 26, 17,
+50, 46, 39, 35, 32, 28, 27,
+63, 50, 45, 39, 26, 21, 10,
+53, 51, 44, 43, 33, 30, 29, 25, 24, 23,
+50, 46, 37, 36, 35, 26,
+49, 47, 46, 31, 28,
+58, 55, 48, 42, 33, 22,
+48, 43, 41, 33,
+53, 52, 48, 42, 38, 33,
+51, 38, 24,
+84, 79, 77, 63, 37, 10,
+59, 54, 50, 49, 40, 39, 36, 28,
+56, 51, 49, 40, 31, 24,
+58, 52, 43, 42, 41,
+64, 59, 56, 47, 46, 40,
+63, 54, 46, 39, 37, 36,
+60, 56, 53, 47, 44, 38, 24,
+61, 58, 53, 48, 43,
+61, 60, 52, 51, 43, 38,
+65, 63, 59, 50, 46,
+73, 72, 67, 62, 58, 57, 41, 22, 11,
+70, 68, 66, 64, 60, 51, 49, 47,
+88, 87, 78, 62, 55, 34, 11,
+67, 61, 55, 52, 48, 41,
+65, 64, 54, 49, 46,
+68, 61, 56, 53, 51,
+68, 67, 60, 58, 53, 52,
+78, 73, 72, 57, 55,
+84, 65, 54, 50, 45, 37,
+69, 66, 65, 59, 56, 49,
+84, 82, 69, 64, 63, 59, 54,
+86, 85, 80, 76, 70, 69, 64, 56,
+83, 74, 73, 68, 61, 58, 55,
+74, 70, 67, 61, 60, 56,
+95, 85, 82, 66, 65, 64,
+90, 76, 74, 68, 66, 56,
+34,
+73, 62, 55,
+83, 78, 72, 67, 62, 55,
+90, 83, 70, 68, 67,
+92, 81, 77, 10,
+90, 86, 70, 66,
+92, 91, 79, 75, 45, 10,
+89, 87, 83, 73, 62, 57,
+94, 91, 84, 77, 45, 10,
+98, 93, 86, 85, 66,
+103, 92, 75,
+102, 95, 84, 69, 65,
+99, 97, 90, 89, 78, 74, 73, 67,
+102, 101, 94, 82, 79, 65, 63, 45,
+95, 93, 80, 69, 66,
+106, 100, 98, 90, 80, 76, 66,
+89, 88, 78, 57,
+116, 99, 89, 87, 57, 34,
+99, 88, 87, 83, 78,
+106, 104, 97, 96, 86, 83, 76, 74, 70,
+110, 103, 94, 92, 79, 77,
+103, 91, 81, 77, 75,
+105, 98, 95, 85, 80,
+112, 110, 101, 91, 84, 79,
+109, 105, 102, 93, 85, 82, 69,
+107, 104, 97, 90,
+111, 107, 99, 96, 90, 83,
+105, 100, 93, 86, 80,
+116, 111, 97, 89, 88, 83,
+115, 106, 105, 98, 86,
+112, 110, 108, 102, 94, 84,
+109, 108, 101, 95, 84, 82,
+118, 110, 92, 91, 81,
+121, 120, 114, 107, 106, 96, 90,
+115, 113, 109, 100, 98, 95, 93,
+120, 115, 104, 100, 90, 86,
+114, 111, 104, 97, 96,
+113, 112, 109, 102, 101,
+113, 108, 105, 102, 95,
+119, 118, 112, 103, 101, 94, 91,
+117, 116, 114, 107, 99, 97,
+119, 113, 110, 108, 101, 94,
+123, 115, 112, 109, 108, 105,
+122, 121, 117, 111, 107, 104,
+126, 124, 123, 121, 120, 113, 106, 105, 100,
+126, 124, 122, 117, 111, 99, 88,
+122, 116, 114, 111,
+125, 119, 110, 103,
+125, 118, 112, 110,
+121, 115, 106, 104,
+124, 122, 120, 115, 114, 104,
+124, 121, 117, 116, 114,
+126, 115, 113,
+126, 122, 121, 116, 115,
+119, 118,
+124, 123, 116, 115
+),
+sumNumNeigh = 710
+)
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Sharedinits.html b/doc/GeoBUGS/Examples/Sharedinits.html
new file mode 100755
index 0000000..3b70547
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Sharedinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Sharedinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha = c(0.14, -0.78), tau.unstr = c(0.25, 2.7), tau.spatial = c(7.5, 9.8),<br>omega.unstr = 9.4, omega.spatial = 4.0, logdelta = 1.34)<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Sharedinits.txt b/doc/GeoBUGS/Examples/Sharedinits.txt
new file mode 100755
index 0000000..d8baa24
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Sharedinits.txt
@@ -0,0 +1,3 @@
+list(alpha = c(0.14, -0.78), tau.unstr = c(0.25, 2.7), tau.spatial = c(7.5, 9.8),
+omega.unstr = 9.4, omega.spatial = 4.0, logdelta = 1.34)
+
diff --git a/doc/GeoBUGS/Examples/Sharedinits1.html b/doc/GeoBUGS/Examples/Sharedinits1.html
new file mode 100755
index 0000000..c51568c
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Sharedinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Sharedinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">list(alpha = c(1.0, 1.0), tau.unstr = c(2.0, 1.0), tau.spatial = c(1.0, 1.0),<br>omega.unstr = 1.0, omega.spatial = 1.0, logdelta = 0.5)<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/GeoBUGS/Examples/Sharedinits1.txt b/doc/GeoBUGS/Examples/Sharedinits1.txt
new file mode 100755
index 0000000..84d35a0
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Sharedinits1.txt
@@ -0,0 +1,3 @@
+list(alpha = c(1.0, 1.0), tau.unstr = c(2.0, 1.0), tau.spatial = c(1.0, 1.0),
+omega.unstr = 1.0, omega.spatial = 1.0, logdelta = 0.5)
+
diff --git a/doc/GeoBUGS/Examples/Sharedmodel.html b/doc/GeoBUGS/Examples/Sharedmodel.html
new file mode 100755
index 0000000..8b19f7f
--- /dev/null
+++ b/doc/GeoBUGS/Examples/Sharedmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Sharedmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Likelihood
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1 : Nareas) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1 : Ndiseases) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> Y[i, k] ~ dpois(mu[i, k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> log(mu[i, k]) <- log(E[i, k]) + alpha[k] + eta[i, k] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"> for(i in 1:Nareas) { <br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"># Define log relative risk in terms of disease-specific (psi) and shared (phi) <br> # random effects <br> # changed order of k and i index for psi (needed because car.normal assumes <br> # right hand index is areas)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> eta[i, 1] <- phi[i] * delta + psi[1, i] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> eta[i, 2] <- phi[i] / delta + psi[2, i] <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Spatial priors (BYM) for the disease-specific random effects
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (k in 1 : Ndiseases) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1 : Nareas) {<br> # convolution prior = sum of unstructured and spatial effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> psi[k, i] <- U.sp[k, i] + S.sp[k, i]<br> # unstructured disease-specific random effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> U.sp[k, i] ~ dnorm(0, tau.unstr[k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br> # spatial disease-specific effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> S.sp[k,1 : Nareas] ~ car.normal(adj[], weights[], num[], tau.spatial[k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Spatial priors (BYM) for the shared random effects
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1:Nareas) {<br> # convolution prior = sum of unstructured and spatial effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> phi[i] <- U.sh[i] + S.sh[i]<br> # unstructured shared random effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> U.sh[i] ~ dnorm(0, omega.unstr) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br> # spatial shared random effects <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> S.sh[1:Nareas] ~ car.normal(adj[], weights[], num[], omega.spatial)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1:sumNumNeigh) {<br> weights[k] <- 1 <br> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Other priors
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3">for (k in 1:Ndiseases) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3"> alpha[k] ~ dflat()
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau.unstr[k] ~ dgamma(0.5, 0.0005) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> tau.spatial[k] ~ dgamma(0.5, 0.0005) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> } <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> omega.unstr ~ dgamma(0.5, 0.0005) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> omega.spatial ~ dgamma(0.5, 0.0005)
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># scaling factor for relative strength of shared component for each disease<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> logdelta ~ dnorm(0, 5.9)<br> # (prior assumes 95% probability that delta^2 is between 1/5 and 5; <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> delta <- exp(logdelta)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># lognormal assumption is invariant to which disease is labelled 1 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># and which is labelled 2)<br> # ratio (relative risk of disease 1 associated with shared component) to <br> # (relative risk of disease 2 associated with shared component)<br> # - see Knorr-Held and Best (2001) for further details<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> RR.ratio <- pow(delta, 2)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># Relative risks and other summary quantities <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># The GeoBUGS map tool can only map vectors, so need to create separate vector<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># of quantities to be mapped, rather than an array (i.e. totalRR[i,k] won't work!)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">for (i in 1 : Nareas) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> SMR1[i] <- Y[i,1] / E[i,1] # SMR for disease 1 (oral)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> SMR2[i] <- Y[i,2] / E[i,2] # SMR for disease 2 (lung)<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> totalRR1[i] <- exp(eta[i,1]) # overall RR of disease 1 (oral) in area i<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> totalRR2[i] <- exp(eta[i,2]) # overall RR of disease 2 (lung) in area i<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># residulal RR specific to disease 1 (oral cancer)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> specificRR1[i]<- exp(psi[1,i]) <br> # residulal RR specific to disease 2 (lung cancer)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> specificRR2[i]<- exp(psi[2,i]) <br> # shared component of risk common to both diseases <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> sharedRR[i] <- exp(phi[i])<br> # Note that this needs to be scaled by delta or 1/delta if the<br> # absolute magnitude of shared RR for each disease is of interest<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> logsharedRR1[i] <- phi[i] * delta<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> logsharedRR2[i] <- phi[i] /delta<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }
</font><font face="Arial" color="#000100" size="3"> <br> # empirical variance of shared effects (scaled for disease 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> var.shared[1] <- sd(logsharedRR1[])*sd(logsharedRR1[])<br> # empirical variance of shared effects (scaled for disease 2)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> var.shared[2] <- sd(logsharedRR2[])*sd(logsharedRR2[])<br> # empirical variance of disease 1 specific effects<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> var.specific[1] <- sd(psi[1,])*sd(psi[1,])<br> # empirical variance of disease 2 specific effects <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> var.specific[2] <- sd(psi[2,])*sd(psi[2,]) <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"># fraction of total variation in relative risks for each disease that is explained <br> # by the shared component<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> frac.shared[1] <- var.shared[1] / (var.shared[1] + var.specific[1])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> frac.shared[2] <- var.shared[2] / (var.shared[2] + var.specific[2])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br>
</font>
</p>
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diff --git a/doc/GeoBUGS/Examples/Sharedmodel.txt b/doc/GeoBUGS/Examples/Sharedmodel.txt
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+ model {
+
+ # Likelihood
+ for (i in 1 : Nareas) {
+ for (k in 1 : Ndiseases) {
+ Y[i, k] ~ dpois(mu[i, k])
+ log(mu[i, k]) <- log(E[i, k]) + alpha[k] + eta[i, k]
+ }
+ }
+
+ for(i in 1:Nareas) {
+ # Define log relative risk in terms of disease-specific (psi) and shared (phi)
+ # random effects
+ # changed order of k and i index for psi (needed because car.normal assumes
+ # right hand index is areas)
+ eta[i, 1] <- phi[i] * delta + psi[1, i]
+ eta[i, 2] <- phi[i] / delta + psi[2, i]
+ }
+
+ # Spatial priors (BYM) for the disease-specific random effects
+ for (k in 1 : Ndiseases) {
+ for (i in 1 : Nareas) {
+ # convolution prior = sum of unstructured and spatial effects
+ psi[k, i] <- U.sp[k, i] + S.sp[k, i]
+ # unstructured disease-specific random effects
+ U.sp[k, i] ~ dnorm(0, tau.unstr[k])
+ }
+ # spatial disease-specific effects
+ S.sp[k,1 : Nareas] ~ car.normal(adj[], weights[], num[], tau.spatial[k])
+ }
+ # Spatial priors (BYM) for the shared random effects
+ for (i in 1:Nareas) {
+ # convolution prior = sum of unstructured and spatial effects
+ phi[i] <- U.sh[i] + S.sh[i]
+ # unstructured shared random effects
+ U.sh[i] ~ dnorm(0, omega.unstr)
+ }
+ # spatial shared random effects
+ S.sh[1:Nareas] ~ car.normal(adj[], weights[], num[], omega.spatial)
+
+ for (k in 1:sumNumNeigh) {
+ weights[k] <- 1
+ }
+
+ # Other priors
+ for (k in 1:Ndiseases) {
+ alpha[k] ~ dflat()
+ tau.unstr[k] ~ dgamma(0.5, 0.0005)
+ tau.spatial[k] ~ dgamma(0.5, 0.0005)
+ }
+ omega.unstr ~ dgamma(0.5, 0.0005)
+ omega.spatial ~ dgamma(0.5, 0.0005)
+ # scaling factor for relative strength of shared component for each disease
+ logdelta ~ dnorm(0, 5.9)
+ # (prior assumes 95% probability that delta^2 is between 1/5 and 5;
+ delta <- exp(logdelta)
+ # lognormal assumption is invariant to which disease is labelled 1
+ # and which is labelled 2)
+ # ratio (relative risk of disease 1 associated with shared component) to
+ # (relative risk of disease 2 associated with shared component)
+ # - see Knorr-Held and Best (2001) for further details
+ RR.ratio <- pow(delta, 2)
+
+ # Relative risks and other summary quantities
+ # The GeoBUGS map tool can only map vectors, so need to create separate vector
+ # of quantities to be mapped, rather than an array (i.e. totalRR[i,k] won't work!)
+ for (i in 1 : Nareas) {
+ SMR1[i] <- Y[i,1] / E[i,1] # SMR for disease 1 (oral)
+ SMR2[i] <- Y[i,2] / E[i,2] # SMR for disease 2 (lung)
+
+ totalRR1[i] <- exp(eta[i,1]) # overall RR of disease 1 (oral) in area i
+ totalRR2[i] <- exp(eta[i,2]) # overall RR of disease 2 (lung) in area i
+ # residulal RR specific to disease 1 (oral cancer)
+ specificRR1[i]<- exp(psi[1,i])
+ # residulal RR specific to disease 2 (lung cancer)
+ specificRR2[i]<- exp(psi[2,i])
+ # shared component of risk common to both diseases
+ sharedRR[i] <- exp(phi[i])
+ # Note that this needs to be scaled by delta or 1/delta if the
+ # absolute magnitude of shared RR for each disease is of interest
+ logsharedRR1[i] <- phi[i] * delta
+ logsharedRR2[i] <- phi[i] /delta
+ }
+ # empirical variance of shared effects (scaled for disease 1)
+ var.shared[1] <- sd(logsharedRR1[])*sd(logsharedRR1[])
+ # empirical variance of shared effects (scaled for disease 2)
+ var.shared[2] <- sd(logsharedRR2[])*sd(logsharedRR2[])
+ # empirical variance of disease 1 specific effects
+ var.specific[1] <- sd(psi[1,])*sd(psi[1,])
+ # empirical variance of disease 2 specific effects
+ var.specific[2] <- sd(psi[2,])*sd(psi[2,])
+
+ # fraction of total variation in relative risks for each disease that is explained
+ # by the shared component
+ frac.shared[1] <- var.shared[1] / (var.shared[1] + var.specific[1])
+ frac.shared[2] <- var.shared[2] / (var.shared[2] + var.specific[2])
+ }
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Manual</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="manual0.bmp" alt="[manual0]">
</font><font face="Courier New" color="#000100" size="6">GeoBUGS User Manual
</font><font face="Arial" color="#000100" size="6"><strong><sup><br>
</sup></strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="4">Version 3.2.3, March 2014
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#000100" size="3"> Andrew Thomas
</font><font face="Arial" color="#000100" size="1"><sup>1
</sup></font><font face="Arial" color="#000100" size="3"> Nicky Best
</font><font face="Arial" color="#000100" size="1"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> Dave Lunn
</font><font face="Arial" color="#000100" size="1"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> <br> Richard Arnold
</font><font face="Arial" color="#000100" size="1"><sup>3
</sup></font><font face="Arial" color="#000100" size="3"> David Spiegelhalter
</font><font face="Arial" color="#000100" size="1"><sup>4
</sup></font><font face="Arial" color="#000100" size="3"> <br><br>
</font><font face="Arial" color="#000100" size="1"><sup>1
</sup></font><font face="Arial" color="#000100" size="3"> Dept of Mathematics & Statistics,<br> University of St Andrews<br> St Andrews<br> Scotland<br><br>
</font><font face="Arial" color="#000100" size="1"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> Department of Epidemiology & Public Health,<br> Imperial College School of Medicine,<br> Norfolk Place,<br> London W2 1PG, UK<br><br>
</font><font face="Arial" color="#000100" size="1"><sup>3
</sup></font><font face="Arial" color="#000100" size="3"> School of Mathematical and Computing Sciences <br> Victoria University, <br> P. O. Box 600, Wellington, <br> New Zealand<br><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="1"><sup>4
</sup></font><font face="Arial" color="#000100" size="1"><sup>
</sup></font><font face="Arial" color="#000100" size="3">MRC Biostatistics Unit,<br> Institute of Public Health,<br> Robinson Way,<br> Cambridge CB2 2SR, UK<br><br> e-mail: bugs at mrc-bsu.cam.ac.uk [general]<br> helsinkiant at gmail.com   [...]
</font><font face="Arial" color="#000100" size="5"><strong><a id="Top">Contents</a>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#0000FF" size="3">
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#Intro">Introduction</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#Import">Importing map polygon files</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#Splus">Splus format</a><br> <a href="#ArcInfo">ArcInfo format</a><br> <a href="#Epimap">Epimap format</a><br> <a href="#ArcView">ArcView format</a><br> <a href="#Load">Loading a polygon file into&n [...]
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#Export">Exporting maps from GeoBUGS into Splus format</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#Adj">Producing adjacency matrices</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#Edit">Editing adjacency matrices</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#Maps">Producing maps</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#Cuts">User-specified cut-points and shading</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#Identify">Identifying individual areas on a map</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#Save">Copying and saving maps</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#Spatial">Spatial distributions</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#car.normal">car.normal and car.l1</a><br> <a href="#car.proper">car.proper</a> <br> <a href="#spatial.exp">spatial.exp and spatial.disc</a><br> <a href="#spatial.exp.pred">spatial.pred and spatial.unipred</a><br> [...]
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#Temporal">Temporal distributions</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#rw">Using car.normal as a random walk prior for <br> temporal smoothing</a><br><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#Examples">Examples</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../GeoBUGS/Examples/Scotland.html">Conditional Autoregressive (CAR) models for disease mapping: <br> Lip cancer in Scotland</a><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../GeoBUGS/Examples/LHA.html">Convolution priors: Lung cancer in a <br> London Health Authority</a><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../GeoBUGS/Examples/Scotland1.html">Proper CAR model: Lip cancer revisited</a><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../GeoBUGS/Examples/Elevation.html">Bayesian kriging and spatial prediction: Surface elevation</a><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../GeoBUGS/Examples/Forest.html">Poisson-gamma spatial moving average (convolution) model: <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#0000FF" size="3"> Distribution of hickory trees in Duke forest</a><br><br> <a href="../GeoBUGS/Examples/Huddersfield.html">Poisson-gamma spatial moving average (convolution) model:<br> Ecological regression of air pollu [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../GeoBUGS/Examples/MVCAR.html">Intrinsic multivariate CAR prior for mapping multiple <br> diseases:Oral cavity cancer and lung cancer in <br> West Yorkshire (UK)</a><br><br> <a href="../G [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#Joint">Joint specification</a><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#Conditional">Conditional specification</a> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#Intrinsic">Intrinsic CAR model</a><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#Proper">Proper CAR model</a><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#MV">Intrinsic Multivariate CAR model</a><br><br> <a href="#Appendix 2">Appendix 2: Technical details of the <br> Poisson-gamma Spatial Moving Average<br> convolution model</a><br><br>& [...]
</font><font face="Arial" color="#000100" size="3"><strong><sub><br>
</sub></strong></font><font face="Arial" color="#000100" size="5"><strong><a id="Intro">
</strong></font><font face="Courier New" color="#000100" size="6">Introduction
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="#Top"> [top]</a>
</font><font face="Arial" color="#000100" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><br>GeoBUGS is an add-on module to WinBUGS which provides an interface for: <br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> <a href="#Maps">
</font><font face="Arial" color="#0000FF" size="3">producing maps
</font><font face="Arial" color="#000100" size="3"></a> of the output from disease mapping and other spatial models<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> <a href="#Adj">
</font><font face="Arial" color="#0000FF" size="3">creating
</font><font face="Arial" color="#000100" size="3"></a> and <a href="#Edit">
</font><font face="Arial" color="#0000FF" size="3">manipulating
</font><font face="Arial" color="#000100" size="3"></a> adjacency matrices that are required as input for the<br> <a href="#car.normal">
</font><font face="Arial" color="#0000FF" size="3">conditional autoregressive models
</font><font face="Arial" color="#000100" size="3"></a> available in OpenBUGS for carrying out<br> spatial smoothing. <br><br>GeoBUGS contains map files for<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> Districts in Scotland (called
</font><font face="Arial" color="#000100" size="3"><strong><em>Scotland
</em></strong></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> Wards in a London Health Authority (called
</font><font face="Arial" color="#000100" size="3"><strong><em>London_HA
</em></strong></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> Counties in Great Britain (called
</font><font face="Arial" color="#000100" size="3"><strong><em>GB_Counties
</em></strong></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> Departements in France (called
</font><font face="Arial" color="#000100" size="3"><strong><em>France
</em></strong></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> Nomoi in Greece (called
</font><font face="Arial" color="#000100" size="3"><strong><em>Greecenomoi
</em></strong></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> Districts in Belgium (called
</font><font face="Arial" color="#000100" size="3"><strong><em>Belgium
</em></strong></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> Communes in Sardinia (called
</font><font face="Arial" color="#000100" size="3"><strong><em>Sardinia
</em></strong></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> Subquarters in Munich (called
</font><font face="Arial" color="#000100" size="3"><strong><em>Munich
</em></strong></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> A 15 x 15 regular grid (called
</font><font face="Arial" color="#000100" size="3"><strong><em>Elevation
</em></strong></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> Wards in West Yorkshire (UK) (called
</font><font face="Arial" color="#000100" size="3"><strong><em>WestYorkshire
</em></strong></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> A 4 x 4 regular grid (called
</font><font face="Arial" color="#000100" size="3"><strong><em>Forest
</em></strong></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> A grid of 750 m
</font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> grid cells covering the town of Huddersfield and surroundings in <br> northern England (called
</font><font face="Arial" color="#000100" size="3"><strong><em>Huddersfield_750m_grid)
</em></strong></font><font face="Arial" color="#000100" size="3"><br><br>A list of the area IDs for each map and the order in which the areas are stored in the map file can be obtained using the <a href="#Export">
</font><font face="Arial" color="#0000FF" size="3">export Splus
</font><font face="Arial" color="#000100" size="3"></a> command. <br><br>GeoBUGS also has facilities for importing user-defined maps reading polygon formats from
</font><font face="Arial" color="#0000FF" size="3"> <a href="#Splus">Splus
</font><font face="Arial" color="#0000FF" size="3"><u></a>
</u></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#0000FF" size="3"> <a href="#ArcInfo">ArcInfo
</font><font face="Arial" color="#0000FF" size="3"><u></a>
</u></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#0000FF" size="3"> <a href="#Epimap">Epimap
</font><font face="Arial" color="#0000FF" size="3"><u></a>
</u></font><font face="Arial" color="#000100" size="3">, plus a link to a program written by Yue Cui for importing
</font><font face="Arial" color="#0000FF" size="3"><a href="#ArcView">ArcView</a>
</font><font face="Arial" color="#000100" size="3"> shape files. <br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Import">
</strong></font><font face="Courier New" color="#000100" size="6">Importing map polygon files
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Polygon files can be imported into GeoBUGS from a variety of other packages:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="3"><a href="#Splus">Splus</a>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="3"><a href="#ArcInfo">ArcInfo</a>
</font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="3"><a href="#Epimap">Epimap</a>
</font><font face="Symbol" color="#000100" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#0000FF" size="3"><a href="#ArcView">ArcView
</font><font face="Arial" color="#0000FF" size="3"><u></a>
</u></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Import files are text files containing:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Number of regions in the map<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> List of labels for each region, with corresponding ID number<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> List of x and y co-ordinates for each polygon, plus the polygon label
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3">The different GeoBUGS import formats are designed to follow as closely as possible the format in which Splus, ArcInfo and EpiMap export polygons, respectively. However, some manual editing of the polygon files exported from these various packages is also necessary before they can be read into GeoBUGS. <br><br>The following simple map is used to illustrate the different import formats. The map contains 3 areas (labelled area 1, area 2 and [...]
</font><font face="Arial" color="#FF0000" size="2"><br> <img src="manual1.bmp" alt="[manual1]"><br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="Splus">
</strong></font><font face="Courier New" color="#000100" size="6">Splus format
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="5"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br> map:3<br>
</font><font face="Arial" color="#FF0000" size="3">Xscale: 1000<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3">Yscale: 1000
</font><font face="Arial" color="#000100" size="3"><br><br> 1 area1<br> 2 area2<br> 3 area3<br><br> area1 0 2<br> area1 1 2<br> area1 1 3<br> area1 0 3<br> NA NA NA<br> area1 2 1 [...]
</font><font face="Arial" color="#000100" size="3"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="3">The Splus import file is in three parts:<br><br>The first line contains the key word 'map' (lower case) followed by a colon and an integer, N, where N is the number of distinct areas in the map (note that one area can consist of more than one polygon). <a id="xscale">The 2nd and 3rd lines are
</font><font face="Arial" color="#000100" size="3"><em>optional
</em></font><font face="Arial" color="#000100" size="3">, and can be used to specify the units for the map scale. By default, GeoBUGS assumes that the polygon coordinates are measured in metres. If the coordinates are measured in kilometres, say, then specify Xscale and Yscale to be 1000. GeoBUGS will then multiply all polygon co-ordinates by Xscale and Yscale as appropriate before storing the map file. If Xscale and Yscale are not specified, then the default units (metres) are assumed.</ [...]
</font><font face="Arial" color="#000100" size="3"><strong><br><br><a id="ArcInfo">
</strong></font><font face="Courier New" color="#000100" size="6">ArcInfo format
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br> map:3<br>
</font><font face="Arial" color="#FF0000" size="3"> Xscale: 1000<br> Yscale: 1000<br>
</font><font face="Arial" color="#000100" size="3"><br> 1 area1<br> 2 area2<br> 3 area3<br><br> regions<br> 99 area1<br> 103 area1<br> 210 area2<br> 211 area3<br> END<br><br>&nbs [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3">The ArcInfo import file is in four parts:<br><br>The first 2 parts are the same as the Splus format. <br><br>The third part begins with a line containing the key word 'regions' (lower case). Below this is a 2 column list giving:<br><br>(column 1) an integer label corresponding to the integer label for one of the polygons listed in the final part of the import file. Each polygon should have a unique integer label, but this can be arbitrary [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="Epimap">
</strong></font><font face="Courier New" color="#000100" size="6">Epimap format
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">map:3<br>
</font><font face="Arial" color="#FF0000" size="1">
</font><font face="Arial" color="#FF0000" size="3">Xscale: 1000<br>
</font><font face="Arial" color="#FF0000" size="1">
</font><font face="Arial" color="#FF0000" size="3">Yscale: 1000<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">1 area1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">2 area2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">3 area3<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">area1, 4<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">0, 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">1, 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">1, 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">0, 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">area1, 4<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">2, 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">4, 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">4, 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">2, 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">area2, 4 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">0, 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">2, 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">2, 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">0, 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">area3, 4 <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">2, 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">3, 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">3, 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">2, 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">END<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3">The Epimap import file is in three parts:<br><br>The first 2 parts are the same as the Splus format. <br><br>The third gives the polygon co-ordinates. The format for each polygon is:<br><br>(row 1, column 1) the label of the area to which the polygon belongs.<br>(row 1, column 2) the number of vertices in the polygon (note the comma separator)<br>Subsequent rows contain a 2-column list of numbers giving the x- and y-coordinates of the pol [...]
</font><font face="Arial" color="#000100" size="3"><strong><a id="ArcView">
</strong></font><font face="Courier New" color="#000100" size="6">ArcView format
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>GeoBUGS does not have an option for loading ArcView shape files directly. However, Ms Yue Cui at the University of Minnesota has written programs in Splus and R for converting shape files into the GeoBUGS Splus format so that they can be loaded in GeoBUGS (http://www.biostat.umn.edu/~yuecui/).
</font><font face="Arial" color="#0000FF" size="3"><br><br><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="Load">
</strong></font><font face="Courier New" color="#000100" size="6">Loading a polygon file into GeoBUGS
</font><font face="Arial" color="#000000" size="3"><strong></a>
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Open the polygon file as a separate text file in OpenBUGS and select the appropriate import option from the
</font><font face="Arial" color="#000100" size="3"><strong><em>Map
</em></strong></font><font face="Arial" color="#000100" size="3"> menu. (To try loading the example map files above, first copy them to a separate file, and focus the window containing this file). If the map has been loaded correctly, a
</font><font face="Arial" color="#000100" size="3"><strong><em>Save As
</em></strong></font><font face="Arial" color="#000100" size="3"> dialog box will appear, prompting you to enter a name for the map file. By default, the map file will be saved in the
</font><font face="Courier" color="#000100" size="3">Maps/Rsrc
</font><font face="Arial" color="#000100" size="3"> subdirectory of your OpenBUGS program, with a
</font><font face="Courier" color="#000100" size="3">.map
</font><font face="Arial" color="#000100" size="3"> extension. You can view this map by selecting
</font><font face="Arial" color="#000100" size="3"><strong><em>Open
</em></strong></font><font face="Arial" color="#000100" size="3"> from the
</font><font face="Arial" color="#000100" size="3"><strong><em>File
</em></strong></font><font face="Arial" color="#000100" size="3"> menu (go to the
</font><font face="Courier" color="#000100" size="3">Maps/Rsrc
</font><font face="Arial" color="#000100" size="3"> subdirectory and select file type:
</font><font face="Courier" color="#000100" size="3">map file (*.map)
</font><font face="Arial" color="#000100" size="3">. You will need to exit OpenBUGS and re-start before the new map will appear on the pull-down list of avaialble maps in the
</font><font face="Arial" color="#000100" size="3"><strong><em>Map Tool
</em></strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong><em>Adjacency Tool
</em></strong></font><font face="Arial" color="#000100" size="3"> of the
</font><font face="Arial" color="#000100" size="3"><strong><em>Map
</em></strong></font><font face="Arial" color="#000100" size="3"> menu.
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Export">
</strong></font><font face="Courier New" color="#000100" size="6">Exporting maps from GeoBUGS into Splus format
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Focus the window containing the map in GeoBUGS and select
</font><font face="Arial" color="#000100" size="3"><strong><em>Export Splus
</em></strong></font><font face="Arial" color="#000100" size="3"> from the
</font><font face="Arial" color="#000100" size="3"><strong><em>Map
</em></strong></font><font face="Arial" color="#000100" size="3"> menu. This will write the map in Splus format to a new window. This command can be used to obtain the list of area IDs and the order in which they are specified in the GeoBUGS map (see top part of export file).<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Adj">
</strong></font><font face="Courier New" color="#000100" size="6">Producing adjacency matrices
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>GeoBUGS includes an option to produce a data file containing the adjacency matrix for any map loaded on the system. This file is in a format required by the
</font><font face="Arial" color="#0000FF" size="3"> <a href="#car.normal">car.normal</a>
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#0000FF" size="3"><a href="#car.normal">car.l1
</font><font face="Arial" color="#000100" size="3"><u></a>
</u></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#0000FF" size="3"> <a href="#mv.car">mv.car</a>
</font><font face="Arial" color="#000100" size="3"> conditional autoregressive distributions available in the OpenBUGS program.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Select the
</font><font face="Arial" color="#000100" size="3"><strong><em>Adjacency Tool
</em></strong></font><font face="Arial" color="#000100" size="3"> option from the
</font><font face="Arial" color="#000100" size="3"><strong><em> Map
</em></strong></font><font face="Arial" color="#000100" size="3"> menu.<br><br>
</font><font face="Arial" color="#000100" size="2"><img src="manual2.bmp" alt="[manual2]"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Select the name of the map you wish to draw from the pull-down menu labelled
</font><font face="Arial" color="#000100" size="3"><strong><em>Map
</em></strong></font><font face="Arial" color="#000100" size="3"> and<br> click on
</font><font face="Arial" color="#000100" size="3"><strong><em>adj map
</em></strong></font><font face="Arial" color="#000100" size="3">. The selected map will then appear in a window.<br><br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> Typing the ID number of a region in the bottom white box and clicking
</font><font face="Arial" color="#000100" size="3"><strong><em>shw region
</em></strong></font><font face="Arial" color="#000100" size="3"> will<br> cause the specified region to be highlighted in red on the map; its neighbours (defined to<br> be any region adjacent to the red region) are highlighted in green. <a id="highlight">A region and its<br> neighbours can also be highlighted by positioning the mouse cursor over the required<br> region on the map and clicking with the left button.</a><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Click on the
</font><font face="Arial" color="#000100" size="3"><strong><em>adj matrix
</em></strong></font><font face="Arial" color="#000100" size="3"> button to produce a text file containing the adjacency matrix in a<br> form suitable for loading as data into OpenBUGS for use with the
</font><font face="Arial" color="#000100" size="3"><strong><em>car.normal
</em></strong></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><strong><em>car.l1
</em></strong></font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">and<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>mv.car
</em></strong></font><font face="Arial" color="#000100" size="3"> distributions. (See
</font><font face="Arial" color="#0000FF" size="3"><a href="#Appendix">appendix 1</a>
</font><font face="Arial" color="#000100" size="3"> for further details about these three<br> distributions).<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">Note: when calculating which areas are adjacent to which others, GeoBUGS includes a<br> 'tolerance' zone of 0.1 metres. This tolerance zone should not lead to spurious neighbours<br> unless you forget to appropriately scale your distance units in the polygon file using the <br>
</font><font face="Arial" color="#0000FF" size="3"><a href="#xscale">Xscale</a>
</font><font face="Arial" color="#000000" size="3">and
</font><font face="Arial" color="#0000FF" size="3"><a href="#xscale">Yscale</a>
</font><font face="Arial" color="#000100" size="3"> options, or your map covers a tiny geographic region (in<br> which case, artificially re-scaling the distance units for your map should overcome any<br> problems). <br><br><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Edit">
</strong></font><font face="Courier New" color="#000100" size="6">Editing adjacency matrices
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#000100" size="3"><br>To remove a region from the set of neighbours for a specific area:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> <a href="#highlight">
</font><font face="Arial" color="#0000FF" size="3">Highlight
</font><font face="Arial" color="#000100" size="3"></a> the specific area in red on the map;<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Place the mouse cursor over the region to be removed from the set of neighbours for the<br> red area;<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Hold down the Ctrl key while clicking with the left mouse button. The removed area will no<br> longer be highlighted in green.<br><br>To add a region to the set of neighbours for a specific area:<br><br>
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> <a href="#highlight">
</font><font face="Arial" color="#0000FF" size="3">Highlight
</font><font face="Arial" color="#000100" size="3"></a> the specific area in red on the map;<br><br>
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Place the mouse cursor over the region to be added to the set of neighbours for the <br> red area
</font><font face="Symbol" color="#000100" size="2"><strong><br>
</strong></font><font face="Symbol" color="#000100" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Hold down the Ctrl key while clicking with the left mouse button. The additional area will<br> then become highlighted in green.<br><br>Once you have finished editing the set of neighbours for each region on your map, <a href="#Adj">
</font><font face="Arial" color="#0000FF" size="3">create the new adjacency matrix
</font><font face="Arial" color="#000100" size="3"></a> by clicking on the
</font><font face="Arial" color="#000100" size="3"><strong><em>adj matrix
</em></strong></font><font face="Arial" color="#000100" size="3"> button.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="5"><strong><a id="Maps">
</strong></font><font face="Courier New" color="#000100" size="6">Producing maps
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Note: in order to produce a map of the mean or other summary statistic of the posterior distribution of a stochastic variable, you must have already set a samples or summary monitor for that parameter and have carried out some updates.<br><br>To produce a map:<br><br>
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Select the
</font><font face="Arial" color="#000100" size="3"><strong><em>Mapping Tool
</em></strong></font><font face="Arial" color="#000100" size="3"> option from the
</font><font face="Arial" color="#000100" size="3"><strong><em>Map
</em></strong></font><font face="Arial" color="#000100" size="3"> menu.<br><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="manual3.bmp" alt="[manual3]"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Select the name of the map you wish to draw from the pull-down menu labelled
</font><font face="Arial" color="#000100" size="3"><strong><em>Map
</em></strong></font><font face="Arial" color="#000100" size="3">.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Type the name of the variable to be mapped in the white box labelled
</font><font face="Arial" color="#000100" size="3"><strong><em> Variable
</em></strong></font><font face="Arial" color="#000100" size="3">.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> If the variable is
</font><font face="Arial" color="#000100" size="3"><em>data
</em></font><font face="Arial" color="#000100" size="3"> (e.g. the raw SMR, expected counts E, or a covariate) pick the<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>value
</em></strong></font><font face="Arial" color="#000100" size="3"> option in the pull down menu labelled
</font><font face="Arial" color="#000100" size="3"><strong><em>Quantity
</em></strong></font><font face="Arial" color="#000100" size="3"> and then click the
</font><font face="Arial" color="#000100" size="3"><strong><em>plot
</em></strong></font><font face="Arial" color="#000100" size="3"> button: a map<br> shaded according to the values of the variable will now appear.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> If the variable is a
</font><font face="Arial" color="#000100" size="3"><em> stochastic
</em></font><font face="Arial" color="#000100" size="3"> quantity (e.g. the relative risks) there are various options<br> which you can select from the
</font><font face="Arial" color="#000100" size="3"><strong><em>Quantity
</em></strong></font><font face="Arial" color="#000100" size="3"> menu:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3"> if you have monitored the variable by setting a
</font><font face="Arial" color="#000100" size="3"><em> summary monitor
</em></font><font face="Arial" color="#000100" size="3">, then you must select<br> the
</font><font face="Arial" color="#000100" size="3"><strong><em>mean(summary)
</em></strong></font><font face="Arial" color="#000100" size="3">option from this menu, as only the posterior means are stored by the<br> summary monitor;<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3"> if you have monitored the variable by setting a
</font><font face="Arial" color="#000100" size="3"><em>samples monitor
</em></font><font face="Arial" color="#000100" size="3"> (which stores the full<br> posterior sample), you can select any of the remaining options from the Quantity menu:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><strong><em>mean(sample)
</em></strong></font><font face="Arial" color="#000100" size="3"> will map the posterior means of the variable;<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><strong><em>percentile
</em></strong></font><font face="Arial" color="#000100" size="3"> will plot posterior quantiles of the variable - if you select this option, you must<br> then type the required percentile in the box labelled
</font><font face="Arial" color="#000100" size="3"><strong><em>quantile
</em></strong></font><font face="Arial" color="#000100" size="3">; <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><strong><em>prob greater
</em></strong></font><font face="Arial" color="#000100" size="3">will map the posterior probability that the value of the variable is greater than<br> or equal to the specified threshold, which you must type in the box labelled
</font><font face="Arial" color="#000100" size="3"><strong><em>threshold
</em></strong></font><font face="Arial" color="#000100" size="3">;<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><strong><em>prob less
</em></strong></font><font face="Arial" color="#000100" size="3"> will map the posterior probability that the value of the variable is less than or<br> equal to the specified threshold, which you must type in the box labelled
</font><font face="Arial" color="#000100" size="3"><strong><em>threshold
</em></strong></font><font face="Arial" color="#000100" size="3">;<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">When you have selected the quantity you want to map, click the
</font><font face="Arial" color="#000100" size="3"><strong><em>plot
</em></strong></font><font face="Arial" color="#000100" size="3"> button to display the<br> map. <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> The numbers in brackets shown on the map legend give the number of areas classified in<br> each category on the map.<br><br>Fig 1. GeoBUGS map of SMRs for Scottish Lip Cancer data <br><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="manual4.bmp" alt="[manual4]"><br><br><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Cuts">
</strong></font><font face="Courier New" color="#000100" size="6">User-specified cut-points and shading
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>GeoBUGS can work with two kinds of cut-points: absolute value cut-points and percentile cut-points. For absolute cut-points, GeoBUGS chooses a default set of breaks based on the absolute value of the variable to be mapped: these are chosen to give equally spaced intervals. For percentile cutpoints, GeoBUGS chooses the 10th, 50th and 90th percentiles of the empirical distribution of the variable to be mapped. The default shading is blu [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Select the
</font><font face="Arial" color="#000100" size="3"><strong><em>custom
</em></strong></font><font face="Arial" color="#000100" size="3"> option from the
</font><font face="Arial" color="#000100" size="3"><strong><em> Palette
</em></strong></font><font face="Arial" color="#000100" size="3"> menu in the top right of the
</font><font face="Arial" color="#000100" size="3"><strong><em>Map Tool
</em></strong></font><font face="Arial" color="#000100" size="3">.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Clicking with the left mouse button on the arrow by each colour will bring up a menu of<br> alternative colours that can be selected.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> After you have selected the new colour scheme, click on the
</font><font face="Arial" color="#000100" size="3"><strong><em>set cuts
</em></strong></font><font face="Arial" color="#000100" size="3"> button to "refresh"<br> the currently selected map or click on the
</font><font face="Arial" color="#000100" size="3"><strong><em> plot
</em></strong></font><font face="Arial" color="#000100" size="3"> button to produce a new map.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> To reset the colour scheme to blue shades, select
</font><font face="Arial" color="#000100" size="3"><strong><em>blues
</em></strong></font><font face="Arial" color="#000100" size="3"> from the Palette menu and click<br> on the
</font><font face="Arial" color="#000100" size="3"><strong><em>set cuts
</em></strong></font><font face="Arial" color="#000100" size="3">button again. <br><br>To edit the absolute value cutpoints:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Select the required number of cutpoints (a maximum of 6 cutpoints is currently allowed)<br> from the menu labelled
</font><font face="Arial" color="#000100" size="3"><strong><em>num cuts
</em></strong></font><font face="Arial" color="#000100" size="3"> under the
</font><font face="Arial" color="#000100" size="3"><strong><em>Cuts
</em></strong></font><font face="Arial" color="#000100" size="3"> menu. <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Type the required values of the cutpoints in the appropriate boxes labelled cut 1, cut 2<br> etc.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Click on the
</font><font face="Arial" color="#000100" size="3"><strong><em>set cuts
</em></strong></font><font face="Arial" color="#000100" size="3"> button to "refresh" the currently selected map or click on the
</font><font face="Arial" color="#000100" size="3"><strong><em>plot<br>
</em></strong></font><font face="Arial" color="#000100" size="3">button to produce a new map.<br><br>To produce maps using cutpoints based on percentiles:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Select the
</font><font face="Arial" color="#000100" size="3"><strong><em>percentile
</em></strong></font><font face="Arial" color="#000100" size="3"> option rather than
</font><font face="Arial" color="#000100" size="3"><strong><em>abs value
</em></strong></font><font face="Arial" color="#000100" size="3"> option for the cutpoints on the left of<br> the
</font><font face="Arial" color="#000100" size="3"><strong><em>Map Tool
</em></strong></font><font face="Arial" color="#000100" size="3">.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Click on the
</font><font face="Arial" color="#000100" size="3"><strong><em>plot
</em></strong></font><font face="Arial" color="#000100" size="3"> button to produce a new map. The default is to set the cutpoints to the<br> 10th, 50th and 90th percentiles of the empirical distribution of values to be mapped.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> To display the absolute values corresponding to these percentiles on the map legend:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3"> reselect the
</font><font face="Arial" color="#000100" size="3"><strong><em>abs value
</em></strong></font><font face="Arial" color="#000100" size="3"> option for cutpoints;<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3"> click on the
</font><font face="Arial" color="#000100" size="3"><strong><em>get cuts
</em></strong></font><font face="Arial" color="#000100" size="3"> button - the absolute values corresponding to the percentiles should<br> now be displayed in the
</font><font face="Arial" color="#000100" size="3"><strong><em>Cuts
</em></strong></font><font face="Arial" color="#000100" size="3"> boxes on the right of the
</font><font face="Arial" color="#000100" size="3"><strong><em> Map Tool
</em></strong></font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3"> click on the
</font><font face="Arial" color="#000100" size="3"><strong><em>set cuts
</em></strong></font><font face="Arial" color="#000100" size="3"> button - the legend labels on the map should now display the<br> absolute values of the cutpoints.<br><br>To use the same set of cutpoints for multiple maps:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Select the window with the map containing the cutpoints you wish to use.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Click on the
</font><font face="Arial" color="#000100" size="3"><strong><em> get cuts
</em></strong></font><font face="Arial" color="#000100" size="3"> button - the cutpoints used for the selected map should now be<br> displayed in the
</font><font face="Arial" color="#000100" size="3"><strong><em>Cuts
</em></strong></font><font face="Arial" color="#000100" size="3">boxes on the right of the
</font><font face="Arial" color="#000100" size="3"><strong><em> Map Tool
</em></strong></font><font face="Arial" color="#000100" size="3">.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Select the window with the map whose cutpoints you wish to change.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> Click on the
</font><font face="Arial" color="#000100" size="3"><strong><em>set cuts
</em></strong></font><font face="Arial" color="#000100" size="3"> button - the map should now be updated using the new cutpoints.<br><br>Some current limitations:<br><br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3"> It is not possible to save user-defined colour schemes once you quit GeoBUGS.<br><br><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Identify">
</strong></font><font face="Courier New" color="#000100" size="6">Identifying individual areas on a map
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>The index, label and value of an individual area on the map can be found by placing the cursor over the area of interest on the map and clicking with the left mouse button. The index (i.e. ID number i of the area, where i=1,...,Number of areas), area label (given in the polygon file) and value of variable currently being mapped for the selected area will be shown in left of the grey bar at the bottom of the WinBUGS program window.<br> [...]
</font><font face="Arial" color="#000100" size="5"><strong><a id="Save">
</strong></font><font face="Courier New" color="#000100" size="6">Copying and saving maps
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Maps produced using the GeoBUGS map tool can be copied and pasted into other Microsoft Windows software such as Word and PowerPoint. To select the map, click anywhere on the map window to focus it, then press the Ctrl and Space keys simultaneouly (a blue border should then appear around the figure); then select 'Copy' from the 'Edit' menu (or Crtl-C). Then paste into the appropriate Word or PowerPoint file etc. To save the map as a po [...]
</font><font face="Arial" color="#000100" size="5"><strong><a id="Spatial">
</strong></font><font face="Courier New" color="#000100" size="6">Spatial distributions
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><br>See <a href="#Appendix">
</font><font face="Arial" color="#0000FF" size="3">appendices</a>
</font><font face="Arial" color="#000100" size="3"> for further tecnhical details about the various spatial distributions implemented in GeoBUGS 1.2.
</font><font face="Arial" color="#000100" size="3"><strong><br><br> <a id="car.normal">
</strong></font><font face="Courier New" color="#000100" size="6">car.normal and car.l1
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"> [<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="3"><br><br>The intrinsic Gaussian CAR prior distribution is specified using the distribution
</font><font face="Arial" color="#000100" size="3"><strong><em>car.normal
</em></strong></font><font face="Arial" color="#000100" size="3"> for the
</font><font face="Arial" color="#000100" size="3"><em>vector
</em></font><font face="Arial" color="#000100" size="3">of random varables
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> = ( S
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">, ....., S
</font><font face="Arial" color="#000100" size="2"><sub>N
</sub></font><font face="Arial" color="#000100" size="3"><sub> ).
</sub></font><font face="Arial" color="#000100" size="3">A robust version of this model is available, which assumes a double exponential (Laplace) rather than Gaussian distribution: this is called
</font><font face="Arial" color="#000100" size="3"><strong><em> car.l1
</em></strong></font><font face="Arial" color="#000100" size="3">. The syntax for these distributions is as follows:<br><br>S[1:N] ~ car.normal(adj[], weights[], num[], tau)<br>S[1:N] ~ car.l1(adj[], weights[], num[], tau)<br><br>where:<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>adj[]
</em></strong></font><font face="Arial" color="#000100" size="3"> : A vector listing the ID numbers of the adjacent areas for each area (this is a sparse representation of the full adjacency matrix for the study region, and can be generated using the
</font><font face="Arial" color="#000100" size="3"><strong><em>Adjacency Tool
</em></strong></font><font face="Arial" color="#000100" size="3">from the
</font><font face="Arial" color="#000100" size="3"><strong><em>Map
</em></strong></font><font face="Arial" color="#000100" size="3"> menu in
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3">.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>weights[]
</em></strong></font><font face="Arial" color="#000100" size="3"> : A vector the same length as
</font><font face="Arial" color="#000100" size="3"><strong><em>adj[]
</em></strong></font><font face="Arial" color="#000100" size="3">giving
</font><font face="Arial" color="#000100" size="3"><em>unnormalised
</em></font><font face="Arial" color="#000100" size="3">weights associated with each pair of areas. For the CAR model described above, taking C
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = 1 (equivalently W
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = 1/ n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ) if areas i and j are neighbours and 0 otherwise, gives a vector of 1's for
</font><font face="Arial" color="#000100" size="3"><strong><em>weights[]
</em></strong></font><font face="Arial" color="#000100" size="3">.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>num[]
</em></strong></font><font face="Arial" color="#000100" size="3">: A vector of length N (the total number of areas) giving the number of neighbours n
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> for each area.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>tau
</em></strong></font><font face="Arial" color="#000100" size="3"> : A scalar argument representing the precision (inverse variance) parameter of the Gaussian CAR prior, or the inverse scale parameter of the Laplace prior (for the latter model, the variance = 2 / tau
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">).<br><br>The first 3 arguments must be entered as data (it is currently not possible to allow the
</font><font face="Arial" color="#000100" size="3"><strong><em>weights
</em></strong></font><font face="Arial" color="#000100" size="3"> to be unknown); the final variable
</font><font face="Arial" color="#000100" size="3"><strong><em>tau
</em></strong></font><font face="Arial" color="#000100" size="3"> is usually treated as unknown and so is assigned a prior distribution. The data variables
</font><font face="Arial" color="#000100" size="3"><strong><em>num
</em></strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong><em>adj
</em></strong></font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">may be created by the
</font><font face="Arial" color="#000100" size="3"><strong><em>adj matrix
</em></strong></font><font face="Arial" color="#000100" size="3"> option of the
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong><em>Adjacency Tool
</em></strong></font><font face="Arial" color="#000100" size="3"> as described <a href="#Adj">
</font><font face="Arial" color="#0000FF" size="3">above
</font><font face="Arial" color="#000100" size="3"></a>. The variable
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3"><strong><em>weights
</em></strong></font><font face="Arial" color="#000100" size="3"> must be created by the user, and must be a vector the same length as
</font><font face="Arial" color="#000100" size="3"><strong><em>adj
</em></strong></font><font face="Arial" color="#000100" size="3">. A common choice is to set all the
</font><font face="Arial" color="#000100" size="3"><strong><em>weights
</em></strong></font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#000100" size="3">equal to 1 since this gives the standard Besag, York and Mollie (1991) CAR model (see section on <a href="#Intrinsic">
</font><font face="Arial" color="#0000FF" size="3">intrinsic CAR models
</font><font face="Arial" color="#000100" size="3"></a> in Appendix 1 for further discussion of weights). The easiest way to do this is to create a loop in your
</font><font face="Arial" color="#000100" size="3"><em>WinBUGS
</em></font><font face="Arial" color="#000100" size="3"> model code:<br><br>for(j in 1:sumNumNneigh) { weights[j] <- 1}<br><br>where
</font><font face="Arial" color="#000100" size="3"><strong><em>sumNumNneigh
</em></strong></font><font face="Arial" color="#000100" size="3"> is the length of
</font><font face="Arial" color="#000100" size="3"><strong><em>adj
</em></strong></font><font face="Arial" color="#000100" size="3">and is also output by the
</font><font face="Arial" color="#000100" size="3"><strong><em>adj matrix
</em></strong></font><font face="Arial" color="#000100" size="3"> option of the
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3"><strong><em>Adjacency Tool
</em></strong></font><font face="Arial" color="#000100" size="3"> .<br><br>Important things to check when using the
</font><font face="Arial" color="#000100" size="3"><strong><em>car.normal
</em></strong></font><font face="Arial" color="#000100" size="3"> or
</font><font face="Arial" color="#000100" size="3"><strong><em>car.l1
</em></strong></font><font face="Arial" color="#000100" size="3"> distributions:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">The
</font><font face="Arial" color="#000100" size="3"><strong><em> car.normal
</em></strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong><em>car.l1
</em></strong></font><font face="Arial" color="#000100" size="3"> distributions use
</font><font face="Arial" color="#FF0000" size="3">unnormalised
</font><font face="Arial" color="#000100" size="3"> weights (see section on<br> <a href="#Intrinsic">
</font><font face="Arial" color="#0000FF" size="3">intrinsic CAR models
</font><font face="Arial" color="#000100" size="3"></a> in Appendix 1).<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3">An area cannot be specified as its own neighbour
</font><font face="Arial" color="#000100" size="3"> so make sure the ID number of the<br> area itself does not appear in as one of its list of neighbours in the
</font><font face="Arial" color="#000100" size="3"><strong><em>adj
</em></strong></font><font face="Arial" color="#000100" size="3"> vector.
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS<br>
</em></font><font face="Arial" color="#000100" size="3">does
</font><font face="Arial" color="#000100" size="3"><em>not
</em></font><font face="Arial" color="#000100" size="3"> check for this, so it is the user's responsibility. <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> The weights must be
</font><font face="Arial" color="#FF0000" size="3">symmetric
</font><font face="Arial" color="#000100" size="3"> ( W
</font><font face="Arial" color="#000100" size="3"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = W
</font><font face="Arial" color="#000100" size="3"><sub>ji
</sub></font><font face="Arial" color="#000100" size="3">).
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><em>does
</em></font><font face="Arial" color="#000100" size="3"> carry out a check for this<br> and returns an error message if non-symmetric weights are detected.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">Take care with priors on tau, and be prepared to carry out sensitivity analysis to this<br> choice.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> The car.normal and car.l1 distributions are parameterised to include a
</font><font face="Arial" color="#FF0000" size="3">sum-to-zero<br> constraint
</font><font face="Arial" color="#000100" size="3"> on the random effects. This means that you must also include a
</font><font face="Arial" color="#FF0000" size="3">separate<br> intercept
</font><font face="Arial" color="#000100" size="3">term in your model, which MUST be assigned an improper uniform prior using the<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>dflat()
</em></strong></font><font face="Arial" color="#000100" size="3"> distribution.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">Because the car.normal and car.l1 distributions are improper, they can only be used as<br>
</font><font face="Arial" color="#FF0000" size="3">prior
</font><font face="Arial" color="#000100" size="3"> distributions, and not as a likelihood.<br><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="car.proper">
</strong></font><font face="Courier New" color="#000100" size="6">car.proper
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"> [<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="3"><br><br>The proper Gaussian CAR prior distribution is specified using the distribution
</font><font face="Arial" color="#000100" size="3"><strong><em>car.proper
</em></strong></font><font face="Arial" color="#000100" size="3"> for the
</font><font face="Arial" color="#000100" size="3"><em>vector
</em></font><font face="Arial" color="#000100" size="3">of random variables
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> = ( S
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">, ....., S
</font><font face="Arial" color="#000100" size="2"><sub>N
</sub></font><font face="Arial" color="#000100" size="3"><sub> ).
</sub></font><font face="Arial" color="#000100" size="3">The syntax for this distributions is as follows:<br><br>S[1:N] ~ car.proper(mu[], C[], adj[], num[], M[], tau, gamma)<br><br>where:<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>mu[]
</em></strong></font><font face="Arial" color="#000100" size="3"> : A vector giving the mean for each area (this can either be entered as data, assigned a prior distribution, or specified deterministically within the model code).<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>C[]
</em></strong></font><font face="Arial" color="#000100" size="3">: A vector the same length as
</font><font face="Arial" color="#000100" size="3"><strong><em>adj[]
</em></strong></font><font face="Arial" color="#000100" size="3">giving
</font><font face="Arial" color="#000100" size="3"><em>normalised
</em></font><font face="Arial" color="#000100" size="3">weights associated with each pair of areas (see sections on <a href="#Conditional">
</font><font face="Arial" color="#0000FF" size="3">conditional specification
</font><font face="Arial" color="#000100" size="3"></a> and <a href="#Proper">
</font><font face="Arial" color="#0000FF" size="3">proper CAR priors
</font><font face="Arial" color="#000100" size="3"></a> in Appendix 1). Note that this differs from the intrinsic
</font><font face="Arial" color="#000100" size="3"><strong><em>car.normal
</em></strong></font><font face="Arial" color="#000100" size="3"> or
</font><font face="Arial" color="#000100" size="3"><strong><em>car.l1
</em></strong></font><font face="Arial" color="#000100" size="3"> distributions, where unnormalised weights should be specified. <br>
</font><font face="Arial" color="#000100" size="3"><strong><em>adj[]
</em></strong></font><font face="Arial" color="#000100" size="3"> : A vector listing the ID numbers of the adjacent areas for each area (this is a sparse representation of the full adjacency matrix for the study region, and can be generated using the
</font><font face="Arial" color="#000100" size="3"><strong><em>Adjacency Tool
</em></strong></font><font face="Arial" color="#000100" size="3">from the
</font><font face="Arial" color="#000100" size="3"><strong><em>Map
</em></strong></font><font face="Arial" color="#000100" size="3"> menu in
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3">.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>num[]
</em></strong></font><font face="Arial" color="#000100" size="3">: A vector of length N (the total number of areas) giving the number of neighbours n
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> for each area.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>M[]
</em></strong></font><font face="Arial" color="#000100" size="3">: A vector of length N giving the diagonal elements M
</font><font face="Arial" color="#000100" size="3"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3"> of the conditional variance matrix (see sections on <a href="#Conditional">
</font><font face="Arial" color="#0000FF" size="3">conditional specification
</font><font face="Arial" color="#000100" size="3"></a> and <a href="#Proper">
</font><font face="Arial" color="#0000FF" size="3">proper CAR priors
</font><font face="Arial" color="#000100" size="3"></a> in Appendix 1)<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>tau
</em></strong></font><font face="Arial" color="#000100" size="3"> : A scalar parameter representing the overall precision (inverse variance) parameter.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>gamma
</em></strong></font><font face="Arial" color="#000100" size="3"> : A scalar parameter representing the overall degree of spatial dependence. This parameter is constrained to lie between bounds given by the inverse of the minimum and maximum eigenvalues of the matrix
</font><font face="Arial" color="#000100" size="3"><strong>M
</strong></font><font face="Arial" color="#000100" size="3"><sup>-
</sup></font><font face="Arial" color="#000100" size="2"><sup>1/2
</sup></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>C
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>M
</strong></font><font face="Arial" color="#000100" size="2"><sup>1/2
</sup></font><font face="Arial" color="#000100" size="3"><sup>
</sup></font><font face="Arial" color="#000100" size="3">(see <a href="#Proper">
</font><font face="Arial" color="#0000FF" size="3">appendix 1</a>
</font><font face="Arial" color="#000100" size="3">).
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS 1.2
</em></font><font face="Arial" color="#000100" size="3"> contains two deterministic functions for calculating these bounds (or they can be calculated externally to
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3"> and input by the user):<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">min.bound(C[], adj[], num[], M[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">max.bound(C[], adj[], num[], M[])<br><br>where the arguments are the same as the corresponding vectors used as arguments to the
</font><font face="Arial" color="#000100" size="3"><strong><em>car.proper
</em></strong></font><font face="Arial" color="#000100" size="3"> distribution. <br><br><br>Important things to check when using the
</font><font face="Arial" color="#000100" size="3"><strong><em>car.proper
</em></strong></font><font face="Arial" color="#000100" size="3">distribution:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong><em>C
</em></strong></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><strong><em>adj
</em></strong></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><strong><em>num
</em></strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong><em>M
</em></strong></font><font face="Arial" color="#000100" size="3"> must be entered as data (it is currently not possible to allow
</font><font face="Arial" color="#000100" size="3"><strong><em>C
</em></strong></font><font face="Arial" color="#000100" size="3">to be<br> unknown);
</font><font face="Arial" color="#000100" size="3"><strong><em>num
</em></strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong><em>adj
</em></strong></font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">may be created by the
</font><font face="Arial" color="#000100" size="3"><strong><em>adj matrix
</em></strong></font><font face="Arial" color="#000100" size="3"> option of the
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS<br>
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong><em>Adjacency Tool
</em></strong></font><font face="Arial" color="#000100" size="3"> as described <a href="#Adj">
</font><font face="Arial" color="#0000FF" size="3">above
</font><font face="Arial" color="#000100" size="3"></a>. The <a href="../GeoBUGS/Examples/Scotland.html">
</font><font face="Arial" color="#0000FF" size="3">Lips example
</font><font face="Arial" color="#000100" size="3"></a> shows a (slightly<br> clumsy) way of creating the
</font><font face="Arial" color="#000100" size="3"><strong><em>C
</em></strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong><em>M
</em></strong></font><font face="Arial" color="#000100" size="3"> vectors within the WinBUGS model code;<br> alternatively, these can be created externally to
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3"> and read in as data.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> The
</font><font face="Arial" color="#000100" size="3"><strong><em> car.proper
</em></strong></font><font face="Arial" color="#000100" size="3">distribution uses
</font><font face="Arial" color="#FF0000" size="3">normalised
</font><font face="Arial" color="#000100" size="3"> weights
</font><font face="Arial" color="#000100" size="3"><strong><em>C
</em></strong></font><font face="Arial" color="#000100" size="3"> (see section on<br> <a href="#Proper">
</font><font face="Arial" color="#0000FF" size="3">proper CAR priors
</font><font face="Arial" color="#000100" size="3"></a> in Appendix 1).<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3">An area cannot be specified as its own neighbour
</font><font face="Arial" color="#000100" size="3"> so make sure the ID number of the<br> area itself does not appear in as one of its list of neighbours in the
</font><font face="Arial" color="#000100" size="3"><strong><em>adj
</em></strong></font><font face="Arial" color="#000100" size="3"> vector.
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS<br>
</em></font><font face="Arial" color="#000100" size="3">does
</font><font face="Arial" color="#000100" size="3"><em>not
</em></font><font face="Arial" color="#000100" size="3"> check for this, so it is the user's responsibility. <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> The
</font><font face="Arial" color="#FF0000" size="3">symmetry constraint
</font><font face="Arial" color="#000100" size="3"> C
</font><font face="Arial" color="#000100" size="3"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> M
</font><font face="Arial" color="#000100" size="3"><sub>jj
</sub></font><font face="Arial" color="#000100" size="3"> = C
</font><font face="Arial" color="#000100" size="3"><sub>ji
</sub></font><font face="Arial" color="#000100" size="3">M
</font><font face="Arial" color="#000100" size="3"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3">must be satisfied.
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><em>does
</em></font><font face="Arial" color="#000100" size="3"> carry out a<br> check for this and returns an error message if lack of symmetry is detected.<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">Take care with priors on tau, and be prepared to carry out sensitivity analysis to this<br> choice.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">Take care with priors on gamma: you must ensure that the prior is constrained between<br> the appropriate bounds. Besag, York and Mollie (1991) suggest that gamma needs to be<br> close to its upper bound before it reflects reasonable spatial dependence, so you may<br> want to try informative priors to represent this, and be prepared to carry out sensitivity<br> a [...]
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="spatial.exp">
</strong></font><font face="Courier New" color="#000100" size="6">spatial.exp and spatial.disc
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Bayesian Gaussian kriging models (multivariate Gaussian distribution with covariance matrix expressed as a parametric function of distance between pairs of points - e.g. see Diggle, Tawn and Moyeed, 1998 and <a href="#Appendix">
</font><font face="Arial" color="#0000FF" size="3">Appendix 1
</font><font face="Arial" color="#000100" size="3"></a>) can be specified using the distributions
</font><font face="Arial" color="#000100" size="3"><strong><em>spatial.exp
</em></strong></font><font face="Arial" color="#000100" size="3">or
</font><font face="Arial" color="#000100" size="3"><strong><em>spatial.disc
</em></strong></font><font face="Arial" color="#000100" size="3"> for the
</font><font face="Arial" color="#000100" size="3"><em>vector
</em></font><font face="Arial" color="#000100" size="3">of random variables
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> = ( S
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">, ....., S
</font><font face="Arial" color="#000100" size="2"><sub>N
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">).
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">The syntax for this distributions is as follows: <br><br> S[1:N] ~ spatial.exp(mu[], x[], y[], tau, phi, kappa)<br> S[1:N] ~ spatial.disc(mu[], x[], y[], tau, alpha)<br><br>where:<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>mu[]
</em></strong></font><font face="Arial" color="#000100" size="3"> : A vector giving the mean for each area (this can either be entered as data, assigned a prior distribution, or specified deterministically within the model code).<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>x[]
</em></strong></font><font face="Arial" color="#000100" size="3">and
</font><font face="Arial" color="#000100" size="3"><strong><em>y[]
</em></strong></font><font face="Arial" color="#000100" size="3">: Vectors of length N giving the x and y coordinates of the location of each point, or the centroid of each area<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>tau
</em></strong></font><font face="Arial" color="#000100" size="3"> : A scalar parameter representing the overall precision (inverse variance) parameter.<br><br>Two options are available for specifying the form of the covariance matrix: the powered exponential function and the 'disc' function (see section on
</font><font face="Arial" color="#0000FF" size="3"><u><a href="#Joint">
</u></font><font face="Arial" color="#0000FF" size="3">Joint Specification
</font><font face="Arial" color="#0000FF" size="3"><u></a>
</u></font><font face="Arial" color="#000100" size="3"> in Appendix1). <br><br>The
</font><font face="Arial" color="#000100" size="3"><strong><em>powered exponential function
</em></strong></font><font face="Arial" color="#000100" size="3"> is implemented using the
</font><font face="Arial" color="#000100" size="3"><strong><em>spatial.exp
</em></strong></font><font face="Arial" color="#000100" size="3"> distribution and has 2 parameters:<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>phi
</em></strong></font><font face="Arial" color="#000100" size="3"> : A scalar parameter representing the rate of decline of correlation with distance between points.
</font><font face="Arial" color="#000100" size="3"><em>Note that the magnitude of this parameter will depend on the units in which the x and y coordinates of each location are measured (e.g. metres, km etc.).
</em></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>kappa
</em></strong></font><font face="Arial" color="#000100" size="3"> : A scalar parameter controlling the amount of spatial smoothing. This is constrained to lie in the interval [0, 2). <br><br>The
</font><font face="Arial" color="#000100" size="3"><strong><em>disc function
</em></strong></font><font face="Arial" color="#000100" size="3"> is implemented using the
</font><font face="Arial" color="#000100" size="3"><strong><em>spatial.disc
</em></strong></font><font face="Arial" color="#000100" size="3"> distribution and has 1 parameter:<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>alpha
</em></strong></font><font face="Arial" color="#000100" size="3"> : A scalar parameter representing the radius of the 'disc' centred at each (x, y) location.
</font><font face="Arial" color="#000100" size="3"><em>Note that the magnitude of this parameter will depend on the units in which the x and y coordinates of each location are measured (e.g. metres, km etc.).
</em></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3"><strong>Warning:
</strong></font><font face="Arial" color="#000100" size="3"> These models can be very
</font><font face="Arial" color="#FF0000" size="3"><em>slow
</em></font><font face="Arial" color="#000100" size="3"> for even moderate sized datasets (the algorithm is of order N
</font><font face="Arial" color="#000100" size="2"><sup>3
</sup></font><font face="Arial" color="#000100" size="3">)! Experience to date also suggests that it may be better to
</font><font face="Arial" color="#FF0000" size="3"><em>hierarchically centre
</em></font><font face="Arial" color="#000100" size="3"> this model. For example, consider the following two alternative parameterisations of the same model:
</font><font face="Courier New" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>Non-hierarchically centred<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (i in 1:N){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">y[i] ~ dnorm(S[i], gamma) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i] <- alpha+beta*z[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">} <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">S[1:N] ~ spatial.exp(mu[], x[], y[], tau, phi,1)
</font><font face="Arial" color="#000100" size="3"><br><br>Hierarchically centred <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (i in 1:N){<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">y[i] ~ dnorm(S[i], gamma) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">S[i] <- alpha+beta*z[i] + W[i]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">mu[i]<-0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">W[1:N] ~ spatial.exp(mu[], x[], y[], tau, phi,1)
</font><font face="Arial" color="#000100" size="3"><br><br>In some simulated examples, the non-hierarchically centred parameterisation has produced incorrect results, while the hierarchically centred parameterisation gives sensible answers. This may be a feature of the single-site updating schemes used in WinBUGS, so interpret your results with care!<br>(Thanks to Alan Gelfand, Shanshan Wu and Alex Schmidt for noting this problem).<br><br>Experience also suggests that there is often very [...]
</font><font face="Arial" color="#000100" size="3"><strong><a id="spatial.exp.pred">
</strong></font><font face="Courier New" color="#000100" size="6">spatial.pred and spatial.unipred
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>Spatial interpolation or prediction at arbitrary locations can be carried out using the
</font><font face="Arial" color="#000100" size="3"><strong><em>spatial.pred
</em></strong></font><font face="Arial" color="#000100" size="3"> or
</font><font face="Arial" color="#000100" size="3"><strong><em>spatial.unipred
</em></strong></font><font face="Arial" color="#000100" size="3"> functions, in conjunction with fitting either the
</font><font face="Arial" color="#000100" size="3"><strong><em>spatial.exp
</em></strong></font><font face="Arial" color="#000100" size="3"> or
</font><font face="Arial" color="#000100" size="3"><strong><em>spatial.disc
</em></strong></font><font face="Arial" color="#000100" size="3"> model to a set of observed data.
</font><font face="Arial" color="#000100" size="3"><strong><em>spatial.pred
</em></strong></font><font face="Arial" color="#000100" size="3"> carries out joint or simultaneous prediction at a set of target locations, whereas
</font><font face="Arial" color="#000100" size="3"><strong><em>spatial.unipred
</em></strong></font><font face="Arial" color="#000100" size="3"> carries out single site prediction. The difference is that the single site prediction yields marginal prediction intervals (i.e. ignoring correlation between prediction locations) whereas joint prediction yields simultaneous prediction intervals for the set of target locations (which will tend to be narrower than the marginal prediction intervals). The predicted means should be the same under joint or single site prediction [...]
</font><font face="Arial" color="#000100" size="2"><sup>3
</sup></font><font face="Arial" color="#000100" size="3">, where P is the number of prediction sites). The syntax for these predictive distributions is:<br><br>Joint prediction:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">T[1:P] ~ spatial.pred(mu.T[], x.T[], y.T[], S[])<br><br>Single site prediction:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(j in 1:P) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">T[j] ~ spatial.unipred(mu.T[j], x.T[j], y.T[j], S[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}<br><br>where:<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>P
</em></strong></font><font face="Arial" color="#000100" size="3"> : Scalar giving the number of prediction locations<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>mu.T[]
</em></strong></font><font face="Arial" color="#000100" size="3"> : vector of length P (or scalar for single site version) specifying the mean for each prediction location (this should be specified in the same way as the mean for the observed data S).<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>x.T[]
</em></strong></font><font face="Arial" color="#000100" size="3">and
</font><font face="Arial" color="#000100" size="3"><strong><em>y.T[]
</em></strong></font><font face="Arial" color="#000100" size="3">: Vectors of length P (or scalars for single site version) giving the x and y coordinates of the location of each prediction point<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>S
</em></strong></font><font face="Arial" color="#000100" size="3"> : The vector of observations to which either the
</font><font face="Arial" color="#000100" size="3"><strong><em>spatial.exp
</em></strong></font><font face="Arial" color="#000100" size="3"> or
</font><font face="Arial" color="#000100" size="3"><strong><em>spatial.disc
</em></strong></font><font face="Arial" color="#000100" size="3"> model has been fitted.<br><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="pois.conv">
</strong></font><font face="Courier New" color="#000100" size="6">pois.conv
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>A conjugate Poisson-gamma spatial moving average distribution can be specified for non-negative counts defined on a spatial lattice (i.e. discrete geographical partition), using the distribution
</font><font face="Arial" color="#000100" size="3"><strong><em>pois.conv
</em></strong></font><font face="Arial" color="#000100" size="3">. This is a discrete version of the Poisson-gamma random field model of Wolpert and Ickstadt (1998) and Best et al (2000a). The basic syntax for this distribution is as follows:
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">S ~ dpois.conv(mu[]) <br><br>where
</font><font face="Arial" color="#000100" size="3"><strong><em>S
</em></strong></font><font face="Arial" color="#000100" size="3"> is a non-negative
</font><font face="Arial" color="#000100" size="3"><em>scalar
</em></font><font face="Arial" color="#000100" size="3"> parameter defined at some (usually spatial) location, and
</font><font face="Arial" color="#000100" size="3"><strong><em>mu[]
</em></strong></font><font face="Arial" color="#000100" size="3"> is a
</font><font face="Arial" color="#000100" size="3"><em>vector
</em></font><font face="Arial" color="#000100" size="3">of length J representing the influence of a set of gamma distributed latent parameters at each of J different locations on the value of S. Hence
</font><font face="Arial" color="#000100" size="3"><strong><em>mu[]
</em></strong></font><font face="Arial" color="#000100" size="3"> must be defined as a convolution of gamma random variables:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (j in 1 : J) { <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">mu[j] <- gamma[j] * k[j]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">gamma[j]
</font><font face="Arial" color="#000100" size="3">~ dgamma(a, b)
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="3"><br>where
</font><font face="Arial" color="#000100" size="3"><strong><em>k[j]
</em></strong></font><font face="Arial" color="#000100" size="3"> is a spatial kernel or spatial 'weight' depending on some measure of distance or spatial proximity between the jth latent location and the location of S, and
</font><font face="Arial" color="#000100" size="3"><strong><em>a
</em></strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong><em>b
</em></strong></font><font face="Arial" color="#000100" size="3"> are hyperparameters to be specified (see
</font><font face="Arial" color="#000100" size="3"><a href="#Appendix 2">
</font><font face="Arial" color="#0000FF" size="3">Appendix 2
</font><font face="Arial" color="#000100" size="3"></a> for further discussion of this distribution, including suitable kernel functions). Usually,
</font><font face="Arial" color="#000100" size="3"><strong><em>k[]
</em></strong></font><font face="Arial" color="#000100" size="3"> is calculated externally and read into WinBUGS as data; alternatively, if k[] depends on unknown parameters, it may be defined as part of the BUGS code and re-computed at each MCMC iteration. However, this is likely to slow down the sampling within WinBUGS by many orders of magnitude, so is not recommended for models with large numbers of latent parameters (i.e. J large).<br><br>More typically, the distribution will be used [...]
</font><font face="Arial" color="#000100" size="3"><em>vector
</em></font><font face="Arial" color="#000100" size="3"> of counts defined on a spatial lattice of N regions, using the following syntax:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (i in 1:N) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">S[i] ~ dpois.conv(mu[i, ]) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for (j in 1 : J) {
</font><font face="Arial" color="#00FF00" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> mu[i, j] <- gamma[j] * k[i, j]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br> <br>where the latent gamma[j] parameters are defined as above, and k[,] is now an N x J matrix with elements k[i,j] representing the 'weight' or contribution of the latent gamma random variable at location j to the expected value of S at location i. <br><br>Conditional on mu, the S[i] have independent Poisson distributions with mean =
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="3"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">mu[i, j]. <br><br>Note that the model may be extended to include observed covariates as well as latent variables in the Poisson mean - see
</font><font face="Arial" color="#0000FF" size="3"><a href="../GeoBUGS/Examples/MVCAR.html">MVCAR Example</a>.
</font><font face="Arial" color="#000100" size="3"><br><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="mv.car">
</strong></font><font face="Courier New" color="#000100" size="6">mv.car
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>The multivariate intrinsic Gaussian CAR prior distribution is specified using the distribution
</font><font face="Arial" color="#000100" size="3"><strong><em>mv.car
</em></strong></font><font face="Arial" color="#000100" size="3"> for the p x N
</font><font face="Arial" color="#000100" size="3"><em>matrix
</em></font><font face="Arial" color="#000100" size="3">of random varables
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> , where columns of
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> represent the spatial units (areas) and rows represent the variables (it is important to ensure the dimensions of S are specified the correct way round). The syntax for this distribution is as follows:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">S[1:p, 1:N] ~ mv.car(adj[], weights[], num[], omega[ , ])<br><br>where:<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>adj[]
</em></strong></font><font face="Arial" color="#000100" size="3"> : A vector listing the ID numbers of the adjacent areas for each area (this is a sparse representation of the full adjacency matrix for the study region, and can be generated using the
</font><font face="Arial" color="#000100" size="3"><strong><em>Adjacency Tool
</em></strong></font><font face="Arial" color="#000100" size="3">from the
</font><font face="Arial" color="#000100" size="3"><strong><em>Map
</em></strong></font><font face="Arial" color="#000100" size="3"> menu in
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3">.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>weights[]
</em></strong></font><font face="Arial" color="#000100" size="3"> : A vector the same length as
</font><font face="Arial" color="#000100" size="3"><strong><em>adj[]
</em></strong></font><font face="Arial" color="#000100" size="3">giving
</font><font face="Arial" color="#000100" size="3"><em>unnormalised
</em></font><font face="Arial" color="#000100" size="3">weights associated with each pair of areas. For the CAR model described above, taking C
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = 1 (equivalently W
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = 1/ n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ) if areas i and j are neighbours and 0 otherwise, gives a vector of 1's for
</font><font face="Arial" color="#000100" size="3"><strong><em>weights[]
</em></strong></font><font face="Arial" color="#000100" size="3">.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>num[]
</em></strong></font><font face="Arial" color="#000100" size="3">: A vector of length N (the total number of areas) giving the number of neighbours n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> for each area.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em>omega[ , ]
</em></strong></font><font face="Arial" color="#000100" size="3"> : A p x p matrix representing the precision (inverse variance) matrix of the multivariate intrinsic Gaussian CAR prior.<br><br>The first 3 arguments must be entered as data (it is currently not possible to allow the
</font><font face="Arial" color="#000100" size="3"><strong><em>weights
</em></strong></font><font face="Arial" color="#000100" size="3"> to be unknown); the final variable
</font><font face="Arial" color="#000100" size="3"><strong><em>omega
</em></strong></font><font face="Arial" color="#000100" size="3"> is usually treated as unknown and so is assigned a prior distribution (which must be a Wishart distribution). The data variables
</font><font face="Arial" color="#000100" size="3"><strong><em>num
</em></strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong><em>adj
</em></strong></font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">may be created by the
</font><font face="Arial" color="#000100" size="3"><strong><em>adj matrix
</em></strong></font><font face="Arial" color="#000100" size="3"> option of the
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong><em>Adjacency Tool
</em></strong></font><font face="Arial" color="#000100" size="3"> as described <a href="#Adj">
</font><font face="Arial" color="#0000FF" size="3">above
</font><font face="Arial" color="#000100" size="3"></a>. The variable
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3"><strong><em>weights
</em></strong></font><font face="Arial" color="#000100" size="3"> must be created by the user, and must be a vector the same length as
</font><font face="Arial" color="#000100" size="3"><strong><em>adj
</em></strong></font><font face="Arial" color="#000100" size="3">. A common choice is to set all the
</font><font face="Arial" color="#000100" size="3"><strong><em>weights
</em></strong></font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#000100" size="3">equal to 1 since this gives the multivariate equivalent of the standard Besag, York and Mollie (1991) CAR model (see sections on <a href="#Intrinsic">
</font><font face="Arial" color="#0000FF" size="3">intrinsic CAR models
</font><font face="Arial" color="#000100" size="3"></a> and <a href="#MV">
</font><font face="Arial" color="#0000FF" size="3">multivariate intrinsic CAR models
</font><font face="Arial" color="#000100" size="3"></a> in Appendix 1 for further discussion of weights). The easiest way to do this is to create a loop in your
</font><font face="Arial" color="#000100" size="3"><em>WinBUGS
</em></font><font face="Arial" color="#000100" size="3"> model code:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">for(j in 1:sumNumNneigh) { weights[j] <- 1}<br><br>where
</font><font face="Arial" color="#000100" size="3"><strong><em>sumNumNneigh
</em></strong></font><font face="Arial" color="#000100" size="3"> is the length of
</font><font face="Arial" color="#000100" size="3"><strong><em>adj
</em></strong></font><font face="Arial" color="#000100" size="3">and is also output by the
</font><font face="Arial" color="#000100" size="3"><strong><em>adj matrix
</em></strong></font><font face="Arial" color="#000100" size="3"> option of the
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3"><strong><em>Adjacency Tool
</em></strong></font><font face="Arial" color="#000100" size="3"> .<br><br>Important things to check when using the
</font><font face="Arial" color="#000100" size="3"><strong><em>mv.car
</em></strong></font><font face="Arial" color="#000100" size="3"> distribution:<br><br>
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> The
</font><font face="Arial" color="#000100" size="3"><strong><em> mv.car
</em></strong></font><font face="Arial" color="#000100" size="3"> distribution uses
</font><font face="Arial" color="#FF0000" size="3">unnormalised
</font><font face="Arial" color="#000100" size="3"> weights, as for the
</font><font face="Arial" color="#000100" size="3"><strong><em>car.normal
</em></strong></font><font face="Arial" color="#000100" size="3"> distribtion.<br>
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3">An area cannot be specified as its own neighbour
</font><font face="Arial" color="#000100" size="3"> so make sure the ID number of the area itself does not appear in as one of its list of neighbours in the
</font><font face="Arial" color="#000100" size="3"><strong><em>adj
</em></strong></font><font face="Arial" color="#000100" size="3"> vector.
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3"> does
</font><font face="Arial" color="#000100" size="3"><em>not
</em></font><font face="Arial" color="#000100" size="3"> check for this, so it is the user's responsibility. <br>
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> The weights must be
</font><font face="Arial" color="#FF0000" size="3">symmetric
</font><font face="Arial" color="#000100" size="3"> ( W
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = W
</font><font face="Arial" color="#000100" size="2"><sub>ji
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">).
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><em>does
</em></font><font face="Arial" color="#000100" size="3"> carry out a check for this and returns an error message if non-symmetric weights are detected.<br>
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">Take care with priors on
</font><font face="Arial" color="#000100" size="3"><strong><em>omega
</em></strong></font><font face="Arial" color="#000100" size="3">, and be prepared to carry out sensitivity analysis to this choice.<br>
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> The
</font><font face="Arial" color="#000100" size="3"><strong><em>mv.car
</em></strong></font><font face="Arial" color="#000100" size="3"> distribution is parameterised to include a
</font><font face="Arial" color="#FF0000" size="3">sum-to-zero constraint
</font><font face="Arial" color="#000100" size="3"> on the random effects. This means that you must also include
</font><font face="Arial" color="#FF0000" size="3">separate intercept
</font><font face="Arial" color="#000100" size="3">terms in your model for each of the p variables, which MUST be assigned improper uniform priors using the
</font><font face="Arial" color="#000100" size="3"><strong><em>dflat()
</em></strong></font><font face="Arial" color="#000100" size="3"> distribution.
</font><font face="Arial" color="#000100" size="3"><em>Note: the mechanism for implementing the sum-to-zero constraint for mv.car in WinBUGS has been tested and appears to be robust; however, we recommend that you nevertheless include a check in your model code to ensure that the constraint has been implemented correctly (e.g. by including a line in your code to calculate the mean across areas of each variable for which the mv.car prior has been assumed). Please report any problems to n.b [...]
</em></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3"> An alternative
</font><font face="Arial" color="#FF0000" size="3">unconstrained
</font><font face="Arial" color="#000100" size="3"> version of the multivariate CAR prior is available in WinBUGS 1.4, called
</font><font face="Arial" color="#000100" size="3"><strong><em>mv.car.uncon
</em></strong></font><font face="Arial" color="#000100" size="3">. The syntax is the same as for mv.car. <br>
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">Because the
</font><font face="Arial" color="#000100" size="3"><strong><em>mv.car
</em></strong></font><font face="Arial" color="#000100" size="3"> (and
</font><font face="Arial" color="#000100" size="3"><strong><em>mv.car.uncon
</em></strong></font><font face="Arial" color="#000100" size="3">) distribution is improper, it can only be used as a
</font><font face="Arial" color="#FF0000" size="3">prior
</font><font face="Arial" color="#000100" size="3"> distribution, and not as a likelihood. <br><br><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="Temporal">
</strong></font><font face="Courier New" color="#000100" size="6">Temporal distributions
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Courier New" color="#000100" size="6">
</font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="rw">
</strong></font><font face="Arial" color="#FF0000" size="3"><strong><em>
</em></strong></font><font face="Arial" color="#000100" size="3"><strong><em>Using car.normal as a random walk prior for temporal smoothing
</em></strong></font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>In one dimension, the intrinsic Gaussian CAR distribution reduces to a Gaussian random walk (see e.g.Fahrmeir and Lang, 2001). Assume we have a set of temporally correlated random effects
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3">, t=1,..., T (where T is the number of equally-spaced time points). In the simplest case of a random walk of order 1, RW(1), we may write<br><br>
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"> |
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Normal
</font><font face="Symbol" color="#000100" size="3">( q
</font><font face="Arial" color="#000100" size="2"><sub>t+1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> ) for t = 1<br>~ Normal
</font><font face="Symbol" color="#000100" size="3">( (q
</font><font face="Arial" color="#000100" size="2"><sub>t-1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">+ q
</font><font face="Arial" color="#000100" size="2"><sub>t+1
</sub></font><font face="Arial" color="#000100" size="3">)/2,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> / 2 ) for t = 2, ...., T-1<br>~ Normal
</font><font face="Symbol" color="#000100" size="3">( q
</font><font face="Arial" color="#000100" size="2"><sub>t-1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> ) for t = T<br><br>where
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">denotes all elements of
</font><font face="Symbol" color="#000100" size="3"><strong>q
</strong></font><font face="Symbol" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">except the
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3">. This is equivalent to specifying <br><br>
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"> |
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Normal
</font><font face="Symbol" color="#000100" size="3">( S
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> C
</font><font face="Arial" color="#000100" size="2"><sub>tk
</sub></font><font face="Symbol" color="#000100" size="3"> q
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> M
</font><font face="Arial" color="#000100" size="2"><sub>tt
</sub></font><font face="Arial" color="#000100" size="3">) for t = 1, ..., T<br><br>where C
</font><font face="Arial" color="#000100" size="2"><sub>tk
</sub></font><font face="Arial" color="#000100" size="3"> = W
</font><font face="Arial" color="#000100" size="2"><sub>tk
</sub></font><font face="Arial" color="#000100" size="3"> / W
</font><font face="Arial" color="#000100" size="2"><sub>t+
</sub></font><font face="Arial" color="#000100" size="3">, W
</font><font face="Arial" color="#000100" size="2"><sub>t+
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> W
</font><font face="Arial" color="#000100" size="2"><sub>tk
</sub></font><font face="Arial" color="#000100" size="3"> and W
</font><font face="Arial" color="#000100" size="2"><sub>tk
</sub></font><font face="Arial" color="#000100" size="3"> = 1 if k = (t-1) or (t+1) and 0 otherwise; M
</font><font face="Arial" color="#000100" size="2"><sub>tt
</sub></font><font face="Arial" color="#000100" size="3"> = 1/W
</font><font face="Arial" color="#000100" size="2"><sub>t+
</sub></font><font face="Arial" color="#000100" size="3">. Hence the RW(1) prior may be fitted using the
</font><font face="Arial" color="#000100" size="3"><strong><em>car.normal
</em></strong></font><font face="Arial" color="#000100" size="3">distribution in WinBUGS, with appropriate specification of the weight and adjacency matrices, and num vector (see the
</font><font face="Arial" color="#0000FF" size="3"> <a href="../GeoBUGS/Examples/Pollution.html">Air Pollution Example
</font><font face="Arial" color="#000100" size="3"></a>)
</font><font face="Arial" color="#000100" size="3"><sub><br>
</sub></font><font face="Arial" color="#000100" size="3"><br>A second order random walk prior is defined as<br><br>
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"> |
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Normal
</font><font face="Symbol" color="#000100" size="3">(
</font><font face="Arial" color="#000100" size="3">2
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t+1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">- q
</font><font face="Arial" color="#000100" size="2"><sub>t+2
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> ) for t = 1<br>~ Normal
</font><font face="Symbol" color="#000100" size="3">(
</font><font face="Arial" color="#000100" size="3">(2
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t-1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">+
</font><font face="Arial" color="#000100" size="3">4
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t+1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">- q
</font><font face="Arial" color="#000100" size="2"><sub>t+2
</sub></font><font face="Arial" color="#000100" size="3">)/5,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> / 5 ) for t = 2 <br>~ Normal
</font><font face="Symbol" color="#000100" size="3">( (-q
</font><font face="Arial" color="#000100" size="2"><sub>t-2
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">+
</font><font face="Arial" color="#000100" size="3">4
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t-1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">+
</font><font face="Arial" color="#000100" size="3">4
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t+1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">- q
</font><font face="Arial" color="#000100" size="2"><sub>t+2
</sub></font><font face="Arial" color="#000100" size="3">)/6,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> / 6 ) for t = 3, ...., T-2<br>~ Normal
</font><font face="Symbol" color="#000100" size="3">( (-q
</font><font face="Arial" color="#000100" size="2"><sub>t-2
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">+ 4q
</font><font face="Arial" color="#000100" size="2"><sub>t-1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">+
</font><font face="Arial" color="#000100" size="3">2
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t+1
</sub></font><font face="Arial" color="#000100" size="3">)/5,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> / 5 ) for t = T-1<br>~ Normal
</font><font face="Symbol" color="#000100" size="3">( -q
</font><font face="Arial" color="#000100" size="2"><sub>t-2
</sub></font><font face="Symbol" color="#000100" size="3">+
</font><font face="Arial" color="#000100" size="3">2
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t-1
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> ) for t = T<br><br>Again this is equivalent to specifying <br><br>
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"> |
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>t
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">~ Normal
</font><font face="Symbol" color="#000100" size="3">( S
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"> C
</font><font face="Arial" color="#000100" size="2"><sub>tk
</sub></font><font face="Symbol" color="#000100" size="3"> q
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> M
</font><font face="Arial" color="#000100" size="2"><sub>tt
</sub></font><font face="Arial" color="#000100" size="3">) for t = 1, ..., T<br><br>where C
</font><font face="Arial" color="#000100" size="2"><sub>tk
</sub></font><font face="Arial" color="#000100" size="3"> is defined as above, but this time with W
</font><font face="Arial" color="#000100" size="2"><sub>tk
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">1 if k = (t-2) or (t+2), W
</font><font face="Arial" color="#000100" size="2"><sub>tk
</sub></font><font face="Arial" color="#000100" size="3"> = 4 if k = (t-1) or (t+1) and t in (3, T-2), W
</font><font face="Arial" color="#000100" size="2"><sub>tk
</sub></font><font face="Arial" color="#000100" size="3"> = 2 if k = (t-1) or (t+1) and t = 2 or T-1, W
</font><font face="Arial" color="#000100" size="2"><sub>tk
</sub></font><font face="Arial" color="#000100" size="3"> = 0 otherwise; M
</font><font face="Arial" color="#000100" size="2"><sub>tt
</sub></font><font face="Arial" color="#000100" size="3"> = 1/W
</font><font face="Arial" color="#000100" size="2"><sub>t+
</sub></font><font face="Arial" color="#000100" size="3">. <br><br>Note that if the observed time points are not equally spaced, it is necessary to include missing values (NA) for the intermediate time points (see the
</font><font face="Arial" color="#0000FF" size="3"><a href="../GeoBUGS/Examples/Pollution.html">Air Pollution Example
</font><font face="Arial" color="#000100" size="3"></a></a>). <br><br>
</font><font face="Arial" color="#0000FF" size="2"><u><br>
</u></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><a id="Appendix">
</font><font face="Courier New" color="#000100" size="6">Appendix 1: Technical details of Structured Multivariate Gaussian and Conditional Autoregressive (CAR) models and hyperprior specification
</font><font face="Arial" color="#000100" size="3">.</a>
</font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br><br>(Note: for clarity of exposition, we parameterise the Normal distribution in terms of the mean and
</font><font face="Arial" color="#000100" size="3"><em>variance
</em></font><font face="Arial" color="#000100" size="3"> in the following discussion. However,
</font><font face="Arial" color="#000100" size="3"><em>WinBUGS
</em></font><font face="Arial" color="#000100" size="3"> parameterisation of the CAR and structured MVN models is in terms of the mean and precision as usual.)<br><br>Assume we have a set of area-specific spatially correlated Gaussian data or random effects S
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, i=1,..., N (where N is the number of areas in the study region). Suppose their joint distribution may be expressed as follows: <br><br>
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> ~ MVN(
</font><font face="Symbol" color="#000100" size="3"><strong>m
</strong></font><font face="Arial" color="#000100" size="3">, v
</font><font face="Symbol" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3">) <br><br>where
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> = ( S
</font><font face="Arial" color="#000100" size="3"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">, ....., S
</font><font face="Arial" color="#000100" size="3"><sub>N
</sub></font><font face="Arial" color="#000100" size="3">), MVN denotes the N-dimensional multivariate normal distribution,
</font><font face="Symbol" color="#000100" size="3"><strong>m
</strong></font><font face="Arial" color="#000100" size="3"> is the 1 x N mean vector, v > 0 controls the overall variability of the S
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> is an N x N positive definite matrix. <br><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="Joint">
</strong></font><font face="Courier New" color="#000100" size="6">Joint specification
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Arial" color="#000100" size="3">[<a href="#Top">
</font><font face="Arial" color="#0000FF" size="3">top</a>
</font><font face="Arial" color="#000100" size="3">]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>We may assume a parametric form for the elements of the between-area correlation matrix:<br>
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = f(d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">;
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="3">)<br>where d
</font><font face="Arial" color="#000100" size="3"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">= distance between areas i and j. WinBUGS 1.4 allows two options for the funtion f(.) (see Richardson (1992) for further details of these functions):<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>1. Powered exponential family<br>
</strong></font><font face="Arial" color="#000100" size="3"><br> f(d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">;
</font><font face="Symbol" color="#000100" size="3">f, k
</font><font face="Arial" color="#000100" size="3">) = exp[
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">(
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">)
</font><font face="Symbol" color="#000100" size="2"><sup>k
</sup></font><font face="Symbol" color="#000100" size="3"><sup>
</sup></font><font face="Arial" color="#000100" size="3">] where
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3">> 0,
</font><font face="Symbol" color="#000100" size="3">k
</font><font face="Arial" color="#000100" size="3"> in (0, 2]<br><br>The parameter
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> controls the rate of decline of correlation with distance:<br><br>
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> large
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">> rapid decay<br>
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3">small
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">> slow decay<br><br>One possible strategy for specifying a prior for
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> is to choose a uniform distribution between
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>min
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">and
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>max
</sub></font><font face="Arial" color="#000100" size="3"> where
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>min
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">and
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>max
</sub></font><font face="Arial" color="#000100" size="3"> are chosen to give a sensible range of values for correlations both at a distance equal to the
</font><font face="Arial" color="#000100" size="3"><em>maximum
</em></font><font face="Arial" color="#000100" size="3"> distance between any pair of areas in the study region, and at a distance equal to the
</font><font face="Arial" color="#000100" size="3"><em>minimum
</em></font><font face="Arial" color="#000100" size="3"> distance between any pair of areas in the study. For example, if the minimum distance is 1 km (say), and the maximum distance is 20 km (say), then values of
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>min
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">= 0.04 and
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="2"><sub>max
</sub></font><font face="Arial" color="#000100" size="3"> = 5 would give a diffuse but plausible prior range of correlations (assuming
</font><font face="Symbol" color="#000100" size="3">k
</font><font face="Arial" color="#000100" size="3"> = 1
</font><font face="Symbol" color="#000100" size="3">)
</font><font face="Arial" color="#000100" size="3"> between 0.007 and 0.96 at a distance of 1 km, and between 0 and 0.45 at a distance of 20 km.
</font><font face="Arial" color="#000100" size="3"><em>Note that it is advisable to choose a value of
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"><sub>min
</sub></font><font face="Arial" color="#000100" size="3"><em>that prevents the correlation at the maximum distance between observations in the study region from being too high, since this can lead to identifiability problems between the overall mean,
</em></font><font face="Symbol" color="#000100" size="3"><strong>m
</strong></font><font face="Arial" color="#000100" size="3"><em>, of the spatial random variables and the correlation parameter,
</em></font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"><em>.
</em></font><font face="Arial" color="#000100" size="3"><br><br>The parameter
</font><font face="Symbol" color="#000100" size="3">k
</font><font face="Arial" color="#000100" size="3">controls the amount by which spatial variations in the data are smoothed. Large values of
</font><font face="Symbol" color="#000100" size="3">k
</font><font face="Arial" color="#000100" size="3"> lead to greater smoothing, with
</font><font face="Symbol" color="#000100" size="3">k
</font><font face="Arial" color="#000100" size="3"> = 2 corresponding to the Gaussian correlation function (although the resulting covariance matrix is nearly singular). It is often difficult to learn much about this parameter, so unless there is a good reason for believing otherwise, it is usually advisable to set
</font><font face="Symbol" color="#000100" size="3">k
</font><font face="Arial" color="#000100" size="3"> = 1 a priori. <br><br>
</font><font face="Arial" color="#000100" size="3"><strong>2. Disc model<br>
</strong></font><font face="Arial" color="#000100" size="3"><br> f(d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">;
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">) = 2 /
</font><font face="Symbol" color="#000100" size="3">p
</font><font face="Arial" color="#000100" size="3"> * {cos
</font><font face="Symbol" color="#000100" size="2"><sup>-
</sup></font><font face="Arial" color="#000100" size="2"><sup>1
</sup></font><font face="Symbol" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">(d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">/
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">)
</font><font face="Symbol" color="#000100" size="3"><sup>
</sup></font><font face="Symbol" color="#000100" size="3">-
</font><font face="Symbol" color="#000100" size="3"><sup>
</sup></font><font face="Arial" color="#000100" size="3">[(d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">/
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">)(1
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Symbol" color="#000100" size="3"><sup>
</sup></font><font face="Arial" color="#000100" size="3">(d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">/
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">))]
</font><font face="Arial" color="#000100" size="2"><sup>1/2
</sup></font><font face="Arial" color="#000100" size="3"> } for d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">< a
</font><font face="Arial" color="#000100" size="3"><br> = 0 for d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">> a
</font><font face="Arial" color="#000100" size="3"><br><br>The parameter
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> controls the rate of decline of correlation with distance:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> large
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">> slow decay<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">small
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">> rapid decay<br><br>The disc function leads to an approximately linear decrease in correlation with increasing distance, with correlation declining to zero at a distance equal to
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">.
</font><font face="Arial" color="#000100" size="3"><em>Again, it is advisable to choose a prior for
</em></font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3"><em>that prevents the correlation at the maximum distance between observations in the study region from being too high, since this can lead to identifiability problems between the overall mean,
</em></font><font face="Symbol" color="#000100" size="3"><strong>m
</strong></font><font face="Arial" color="#000100" size="3"><em>, of the spatial random variables and the correlation parameter,
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><em>. An upper prior bound on
</em></font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><em> equal to a small multiple of the maximum distance in the study region is therefore a sensible 'default' choice. The minimum value allowed a priori for
</em></font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><em> should also be chosen carefully since values of
</em></font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"><em> less than the minimum distance between observations in the study region will not be identifiable.<br>
</em></font><font face="Arial" color="#000100" size="3"><br>Exploratory analysis using variograms maybe be helpful to help chose an appropriate specification for the correlation function and associated parameters. <br><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="Conditional">Conditional specification</a>
</strong></font><font face="Arial" color="#000100" size="5"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>By writing the between-area covariance matrix in the following form:<br> v
</font><font face="Symbol" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> = v(
</font><font face="Arial" color="#000100" size="3"><strong>I
</strong></font><font face="Arial" color="#000100" size="3"> -
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"><strong>C
</strong></font><font face="Arial" color="#000100" size="3">)
</font><font face="Arial" color="#000100" size="2"><sup>-1
</sup></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>M<br><br>
</strong></font><font face="Arial" color="#000100" size="3">where
</font><font face="Arial" color="#000100" size="3"><strong>I
</strong></font><font face="Arial" color="#000100" size="3">= N x N identity matrix<br>
</font><font face="Arial" color="#000100" size="3"><strong>M
</strong></font><font face="Arial" color="#000100" size="3">= N x N diagonal matrix, with elements M
</font><font face="Arial" color="#000100" size="2"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3"> proportional to the conditional variance of S
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> | S
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="3"><strong>C
</strong></font><font face="Arial" color="#000100" size="3">= N x N weight matrix, with elements C
</font><font face="Arial" color="#000100" size="3"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> reflecting spatial association between areas i and j<br>
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3">= controls overall strength of spatial dependence<br><br>and using standard multivariate normal theory (e.g. Johnson and Kotz, 1972; Besag and Kooperberg, 1995), the joint multivariate Gaussian model can be expressed in the form of a set of conditional distributions<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> |
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal (
</font><font face="Symbol" color="#000100" size="3">m
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">+
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3">C
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> (s
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">-m
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">),
</font><font face="Symbol" color="#000100" size="3">f
</font><font face="Arial" color="#000100" size="3"> M
</font><font face="Arial" color="#000100" size="2"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3"> ), <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">(here
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> denotes summation over j = 1 to N, not covariance matrix, and
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> denotes all the elements of
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> except S
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>From a modelling perspective, use of the joint formulation requires specification of the elements of the covariance matrix
</font><font face="Symbol" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> (see above), while use of the conditional formulation reduces to specification of the matrices
</font><font face="Arial" color="#000100" size="3"><strong>C
</strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong>M
</strong></font><font face="Arial" color="#000100" size="3"> and the spatial dependence parameter
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3">. Various constraints are needed on the values of
</font><font face="Arial" color="#000100" size="3"><strong>C
</strong></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><strong>M
</strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"> in order to ensure that
</font><font face="Symbol" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> is symmetric positive definite:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>* S
</strong></font><font face="Arial" color="#000100" size="3"> is only symmetric if C
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> M
</font><font face="Arial" color="#000100" size="2"><sub>jj
</sub></font><font face="Arial" color="#000100" size="3"> = C
</font><font face="Arial" color="#000100" size="2"><sub>ji
</sub></font><font face="Arial" color="#000100" size="3"> M
</font><font face="Arial" color="#000100" size="2"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3"><sub><br>
</sub></font><font face="Arial" color="#000100" size="1">
</font><font face="Symbol" color="#000100" size="3"><strong>*
</strong></font><font face="Arial" color="#000100" size="3">Var( S
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> | S
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">) = vM
</font><font face="Arial" color="#000100" size="2"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3"> > 0 so M
</font><font face="Arial" color="#000100" size="2"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3"> must be > 0
</font><font face="Symbol" color="#000100" size="3"><strong><br> *
</strong></font><font face="Arial" color="#000100" size="3">To ensure S is positive definite,
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"> must lie between
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"><sub>min
</sub></font><font face="Arial" color="#000100" size="3">and
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"><sub>max
</sub></font><font face="Arial" color="#000100" size="3">where
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"><sub>min
</sub></font><font face="Arial" color="#000100" size="2"><sup>-1
</sup></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3"><br> g
</font><font face="Arial" color="#000100" size="3"><sub>max
</sub></font><font face="Arial" color="#000100" size="2"><sup>-1
</sup></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">are the smallest and largest eigenvalues of
</font><font face="Arial" color="#000100" size="3"><strong>M
</strong></font><font face="Arial" color="#000100" size="2"><sup>-1/2
</sup></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>C
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>M
</strong></font><font face="Arial" color="#000100" size="2"><sup>1/2
</sup></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3"><strong><br> *
</strong></font><font face="Arial" color="#000100" size="3">In practice, we often expect positive spatial dependence, so constrain prior for
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"> to be between 0 and
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"><sub>max
</sub></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Symbol" color="#000100" size="3"><strong> *
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"> = 0 implies no spatial dependence
</font><font face="Arial" color="#000100" size="3"><sub><br><br>
</sub></font><font face="Arial" color="#000100" size="3"><strong><a id="Intrinsic">
</strong></font><font face="Courier New" color="#000100" size="6">Intrinsic CAR model
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Courier New" color="#000100" size="6">
</font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="3"><strong><sub><br>
</sub></strong></font><font face="Arial" color="#000100" size="3"><br>Besag, York and Mollie (1991) propose an intrinsic version of this CAR model in which the covariance matrix
</font><font face="Symbol" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> is not positive definite. Their model corresponds to choosing C
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = 1/n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> if areas i and j are adjacent and C
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = 0 otherwise (with C
</font><font face="Arial" color="#000100" size="2"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3"> also set to 0), M
</font><font face="Arial" color="#000100" size="2"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3"> = 1/n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, and setting
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>max
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">which turns out to always be 1 with this particular choice of C
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> and M
</font><font face="Arial" color="#000100" size="2"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3">. Here, n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is the number of areas which are adjacent to area i. Comparison with the equations above shows that this leads to the following model for the conditional distribution of S
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> |
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> :<br><br>S
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> |
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal ( S.bar
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">, v / n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">)<br><br>where S.bar
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub> in
</sub></font><font face="Symbol" color="#000100" size="3"><sub>d
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> / n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">and
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> denotes the set of labels of the "neighbours" of area i. Hence S
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> has a normal distribution with conditional mean given by the average of the neighbouring S
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">'s and conditional variance inversely proportional to the number of neighbours n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> . Note that an equivalent specification is take
</font><font face="Arial" color="#000100" size="3"><em>unnormalised
</em></font><font face="Arial" color="#000100" size="3">weights W
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = 1 if areas i and j are adjacent and W
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = 0 otherwise, and set C
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = W
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> / W
</font><font face="Arial" color="#000100" size="2"><sub>i+
</sub></font><font face="Arial" color="#000100" size="3"> where W
</font><font face="Arial" color="#000100" size="2"><sub>i+
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> W
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">. The
</font><font face="Arial" color="#000100" size="3"><strong><em>car.normal
</em></strong></font><font face="Arial" color="#000100" size="3"> and (
</font><font face="Arial" color="#000100" size="3"><strong><em>car.l1
</em></strong></font><font face="Arial" color="#000100" size="3">) distributions in
</font><font face="Arial" color="#000100" size="3"><em>GeoBUGS
</em></font><font face="Arial" color="#000100" size="3"> requires the user to specify
</font><font face="Arial" color="#000100" size="3"><em>unnormalised weights
</em></font><font face="Arial" color="#000100" size="3">.<br><br>Since the CAR model defined above is improper (the overall mean of the S
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">is not defined), it can only be used as a prior distribution for spatially distributed random effects, and not as a likelihood for data. It is often convenient to assume that suchrandom effects have zero mean. Besag and Kooperberg (1995) show that constraining the random effects to sum to zero and specifying a separate intercept term with a location invariant Uniform(-infty, +infty) prior is equivalent to the unconstrained parameter [...]
</font><font face="Arial" color="#000100" size="3"><strong><em>dflat()
</em></strong></font><font face="Arial" color="#000100" size="3"> which corresponds to an improper (flat) prior on the whole real line. This prior must always be used for the intercept term in a model including CAR random effects.<br><br>We must also specify prior distributions for the overall variance parameter v. As usual in WinBUGS, the
</font><font face="Arial" color="#000100" size="3"><strong><em>car.normal
</em></strong></font><font face="Arial" color="#000100" size="3"> (and
</font><font face="Arial" color="#000100" size="3"><strong><em>car.l1
</em></strong></font><font face="Arial" color="#000100" size="3">) distributions are parameterised in terms of the precision
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">= 1/
</font><font face="Arial" color="#000100" size="3">v
</font><font face="Symbol" color="#000100" size="3"> .
</font><font face="Arial" color="#000100" size="3">Care is needed when choosing a prior for
</font><font face="Symbol" color="#000100" size="3"> t
</font><font face="Arial" color="#000100" size="3"> since the posterior variance of the random effects can be quite sensitive. One option is a gamma
</font><font face="Arial" color="#000100" size="3"> distribution with shape and inverse scale parameters both equal to 0.01. This has a mean of 0.01/0.01 = 1 and a large variance of 0.01/(0.01)
</font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> = 100; however, this tends to place most of the prior mass away from zero (on the scale of the random effects standard deviation), and so in situations when the true spatial dependence between areas is negligible (i.e. standard deviation close to zero) this may induce artefactual spatial structure in the posterior. Kelsall and Wakefield (1999) suggest an alternative gamma(0.5, 0.0005) prior for the precision parameter of the spatia [...]
</font><font face="Arial" color="#000100" size="3"><strong><a id="Proper">
</strong></font><font face="Courier New" color="#000100" size="6">Proper CAR model
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="3"><br><br>If
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3"> is constrained to lie in the interval (
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>min
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>max
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">) where
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>min
</sub></font><font face="Arial" color="#000100" size="2"><sup>-1
</sup></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>max
</sub></font><font face="Arial" color="#000100" size="2"><sup>-1
</sup></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">are the smallest and largest eigenvalues of
</font><font face="Arial" color="#000100" size="3"><strong>M
</strong></font><font face="Arial" color="#000100" size="2"><sup>-1/2
</sup></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>C
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>M
</strong></font><font face="Arial" color="#000100" size="2"><sup>1/2
</sup></font><font face="Arial" color="#000100" size="3"> as defined above, rather than being fixed to its maximum as in the intrinsic CAR, then the resulting distribution is proper provided the constraints on
</font><font face="Arial" color="#000100" size="3"><strong>C
</strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong>M
</strong></font><font face="Arial" color="#000100" size="3"> are still satisfied. The choice C
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = 1/n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> if areas i and j are adjacent and C
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = 0 otherwise (with C
</font><font face="Arial" color="#000100" size="2"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3"> also set to 0) and M
</font><font face="Arial" color="#000100" size="2"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3"> = 1/n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, where n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is the number of areas which are adjacent to area i is still valid for the proper CAR. In the context of disease mapping Cressie and Chan (1989) and Stern and Cressie (1999) choose an alternative parameterisation:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> M
</font><font face="Arial" color="#000100" size="2"><sub>ii
</sub></font><font face="Arial" color="#000100" size="3"> = 1/E
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> (the inverse of the expected count or population size in area i)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> C
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = (E
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> / E
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)
</font><font face="Arial" color="#000100" size="2"><sup>1/2
</sup></font><font face="Arial" color="#000100" size="3"><sup>
</sup></font><font face="Arial" color="#000100" size="3">for neighbouring areas i, j and 0 otherwise<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="MV">
</strong></font><font face="Courier New" color="#000100" size="6">Multivariate intrinsic CAR model
</font><font face="Arial" color="#000100" size="3"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="3"><br><br>Assume we have a multivariate p-dimensional vector of spatially correlated Gaussian data or random effects in each area,
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> = (S
</font><font face="Arial" color="#000100" size="2"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3"> , S
</font><font face="Arial" color="#000100" size="2"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3">,....., S
</font><font face="Arial" color="#000100" size="2"><sub>pi
</sub></font><font face="Arial" color="#000100" size="3"> )', i=1,..., N. The CAR models discussed above extend naturally to a multivariate setting by replacing the univariate Gaussian conditional distribution for S
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> | S
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">with a multivariate conditional distribution. In the case of the intrinsic CAR prior with 0-1 adjacency weights as used by Besag, York and Mollie (1991), and taking the case of p = 2 for simplicity, this gives:<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> | (
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="2"><sub>1(
</sub></font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>i)
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="2"><sub>2(
</sub></font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>i)
</sub></font><font face="Arial" color="#000100" size="3">) ~ Bivariate Normal (
</font><font face="Arial" color="#000100" size="3"><strong>S.bar
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><strong>V
</strong></font><font face="Arial" color="#000100" size="3"> / n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">), <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">(here (
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="2"><sub>1(
</sub></font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>i)
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="2"><sub>2(
</sub></font><font face="Symbol" color="#000100" size="2"><sub>-
</sub></font><font face="Arial" color="#000100" size="2"><sub>i)
</sub></font><font face="Arial" color="#000100" size="3">) denotes the elements of the 2 x N matrix S excluding the ith area (column))<br><br>where
</font><font face="Arial" color="#000100" size="3"><strong>S.bar
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">(
</font><font face="Arial" color="#000100" size="3">S.bar
</font><font face="Arial" color="#000100" size="2"><sub>i1
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">,
</font><font face="Symbol" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#000100" size="3">S.bar
</font><font face="Arial" color="#000100" size="2"><sub>i2
</sub></font><font face="Arial" color="#000100" size="3">) with S.bar
</font><font face="Arial" color="#000100" size="2"><sub>ip
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>j in
</sub></font><font face="Symbol" color="#000100" size="2"><sub>d
</sub></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>jp
</sub></font><font face="Arial" color="#000100" size="3"> / n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">and, as in the univariate case,
</font><font face="Symbol" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">denote the set of labels of the "neighbours" of area i and the number of neighbours, respectively.
</font><font face="Arial" color="#000100" size="3"><strong>V
</strong></font><font face="Arial" color="#000100" size="3"> is a 2 x 2 covariance matix with diagonal elements v
</font><font face="Arial" color="#000100" size="2"><sub>11
</sub></font><font face="Arial" color="#000100" size="3"> and v
</font><font face="Arial" color="#000100" size="2"><sub>22
</sub></font><font face="Arial" color="#000100" size="3"> representing the conditional variances of S
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> and S
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">respectively, and off-diagonal element v
</font><font face="Arial" color="#000100" size="2"><sub>12
</sub></font><font face="Arial" color="#000100" size="3"> representing the (conditional) within-area covariance between S
</font><font face="Arial" color="#000100" size="2"><sub>1
</sub></font><font face="Arial" color="#000100" size="3"> and S
</font><font face="Arial" color="#000100" size="2"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">. In general
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> has a p-dimensional multivariate normal distribution with pth element of the conditional mean vector given by the average of the neighbouring S
</font><font face="Arial" color="#000100" size="2"><sub>jp
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">'s and conditional covariance matrix inversely proportional to the number of neighbours n
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, with pth diagonal element representing the conditional variance of the pth component of
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3"> and off-diagonal elements representing the conditional covariances between each pair of the p elements of
</font><font face="Arial" color="#000100" size="3"><strong>S
</strong></font><font face="Arial" color="#000100" size="3">. <br><br>Gelfand and Vounatsou (2003) discuss a multivariate generalisation of the proper version of CAR distribution, but only the improper intrinsic multivariate CAR is currently implemented in WinBUGS. <br><br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Appendix 2">
</strong></font><font face="Courier New" color="#000100" size="6">Appendix 2: Technical details of the Poisson-gamma Spatial Moving Average convolution model.
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="3"><br><br>Spatial moving average models are a flexible class of models that have been used to describe continuous spatial processes, particularly in geostatistical applications. Such models are constructed by integrating a simple two-dimensional random noise process (for example, a grid of iid Gaussian random variables) with a smoothing kernel that is a function of distance and, possibly, location. The kernel can be thought of as a device t [...]
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, i=1,..., N (where N is the number of areas in the study region). Ickstadt and Wolpert (1998) and Best et al (2000b) model spatial dependence at the level of the Poisson mean, and assume that the counts S
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> are conditionally independent given this mean:<br><br> S
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Poisson(
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">) <br><br>The model for each
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">is constructed by specifying an arbitrary grid of latent iid gamma random variables
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> (j=1,...,J where J is the total number of grid cells defining the latent process) covering the study region. These are then convolved with a kernel matrix whose elements, k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">, represent the relative contribution of the latent variable in grid cell j to the Poisson mean in area i:<br><br>
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2"><sub>
</sub></font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">* k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3"><br><br>Best et al (2000b) assume an isotropic, stationary Gaussian kernel function (although other kernel forms are easily accommodated, such as an adjacency-based kernel - see the
</font><font face="Arial" color="#0000FF" size="3"><a href="../GeoBUGS/Examples/Forest.html">'Forest Example'</a>
</font><font face="Arial" color="#000100" size="3">):<br><br> k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> / (2
</font><font face="Symbol" color="#000100" size="3">p r
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">) exp(
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> / 2
</font><font face="Symbol" color="#000100" size="3">r
</font><font face="Arial" color="#000100" size="2"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">)<br><br>where
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> can be thought of as a scale factor for the
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Arial" color="#000100" size="3">'s, d
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> is the distance between the centroid of area i and the centroid of latent grid cell j, and
</font><font face="Symbol" color="#000100" size="3">r
</font><font face="Arial" color="#000100" size="3"> is the spatial range parameter governing how rapidly the influence of the latent gamma random variables on the area-specific Poisson means declines with distance. <br><br>One interpretation of Poisson-gamma moving average model is to view the gamma random variables as representing the location and magnitude of unmeasured risk factors, and the area-specific Poisson means
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">as representing the cumulative effect of these risk factors in each area, weighted by their distance from the area according to the kernel 'weights' k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">. <br><br>The model may be extended to include observed covariates and an offset adjustment (e.g. to account for different populations in different areas). Observed covariates are included as additive terms in the linear predictor
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">as in a standard identity link Poisson regression:<br><br>
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">=
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">X
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">+
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">* k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3"><br><br>where X
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">is the value of the kth observed covariate in area i. Note that due to the identity link, all covariates and regression coefficients must take positive values, yielding an interpretation as additive excess risk factors. The latent terms
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">* k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">may then be thought of as a spatial (non-negative) random effect for area i. Adjustment for an offset - say the population living in each area, N
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> - is easily achieved by setting
</font><font face="Symbol" color="#000100" size="3"><br><br> l
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">= p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> N
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> <br> p
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">X
</font><font face="Arial" color="#000100" size="2"><sub>ik
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">+
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">* k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3"><br><br>Note that Best et al (2004) discuss how to standardise the offset N
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> for different age and sex distributions within each area in an epidemiological application of these models. <br><br>Estimation of the
</font><font face="Arial" color="#000100" size="3"><strong><em>pois.conv
</em></strong></font><font face="Arial" color="#000100" size="3"> distribution is carried out in WinBUGS 1.4 using a data augmentation scheme to exploit the Poisson-gamma conjugacy of the full conditionals for the
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">parameters (see Ickstadt and Wolpert (1998) and Best et al (2000b) for details). It is also a good idea to assume gamma prior distributions for any other uncertain parameters in the linear predictor
</font><font face="Symbol" color="#000100" size="3">l
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> (e.g. the
</font><font face="Symbol" color="#000100" size="3">b
</font><font face="Arial" color="#000100" size="2"><sub>k
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">parameters above) to exploit this conjugacy, although it is possible to assume any suitable prior distribution with positive support for these other parameters. Hyperprior specification is discussed in detail by Ickstadt and Wolpert (1998) and Best et al (2000b). Note however that the prior shape (a) and precision (b) parameters of the latent gamma variables should be chosen such that
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">has prior mean proportional to the area of the j
</font><font face="Arial" color="#000100" size="2"><sup>th
</sup></font><font face="Arial" color="#000100" size="3"> latent grid cell. This makes the model spatially extensible in the sense that any partition of the latent gamma random variables will lead to identical probability distributions for the kernel-weighted sums
</font><font face="Symbol" color="#000100" size="3">S
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Symbol" color="#000100" size="3">g
</font><font face="Symbol" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"><sub>
</sub></font><font face="Arial" color="#000100" size="3">* k
</font><font face="Arial" color="#000100" size="2"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Refs">
</strong></font><font face="Courier New" color="#000100" size="6">References
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3">[<a href="#Top">top</a>]
</font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br>Besag, J., York, J. and Mollie, A. (1991). Bayesian image restoration, with two applications in spatial statistics.
</font><font face="Arial" color="#000100" size="2"><em> Annals of the Institute of Statistical Mathematics
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>43
</strong></font><font face="Arial" color="#000100" size="2">, 1--59, (With discussion).<br><br>Besag, J. and Kooperberg, C.L. (1995). On conditional and intrinsic autoregressions.
</font><font face="Arial" color="#000100" size="2"><em>Biometrika
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>82
</strong></font><font face="Arial" color="#000100" size="2">, 733--746.
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="2">Best, N.G., Richardson, S. and Thomson, A. (2004). A comparison of Bayesian spatial models for disease mapping.
</font><font face="Arial" color="#000100" size="2"><em>Statistical Methods in Medical Research
</em></font><font face="Arial" color="#000100" size="2"> (to appear).<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2">Best, N.G., Ickstadt, K.and Wolpert, R.L. and Briggs, D.J. (2000a).
</font><font face="Arial" color="#000100" size="2"><em>Journal of the American Statistical Association
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong> 95
</strong></font><font face="Arial" color="#000100" size="2">, 1076-1088.<br><br>Best, N.G., Ickstadt, K., Wolpert, R.L. and Briggs, D.J. (2000b). Combining models of health and exposure data: the SAVIAH study. In
</font><font face="Arial" color="#000100" size="2"><em>Spatial Epidemiology: Methods and Applications
</em></font><font face="Arial" color="#000100" size="2">. P. Elliott, J.C. Wakefield, N.G. Best and D.J. Briggs (eds), Oxford: Oxford University Press, p. 393-414.<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2">Clayton, D.G and Kaldor, J. (1987). Empirical Bayes estimates of age-standardized relative risks for use in disease mapping.
</font><font face="Arial" color="#000100" size="2"><em>Biometrics
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>43
</strong></font><font face="Arial" color="#000100" size="2">, 671--681.<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2">Cressie, N.A. and Chan, N.H. (1989). Spatial modeling of regional variables.
</font><font face="Arial" color="#000100" size="2"><em>Journal of the American Statistical Association
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>84
</strong></font><font face="Arial" color="#000100" size="2">, 393--401.
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"><br>Diggle, P.J., Tawn, J.A. and Moyeed, R.A. (1998). Model-based geostatistics.
</font><font face="Arial" color="#000100" size="2"><em>Applied Statistics
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>47
</strong></font><font face="Arial" color="#000100" size="2">, 299-350.<br><br>Fahrmeir, L. and Lang, S. (2001). Bayesian inference for generlaized additive mixed models based on Markov random field priors.
</font><font face="Arial" color="#000100" size="2"><em>Applied Statistics
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>50
</strong></font><font face="Arial" color="#000100" size="2">, 201-220.<br><br>Gelfand, A. and Vounatsou, P. (2003). Proper multivariate conditional autoregressive models for spatial data analysis.
</font><font face="Arial" color="#000100" size="2"><em>Biostatistics
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>4
</strong></font><font face="Arial" color="#000100" size="2">, 11-25.<br><br>Ickstadt, K. and Wolpert, R.L. (1998). Multiresolution assessment of forest inhomogeneity. In
</font><font face="Arial" color="#000100" size="2"><em>Case Studies in Bayesian Statistics, Volume 3.
</em></font><font face="Arial" color="#000100" size="2">Lecture Notes in Statistics,
</font><font face="Arial" color="#000100" size="2"><strong>121
</strong></font><font face="Arial" color="#000100" size="2">. C. Gatsonis, J.S. Hodges, R.E. Kass, R. McCulloch, P. Rossi and N.D. Singpurwalla (eds), New York: Springer-Verlag, p. 371-386.<br><br>Johnson, N.L. and Kotz, S. (1972).
</font><font face="Arial" color="#000100" size="2"><em>Distributions in Statistics: continuous multivariate
</em></font><font face="Arial" color="#000100" size="2">. Wiley: New York.<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2">Kelsall, J.E. and Wakefield, J.C. (1999). Discussion of "Bayesian models for spatially correlated disease and exposure data", by Best
</font><font face="Arial" color="#000100" size="2"><em>et al.
</em></font><font face="Arial" color="#000100" size="2"> In
</font><font face="Arial" color="#000100" size="2"><em> Bayesian Statistics 6
</em></font><font face="Arial" color="#000100" size="2">. J.M. Bernardo, J.O. Berger, A.P. Dawid and A.F.M. Smith (eds), Oxford: Oxford University Press, p. 151.<br><br>Knorr-Held L. and Best N.G. (2001). A shared component model for joint and selective clustering of two diseases.
</font><font face="Arial" color="#000100" size="2"><em>Journal of the Royal Statistical Society, Series A
</em></font><font face="Arial" color="#000100" size="2">.
</font><font face="Arial" color="#FF00FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>Mollie, A. (1996). Bayesian mapping of disease. In
</font><font face="Arial" color="#000100" size="2"><em>Markov Chain Monte Carlo in Practice
</em></font><font face="Arial" color="#000100" size="2">. W.R. Gilks, S. Richardson and D.J. Spiegelhalter (eds.), New York: Chapman & Hall, pp. 359--379.<br><br>Richardson, S. (1992). Statistical methods for geographical correlation studies. In
</font><font face="Arial" color="#000100" size="2"><em>Geographical and Environmental Epidemiology
</em></font><font face="Arial" color="#000100" size="2">. P. Elliott, J. Cuzick, D. English and R. Stern (eds.), Oxford: Oxford University Press, p. 181-204.<br><br>Shaddick, G. and Wakefield, J. (2002). Modelling daily multivariate pollutant data at multiple sites.
</font><font face="Arial" color="#000100" size="2"><em>Applied Statistics
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>51
</strong></font><font face="Arial" color="#000100" size="2">, 351-372.<br><br>Stern, H.S. and Cressie, N.A. (1999). Inference for extremes in disease mapping. In
</font><font face="Arial" color="#000100" size="2"><em>Disease mapping and risk assessment for public health
</em></font><font face="Arial" color="#000100" size="2">. A. Lawson, A. Biggeri, D. Bohning, E. Lesaffre, J-F. Viel and R. Bertollini (eds.), Chichester: Wiley, p. 63--84.<br><br>Wakefield, J.C., Best, N.G., and Waller, L.A. (2000). Bayesian Approaches to Disease Mapping. In
</font><font face="Arial" color="#000100" size="2"><em>Spatial Epidemiology: Methods and Applications
</em></font><font face="Arial" color="#000100" size="2">. P. Elliott, J.C. Wakefield, N.G. Best and D.J. Briggs (eds), Oxford: Oxford University Press, p. 104-127.<br><br>Wolpert, R.L. and Ickstadt, K. (1998). Poisson/Gamma random field models for spatial statistics.
</font><font face="Arial" color="#000100" size="2"><em>Biometrika
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>85
</strong></font><font face="Arial" color="#000100" size="2">, 251-267.
</font>
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<html>
<head>
<title>AttributesMenu</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="attributesmenu0.bmp" alt="[attributesmenu0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">The Attributes Menu
</font><font face="Arial" color="#000100" size="6"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#GeneralProperties">General properties</a><br> <a href="#Weight">Weight</a><br> <a href="#FixedSize">Fixed Size...</a><br> <a href="#Size">Size...</a><br> <a href="#FixedColor">Fixed Color</a><br> <a href="#Color">Color...</a><br> <a href="#DefaultFont">Default Font</a><br> &nb [...]
</font><font face="Arial" color="#0000FF" size="4"> <br>
</font><font face="Arial" color="#000100" size="2"><br><a id="GeneralProperties">
</font><font face="Courier New" color="#000100" size="5">General properties</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The commands change the appearance of text in documents. They either act on the highlighted text or affect the appearance of subsequently entered text.<br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Weight">Weight</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">The commands in this group set the weight of the highlighted text. The weight can either be Regular, Bold, Italic or Underline. If the entire highlighted text is of one single weight a tick mark will appear against the relevant weight.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="FixedSize">
</font><font face="Courier New" color="#000100" size="5">Fixed Size
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">The commands in this group change the size of the highlighted text to a predefined font size. Sizes available are 8, 9, 10, 12, 16, 20 and 24pts. If the entire highlighted text is of one single font size a tick mark will appear against the relevant size.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Size">Size...</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command opens a non modal dialog box which allows the user to choose the font size for the highlighted text.<br><br> <img src="attributesmenu1.bmp" alt="[attributesmenu1]"><br> <br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="FixedColor">
</font><font face="Courier New" color="#000100" size="5">Fixed Color
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">The commands in this group change the color of the highlighted text to a predefined color. Colors available are Default Color, Black, Red, Green, and Blue. If the entire highlighted text is of one single color a tick mark will appear against this color.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Color">
</font><font face="Courier New" color="#000100" size="5">Color...</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command opens a modal dialog box which allows the user to choose the color for the highlighted text.<br>
</font><font face="Arial" color="#0000FF" size="3"><br> <img src="attributesmenu2.bmp" alt="[attributesmenu2]"><br> <br> <br><a id="DefaultFont">
</font><font face="Courier New" color="#000100" size="5">Default Font
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command changes the highlighted text to be in the default font. If the entire highlighted text is in the default font a tick mark will appear against this option.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Font">
</font><font face="Courier New" color="#000100" size="5">Font...</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command opens a modal dialog box which allows the user to choose the font for the highlighted text. The color of the text can also be chosen from a restricted range of options. This command is useful for entering Greek characters into a document.<br><br> <img src="attributesmenu3.bmp" alt="[attributesmenu3]"><br> <br> [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Typeface">Typeface...</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command is a simplified version of the Font... command without the ability to change the color of the text.
</font>
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<html>
<head>
<title>CompoundDocuments</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="compounddocuments0.bmp" alt="[compounddocuments0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Arial" color="#000100" size="6"><strong><sup>
</sup></strong></font><font face="Courier New" color="#000100" size="6">Compound Documents
</font><font face="Arial" color="#000100" size="2"><br><br><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#WhatIsACompoundDocument">What is a compound document?</a><br> <a href="#WorkingWithCompoundDocuments">Working with compound documents</a><br> <a href="#EditingCompoundDocuments">Editing compound documents</a><br> <a href="#CompoundDocumentsAndEMail">Compound documents and e-mail</a><br> [...]
</font><font face="Arial" color="#0000FF" size="4">
</font><font face="Arial" color="#0000FF" size="2"><u><br><br>
</u></font><font face="Arial" color="#000100" size="2"><a id="WhatIsACompoundDocument">
</font><font face="Courier New" color="#000100" size="5">What is a compound document?</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents"> [top]</a>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">A compound document contains various types of information (formatted text, tables, formulae, plots, graphs etc) displayed in a single window and stored in a single file. The tools needed to create and manipulate these information types are always available, so there is no need to continuously move between different programs. The
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> software has been designed so that it produces output directly to a compound document and can get its input directly from a compound document. To see an example of a compound document
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Examples/Rats.html">click here</a>.
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> is written in Component Pascal using the BlackBox development framework: see http://www.oberon.ch.
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3">In
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> a document can be a description of a statistical analysis, the user interface to the software, and the resulting output.<br><br>Compound documents are stored in binary files with the .odc extension.
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="WorkingWithCompoundDocuments">Working with compound documents
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents"> [top]</a>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3">A compound document is like a word-processor document that contains special rectangular embedded regions or elements, each of which can be manipulated by standard word-processing tools -- each rectangle behaves like a single large character, and can be focused, selected, moved, copied, deleted etc. If an element is "focused" the tools to manipulate its interior become available.<br><br>The
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> software works with many different types of elements, the most interesting of which are Doodles, which allow statistical models to be described in terms of graphs.
</font><font face="Arial" color="#000100" size="3"><em>DoodleBUGS
</em></font><font face="Arial" color="#000100" size="3"> is a specialised graphics editor and is described fully in
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Manuals/DoodleBUGS.html"><br>DoodleBUGS: The Doodle Editor
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">. Other elements are rather simpler and are used to display plots of an analysis.<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="EditingCompoundDocuments">Editing compound documents
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents"> [top]</a>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> contains a built-in word processor, which can be used to manipulate any output produced by the software. If a more powerful editing tool is needed
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> documents or parts of them can be pasted into a standard OLE enabled word processor.<br><br>Each open document either displays a caret or a selection of highlighted text. New keyboard input is inserted at the caret position. Text is selected by holding down the left mouse button while dragging the mouse over a region of text. A single word of text can be selected by double clicking on it.
</font><font face="Arial" color="#FF0000" size="3">Warning: if selection of text is highlighted and a key pressed the selection will be replaced by the character typed. (This can be un-done by selecting Undo from the Edit menu.)
</font><font face="Arial" color="#000100" size="3">. The text can be unselected by pressing the "Esc" key or clicking the mouse outside the highlighted selection. <br><br>A single embedded element can be selected by single clicking into it with the left mouse button. A selected element is distinguished by a thin bounding rectangle. If this bounding rectangle contains small solid squares at the corners and mid sides it can be resized by dragging these with the mouse. An embedded [...]
</font><font face="Arial" color="#000100" size="2"><br><a id="CompoundDocumentsAndEMail">
</font><font face="Courier New" color="#000100" size="5">Compound documents and e-mail</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents"> [top]</a>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> compound documents contain non-ascii characters, but the Encode Document command in the Tools menu produces an ascii representation of the focus document. The original document can be recovered from this encoded form by using the Decode command of the Tools menu. This allows, for example, Doodles to be sent by e-mail.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="PrintingCompoundDocumentsAndDoodles">
</font><font face="Courier New" color="#000100" size="5">Printing compound documents
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents"> [top]</a>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">These can be printed directly from the File Print... menu. We find it useful to have printing set up to produce pdf files. CutePDF is a freely available Windows PDF printer that does this.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="ReadingInTextFiles">
</font><font face="Courier New" color="#000100" size="5">Reading in plain text files
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents"> [top]</a>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3">Open these using the File Open... menu option and pick 'txt' as the file type in the dialog box. The contents of text files can be copied into documents, or text files can be converted into odc documents by using the File Save As... menu option and picking 'odc' as the file type in the dialog box.<br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Compound documents and Linux">Compound documents and Linux</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents"> [top]</a>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The OpenBUGS implementation for Intel Linux machines accepts only ASCII file input for all input types, and all output is in ASCII format. Graphic output is not available in the Linux version of the program.<br>
</font>
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<html>
<head>
<title>Contents</title>
</head>
<body>
<p>
<font face="Courier New" color="#0000FF" size="3"><img src="contents0.bmp" alt="[contents0]">
</font><font face="Courier New" color="#000100" size="5"><a id="ManualContents">
</font><font face="Courier New" color="#000100" size="6">OpenBUGS User Manual
</font><font face="Arial" color="#000100" size="6"><strong><br>
</strong></font><font face="Courier New" color="#000100" size="6"><br> Contents
</font><font face="Courier New" color="#000100" size="5"></a>
</font><font face="Courier New" color="#000100" size="3"><br><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/Introduction.html">Introduction
</strong></font><font face="Courier New" color="#0000FF" size="3"></a>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/Tutorial.html">Tutorial
</strong></font><font face="Courier New" color="#0000FF" size="3"></a> <br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/CompoundDocuments.html">Compound Documents
</strong></font><font face="Courier New" color="#0000FF" size="3"></a>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/ModelSpecification.html">Model Specification
</strong></font><font face="Courier New" color="#0000FF" size="3"></a> <br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/Scripts.html">Scripts and Batch-mode</a>
</strong></font><font face="Courier New" color="#0000FF" size="3">
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/DoodleBUGS.html">DoodleBUGS:The Doodle Editor
</strong></font><font face="Courier New" color="#0000FF" size="3"></a> <br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/FileMenu.html">The File Menu
</strong></font><font face="Courier New" color="#0000FF" size="3"></a>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/EditMenu.html">The Edit Menu
</strong></font><font face="Courier New" color="#0000FF" size="3"></a> <br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/AttributesMenu.html">The Attributes Menu
</strong></font><font face="Courier New" color="#0000FF" size="3"></a>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/ToolsMenu.html">The Tools Menu
</strong></font><font face="Courier New" color="#0000FF" size="3"></a> <br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/TextMenu.html">The Text Menu
</strong></font><font face="Courier New" color="#0000FF" size="3"></a>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/InfoMenu.html">The Info Menu
</strong></font><font face="Courier New" color="#0000FF" size="3"></a> <br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/ModelMenu.html">The Model Menu
</strong></font><font face="Courier New" color="#0000FF" size="3"></a>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/InferenceMenu.html">The Inference Menu
</strong></font><font face="Courier New" color="#0000FF" size="3"></a> <br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/ExamplesMenu.html">The Examples Menu
</strong></font><font face="Courier New" color="#0000FF" size="3"></a>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/ManualsMenu.html">The Manuals Menu
</strong></font><font face="Courier New" color="#0000FF" size="3"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/HelpMenu.html">The Help Menu
</strong></font><font face="Courier New" color="#0000FF" size="3"></a>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/WinBUGSGraphics.html">OpenBUGS Graphics
</strong></font><font face="Courier New" color="#0000FF" size="3"></a> <br><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/TipsTroubleshooting.html">Tips and Troubleshooting
</strong></font><font face="Courier New" color="#0000FF" size="3"></a> <br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/Tricks.html">Advanced use of the BUGS Language
</strong></font><font face="Courier New" color="#0000FF" size="3"></a> <br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Manuals/References.html">References
</strong></font><font face="Courier New" color="#0000FF" size="3"></a><br>
</font>
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<html>
<head>
<title>DoodleBUGS</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="doodlebugs0.bmp" alt="[doodlebugs0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">DoodleBUGS: The Doodle Editor
</font><font face="Arial" color="#000100" size="2"><br><br><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#GeneralProperties">General properties</a><br> <a href="#CreatingANode">Creating a node</a><br> <a href="#SelectingANode">Selecting a node</a><br> <a href="#DeletingANode">Deleting a node</a><br> <a href="#MovingANode">Moving a node</a><br> <a href="#CreatingAPlate">Creating [...]
</font><font face="Arial" color="#000100" size="2"><br><a id="GeneralProperties">
</font><font face="Courier New" color="#000100" size="5">General properties
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Doodles consist of three elements:
</font><font face="Arial" color="#000100" size="3"><em>nodes
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><em>plates
</em></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><em>edges
</em></font><font face="Arial" color="#000100" size="3">. The graph is built up out of these elements using the mouse and keyboard. The
</font><font face="Arial" color="#000100" size="3"><em>Doodle
</em></font><font face="Arial" color="#000100" size="3"> menu contains options that apply to the whole
</font><font face="Arial" color="#000100" size="3"><em>Doodle
</em></font><font face="Arial" color="#000100" size="3">. These menu options are described below.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>New...
</em></strong></font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">Dialog box for creating a new
</font><font face="Arial" color="#000100" size="3"><em>Doodle
</em></font><font face="Arial" color="#000100" size="3">. Allows a choice of size of the Doodle graphic and the size of the nodes in the Doodle.<br><br> <img src="doodlebugs1.bmp" alt="[doodlebugs1]"><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>No grid, grid 1mm, grid 2mm, grid 5mm:
</em></strong></font><font face="Arial" color="#000100" size="3"> options for the snap grid the snap grid to which the centre of each node and each corner of each plate is constrained to lie.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>Scale Model:
</em></strong></font><font face="Arial" color="#000100" size="3">shrinks the Doodle so that
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">the size of each node and plate plus the separation between them is reduced by a constant factor. The Doodle will move towards the top left corner of the window. This command is useful if you run out of space while drawing the Doodle. Note that the Doodle
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">will still be constrained by the snap grid, and if the snap is coarse then the Doodle
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">could be badly distorted.<br><br> <img src="doodlebugs2.bmp" alt="[doodlebugs2]"><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>Remove Selection:
</em></strong></font><font face="Arial" color="#000100" size="3"> removes the highlighting from the selected node or plate of the Doodle
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">if any.<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="CreatingANode">Creating a node
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Point the mouse cursor to an empty region of the
</font><font face="Arial" color="#000100" size="3"><em>Doodle
</em></font><font face="Arial" color="#000100" size="3"> window and click. A new grey elipse will appear centered at the mouse cursor position. A flashing caret appears next to the blue word
</font><font face="Arial" color="#000100" size="3"><em>name
</em></font><font face="Arial" color="#000100" size="3">. Typed characters will appear both at this caret and within the outline of the elipse.<br><br>When first created the node will be of type
</font><font face="Arial" color="#000100" size="3"><em>stochastic
</em></font><font face="Arial" color="#000100" size="3"> and have associated density
</font><font face="Arial" color="#000100" size="3"><em>dnorm.
</em></font><font face="Arial" color="#000100" size="3"><br><br>The type of the node can be changed by clicking on the blue word
</font><font face="Arial" color="#000100" size="3"><em>type
</em></font><font face="Arial" color="#000100" size="3"> at the top of the doodle. A menu will drop down giving a choice of
</font><font face="Arial" color="#000100" size="3"><em>stochastic
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><em>logical
</em></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><em>constant
</em></font><font face="Arial" color="#000100" size="3"> for the node type. Constant nodes are shown as rectangular boxes.<br><br>The name of a node starts with a letter and can also contain digits and the period character "." The name must not contain two successive periods and must not end with a period. Vectors are denoted using a square bracket notation, with indices separated by commas. A colon-separated pair of integers is used to denote an index range of a multivariate no [...]
</font><font face="Arial" color="#000100" size="3"><strong>Stochastic:
</strong></font><font face="Arial" color="#000100" size="3"> Associated with stochastic nodes is a density. Click on the blue word
</font><font face="Arial" color="#000100" size="3"><em>density
</em></font><font face="Arial" color="#000100" size="3"> to see the choice of densities available (this will not necessarily include all those available in the
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language and described in
</font><font face="Arial" color="#0000FF" size="3"><a href="../Manuals/ModelSpecification.html#ContentsAII">
</font><font face="Arial" color="#0000FF" size="3"><u>Appendix II Functions and functionals
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">). For each density the appropriate name(s) of the parameters are displayed in blue. For some densities default values of the parameters will be displayed in black next to the parameter name. When edges are created pointing into a stochastic node these edges are associated with the parameters in a left to right order. To change the association of edges with parameters click on one of the blue parameter names, a menu will drop down from wh [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><strong>Logical:
</strong></font><font face="Arial" color="#000100" size="3"> Associated with logical nodes is a link, which can be selected by clicking on the blue word
</font><font face="Arial" color="#000100" size="3"><em>link
</em></font><font face="Arial" color="#000100" size="3">. Logical nodes also require a
</font><font face="Arial" color="#000100" size="3"><em>value
</em></font><font face="Arial" color="#000100" size="3"> to be evaluated (modified by the chosen link) each time the value of the node is required. To type input in the value field click the mouse on the blue word
</font><font face="Arial" color="#000100" size="3"><em>value
</em></font><font face="Arial" color="#000100" size="3">. The value field of a logical node corresponds to the right hand side of a logical relation in the
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language and can contain the same functions. The value field must be completed for all logical nodes.<br><br>We emphasise that the
</font><font face="Arial" color="#000100" size="3"><em>value
</em></font><font face="Arial" color="#000100" size="3"> determines the value of the node and the logical links in the Doodle are for cosmetic purposes only.<br><br>
</font><font face="Arial" color="#000000" size="3">It is possible to define two nodes in the same Doodle with the same name - one as logical and one as stochastic - in order to use the data transformation facility described in
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Manuals/ModelSpecification.html#DataTransformations">Data transformations</a>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong>Constants:
</strong></font><font face="Arial" color="#000100" size="3"> Constant nodes can be given a name or a numerical value.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="SelectingANode">
</font><font face="Courier New" color="#000100" size="5">Selecting a node
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Point the mouse cursor inside the node and left-mouse-click.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="DeletingANode">
</font><font face="Courier New" color="#000100" size="5">Deleting a node
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Select a node and press
</font><font face="Arial" color="#000100" size="3"><em>ctrl + delete
</em></font><font face="Arial" color="#000100" size="3"> key combination.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="MovingANode">
</font><font face="Courier New" color="#000100" size="5">Moving a node
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Select a node and then point the mouse into selected node. Hold mouse button down and drag node. The cursor keys may also be used to move the centre of the node to the next snap grid point.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="CreatingAPlate">
</font><font face="Courier New" color="#000100" size="5">Creating a plate
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Point the mouse cursor to an empty region of the
</font><font face="Arial" color="#000100" size="3"><em>Doodle
</em></font><font face="Arial" color="#000100" size="3"> window and click while holding the
</font><font face="Arial" color="#000100" size="3"><em>Ctrl
</em></font><font face="Arial" color="#000100" size="3"> key down.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="SelectingAPlate">
</font><font face="Courier New" color="#000100" size="5">Selecting a plate
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Point the mouse into the lower or right hand border of the plate and click.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="DeletingAPlate">
</font><font face="Courier New" color="#000100" size="5">Deleting a plate
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Select a plate and press
</font><font face="Arial" color="#000100" size="3"><em>ctrl + delete
</em></font><font face="Arial" color="#000100" size="3"> key combination.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="MovingAPlate">
</font><font face="Courier New" color="#000100" size="5">Moving a plate
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Select a plate and then point the mouse into the lower or right hand border of the selected plate. Hold the mouse button down and drag the plate. The cursor keys may also be used to move the cornor of the node to the next snap grid point. If the
</font><font face="Arial" color="#000100" size="3"><em>Ctrl
</em></font><font face="Arial" color="#000100" size="3"> key is held down while moving a plate any nodes within the plate will move with the plate.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="ResizingAPlate">
</font><font face="Courier New" color="#000100" size="5">Resizing a plate
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Select a plate and then point the mouse into the small region at the lower right where the two borders intercept. Hold the mouse button down and drag to resize the plate.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="CreatingAnEdge">
</font><font face="Courier New" color="#000100" size="5">Creating an edge
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Select node into which the edge should point and then click into its parent while holding down the
</font><font face="Arial" color="#000100" size="3"><em>ctrl
</em></font><font face="Arial" color="#000100" size="3"> key.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="DeletingAnEdge">
</font><font face="Courier New" color="#000100" size="5">Deleting an edge
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Select node whose incoming edge is to be deleted and then click into its parent while holding down the
</font><font face="Arial" color="#000100" size="3"><em>ctrl
</em></font><font face="Arial" color="#000100" size="3"> key.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="MovingADoodle">
</font><font face="Courier New" color="#000100" size="5">Moving a Doodle
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">After constructing a Doodle, it can be moved into a document that may also contain data, initial values, and other text and graphics. This can be done by choosing
</font><font face="Arial" color="#000100" size="3"><em> Select Document
</em></font><font face="Arial" color="#000100" size="3"> from the
</font><font face="Arial" color="#000100" size="3"><em>Edit
</em></font><font face="Arial" color="#000100" size="3"> menu, and then either copying and pasting, or dragging, the Doodle.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="ResizingADoodle">
</font><font face="Courier New" color="#000100" size="5">Resizing a Doodle
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">To change the size of Doodle which is already in a document containing text, click once into the Doodle with the left mouse button. A narrow border with small solid squares at the corners and mid-sides will appear. Drag one of these squares with the mouse until the Doodle is of the required size.<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font>
</p>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>EditMenu</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="editmenu0.bmp" alt="[editmenu0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">The Edit Menu
</font><font face="Arial" color="#000100" size="6"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Contents">Contents</a>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#GeneralProperties">General properties</a><br> <a href="#Undo">Undo</a><br> <a href="#Redo">Redo</a><br> <a href="#Cut">Cut</a><br> <a href="#Copy">Copy</a><br> <a href="#Paste">Paste</a><br> <a href="#Delete">Delete</a><br> <a href="#PasteObject">Paste Object</a><br> &n [...]
</font><font face="Arial" color="#0000FF" size="4"><br>
</font><font face="Arial" color="#000100" size="2"><a id="GeneralProperties">
</font><font face="Courier New" color="#000100" size="5">General properties
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The commands in this menu apply to the editing of documents. OpenBUGS is build using a component framework. One component of this framework is a powerful document editor.<br><br>
</font><font face="Arial" color="#0000FF" size="4"><br><a id="Undo">
</font><font face="Courier New" color="#000100" size="5">Undo
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command un-does the last editing action carried out by the user. The full name of this command changes depending on what type of editing action is to be un-done<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Redo">
</font><font face="Courier New" color="#000100" size="5">Redo
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command restores the last editing action carried out by the user if it has been undone. The full name of this command changes depending on what type of editing action is to be re-done.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Cut">
</font><font face="Courier New" color="#000100" size="5">Cut
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command cuts the highlighted section of the document to the Windows clip board.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Copy">
</font><font face="Courier New" color="#000100" size="5">Copy
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command copies the highlighted section of the document to the Windows clip board.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Paste">
</font><font face="Courier New" color="#000100" size="5">Paste
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command copies the contents of the Windows clip board to the caret position in the document.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Delete">
</font><font face="Courier New" color="#000100" size="5">Delete</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command deletes the highlighted section from the document.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="CopyProperties"><a id="PasteObject">
</font><font face="Courier New" color="#000100" size="5">Paste Object</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>This command copies the contents of the Windows clip board to the caret position in the document. <br>
</font><font face="Arial" color="#0000FF" size="3"><br><br><a id="PasteSpecial">
</font><font face="Courier New" color="#000100" size="5">Paste Special...</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command copies the contents of the Windows clip board to the caret position in the document. But in addition it allows the user to choose the format in which the object is copied into the document.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="PastetoWindow">
</font><font face="Courier New" color="#000100" size="5">Paste to Window
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command copies the contents of the Windows clip board to a new window.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="InsertObject">Insert Object...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command inserts an OLE object at the current caret position. A modal dialog box pops up giving a choice of OLE objects to insert<br><br> <img src="editmenu1.bmp" alt="[editmenu1]"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="ObjectProperties">
</font><font face="Courier New" color="#000100" size="5">Object Properties...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command allows the user to change the font and font style, size, color and effects.
</font><font face="Arial" color="#0000FF" size="3"><br><br><br><a id="BitmapImageObject">
</font><font face="Courier New" color="#000100" size="5">Bitmap Image Object
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command allows the user to open or edit an in-line bitmap image.
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><br><br>
</font><font face="Courier New" color="#000100" size="5">Select Document
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command selects the document in the window.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="SelectAll">
</font><font face="Courier New" color="#000100" size="5">Select All</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command selects the contents of the entire document.
</font><font face="Arial" color="#0000FF" size="3"><br><br><br><a id="SelectNextObject">
</font><font face="Courier New" color="#000100" size="5">Select Next Object
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br><br><a id="Preferences">
</font><font face="Courier New" color="#000100" size="5">Preferences...</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command opens a dialog that allows the user to set certain preferences for documents. In addition there is an option that affects the status bar, the line of information at the bottom of the main OpenBUGS window. By default (option Simple) this line just shows error messages, but it can be hidden (option No) or made to show how much memory OpenBUGS is using (option Double). Ticking the thick caret box can make the caret easier to see.<br>
</font><font face="Arial" color="#0000FF" size="3"><br> <img src="editmenu2.bmp" alt="[editmenu2]">
</font><font face="Arial" color="#000100" size="4"><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Manuals/ExamplesMenu.html b/doc/Manuals/ExamplesMenu.html
new file mode 100755
index 0000000..60b13d2
--- /dev/null
+++ b/doc/Manuals/ExamplesMenu.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ExamplesMenu</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="examplesmenu0.bmp" alt="[examplesmenu0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Examples Menu
</font><font face="Arial" color="#000100" size="6"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="3">This menu gives access to the various volumes of examples illustrating the use of the OpenBUGS software. The first group of options opens the contents pages of the example volumes as hyper-text documents. Clicking on the blue links will open further windows displaying the individual examples. The second group of options prints a copy of the examples. If a physical printer is the default printer the result is a paper. If the defau [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Manuals/FileMenu.html b/doc/Manuals/FileMenu.html
new file mode 100755
index 0000000..80a12b8
--- /dev/null
+++ b/doc/Manuals/FileMenu.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>FileMenu</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="filemenu0.bmp" alt="[filemenu0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">The File Menu
</font><font face="Arial" color="#000100" size="6"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#GeneralProperties">General properties</a><br> <a href="#New">New</a><br> <a href="#Open">Open...</a><br> <a href="#OpenStationary">Open Stationary...</a><br> <a href="#Save">Save...</a><br> <a href="#SaveAs">Save As...</a><br> <a href="#SaveCopyAs">Save Copy As...</a><br>  [...]
</font><font face="Arial" color="#0000FF" size="4"> <br>
</font><font face="Arial" color="#000100" size="2"><br><a id="GeneralProperties">
</font><font face="Courier New" color="#000100" size="5">General properties
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The commands in this menu apply to documents. There are options for creating, opening and saving documents<br><br><br><a id="New">
</font><font face="Courier New" color="#000100" size="5">New
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">Creates a new document and opens it in a window<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Open">
</font><font face="Courier New" color="#000100" size="5">Open...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">Opens an existing document that has been saved to a file. A modal dialog showing a list of files<br>pops up.<br><br> <img src="filemenu1.bmp" alt="[filemenu1]"><br> <br>The types of files show in the list can be changed by using the 'Files of type' pull down list. By default the files list are ones storing documents. The location of the list of files displayed can be ch [...]
</font><font face="Courier New" color="#000100" size="5"><a id="OpenStationary"><a id="Save">Save...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">Saves a document to a file. If the document has already been saved to a file it is saved to this file. If the document has never been saved to a file 'Save' behaves as 'Save As*, see the next section.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="SaveAs">Save As...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">Save a document to a different file than the one it was originally stored in.<br><br> <img src="filemenu2.bmp" alt="[filemenu2]"><br> <br>The name of the file to which the document is to be saved can be typed in the 'File name' field or a existing file can be picked from the main dialog. The location where the file is to be stored can be changed using the 'Save in' pull [...]
</font><font face="Arial" color="#0000FF" size="3"><a id="SaveCopyAs"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Close">Close
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">Closes the top window. If the document in the top window has changed since it was last saved to file a dialog box will pop up asking the user if they want to save the document before closing the window.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="PageSetup">
</font><font face="Courier New" color="#000100" size="5">Page Setup...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">Options for changing the appearance of documents.<br><br> <img src="filemenu3.bmp" alt="[filemenu3]"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Print">
</font><font face="Courier New" color="#000100" size="5">Print...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">Prints the document in the top window. A modal dialog box pops up allowing the user to choose which printer to use etc. We have found CutePDF Writer very useful, this 'printer' produces PDF documents that can be saved to file and then printed to paper later on.<br><br> <img src="filemenu4.bmp" alt="[filemenu4]"><br> <br><br>
</font><font face="Courier New" color="#000100" size="5">Send Document...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">No action is taken.<br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Exit">
</font><font face="Courier New" color="#000100" size="5">Send Note...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">No action is taken.<br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Exit">
</font><font face="Courier New" color="#000100" size="5">Exit</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">Closes the OpenBUGS program. The user will be prompted to save any documents that have changed. The state of the MCMC simulation will be lost. OpenBUGS can also be closed by clicking on the red button at the extreme right of the menu bar. This can easily be done by accident, so to prevent the unintended loss of the MCMC simulation a modal dialog box will pop up asking the user if they really want to quit OpenBUGS. The internalize/external [...]
</font><font face="Arial" color="#0000FF" size="3"><a href="../Manuals/ModelMenu.html#Externalize">Externalize
</font><font face="Arial" color="#000100" size="3"></a>.
</font><font face="Arial" color="#000100" size="1">
</font><font face="Times New Roman" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="1">
</font><font face="Times New Roman" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="1">
</font><font face="Times New Roman" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="1">
</font><font face="Times New Roman" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="1">
</font><font face="Times New Roman" color="#000100" size="3">
</font>
</p>
</body>
</html>
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diff --git a/doc/Manuals/GNU-Licence.html b/doc/Manuals/GNU-Licence.html
new file mode 100755
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+++ b/doc/Manuals/GNU-Licence.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GNU-Licence</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2">GNU GENERAL PUBLIC LICENSE<br><br>Version 2, June 1991 <br><br>Copyright (C) 1989, 1991 Free Software Foundation, Inc. <br>59 Temple Place - Suite 330, Boston, MA 02111-1307, USA<br><br>Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.<br><br>Preamble<br><br>The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU Genera [...]
</font>
</p>
</body>
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diff --git a/doc/Manuals/HelpMenu.html b/doc/Manuals/HelpMenu.html
new file mode 100755
index 0000000..b0c05b5
--- /dev/null
+++ b/doc/Manuals/HelpMenu.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>HelpMenu</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="helpmenu0.bmp" alt="[helpmenu0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Help Menu
</font><font face="Arial" color="#000100" size="6"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="3">This menu gives short cuts to documentation about distributions and functions that can be used in OpenBUGS models. It also shows a copy of the licence agreement under which the OpenBUGS software is distributed and displays a message box giving a brief summary of the version and history of the software.
</font>
</p>
</body>
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diff --git a/doc/Manuals/InferenceMenu.html b/doc/Manuals/InferenceMenu.html
new file mode 100755
index 0000000..1f654ce
--- /dev/null
+++ b/doc/Manuals/InferenceMenu.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>InferenceMenu</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="inferencemenu0.bmp" alt="[inferencemenu0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">The Inference Menu
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents</a>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#GeneralProperties">General properties</a><br> <a href="#Samples">Samples...</a><br> <a href="#Compare">Compare...</a><br> <a href="#Correlations">Correlations...</a><br> <a href="#Summary">Summary...</a><br> <a href="#Rank">Rank...</a><br> <a href="#DIC">DIC...</a><br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="GeneralProperties">
</font><font face="Courier New" color="#000100" size="5">General properties</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">[top]</a>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3">These menu items open dialog boxes for making inferences about parameters of the model. The commands are divided into three sections: the first three commands concern an entire set of monitored values for a variable; the next two commands are space-saving short-cuts that monitor running statistics; and the final command, DIC..., concerns evaluation of the
</font><font face="Arial" color="#000000" size="3"><em>Deviance Information Criterion
</em></font><font face="Arial" color="#000000" size="3"> proposed by
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Manuals/References.html#DICPaper">Spiegelhalter et al. (2002
</font><font face="Arial" color="#0000FF" size="3"><u>)
</u></font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000000" size="3">.
</font><font face="Arial" color="#000000" size="3"><strong>Users should ensure their simulation has converged before using Summary..., Rank... or DIC...
</strong></font><font face="Arial" color="#000000" size="3"><em>
</em></font><font face="Arial" color="#000000" size="3">Note that if the MCMC simulation has an adaptive phase it will not be possible to make inference using values sampled before the end of this phase.
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="Samples">
</font><font face="Courier New" color="#000100" size="5">Samples...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">[top]</a>
</font><font face="Arial" color="#000100" size="2"><br><br> <img src="inferencemenu1.bmp" alt="[inferencemenu1]"><br><br>
</font><font face="Arial" color="#000100" size="3">This command opens a non-modal dialog for analysing stored samples of variables produced by the MCMC simulation. <br><br>It is incorrect to make statistical inference about the model when the simulation is in an adaptive phase. For this reason some of the buttons in the samples dialog will be grayed out during any adaptive phase.<br><br>The dialog fields are:<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>node:
</em></strong></font><font face="Arial" color="#000100" size="3">The variable of interest must be typed in this text field. If the variable of interest is an array, slices of the array can be selected using the notation variable[lower0:upper0, lower1:upper1, ...].
</font><font face="Arial" color="#000000" size="3">The buttons at the bottom of the dialog act on this variable. A star '*' can be entered in the node text field as shorthand for all the stored samples. These buttons are arranged in two groups: the first group is associated with quantities of substantive interest while the second group gives information about how well the simulation is performing.<br><br>
</font><font face="Arial" color="#000000" size="3"><em><a id="DevianceDefinition">OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> automatically sets up a logical node to measure a quantity known as
</font><font face="Arial" color="#000000" size="3"><em>deviance</a>
</em></font><font face="Arial" color="#000000" size="3">; this may be accessed, in the same way as any other variable of interest, by typing its name, i.e. "deviance", in the
</font><font face="Arial" color="#000000" size="3"><em>node
</em></font><font face="Arial" color="#000000" size="3"> field of the
</font><font face="Arial" color="#000000" size="3"><em>Sample Monitor Tool
</em></font><font face="Arial" color="#000000" size="3">. The definition of deviance is -2 * log(likelihood): 'likelihood' is defined as p(
</font><font face="Arial" color="#000000" size="3"><em>y
</em></font><font face="Arial" color="#000000" size="3"> |
</font><font face="Arial" color="#000000" size="3"><em>theta
</em></font><font face="Arial" color="#000000" size="3"> ), where
</font><font face="Arial" color="#000000" size="3"><em>y
</em></font><font face="Arial" color="#000000" size="3"> comprises all stochastic nodes given values (i.e. data), and
</font><font face="Arial" color="#000000" size="3"><em>theta
</em></font><font face="Arial" color="#000000" size="3"> comprises the
</font><font face="Arial" color="#000000" size="3"><em>stochastic parents
</em></font><font face="Arial" color="#000000" size="3"> of
</font><font face="Arial" color="#000000" size="3"><em>y
</em></font><font face="Arial" color="#000000" size="3"> - 'stochastic parents' are the stochastic nodes upon which the distribution of
</font><font face="Arial" color="#000000" size="3"><em>y
</em></font><font face="Arial" color="#000000" size="3"> depends, when collapsing over all logical relationships.<br>
</font><font face="Arial" color="#000000" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3"><strong><em>beg
</em></strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong><em>end:
</em></strong></font><font face="Arial" color="#000100" size="3"> numerical fields used to select a subset of the stored sample for analysis.<br><br>
</font><font face="Arial" color="#000000" size="3"><strong><em>thin:
</em></strong></font><font face="Arial" color="#000000" size="3">numerical field used to select every
</font><font face="Arial" color="#000000" size="3"><em>k
</em></font><font face="Arial" color="#000000" size="3"><sup>th
</sup></font><font face="Arial" color="#000000" size="3"> iteration of each chain to contribute to the statistics being calculated, where
</font><font face="Arial" color="#000000" size="3"><em>k
</em></font><font face="Arial" color="#000000" size="3"> is the value of the field. Note the difference between this and the thinning facility on the
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Manuals/ModelMenu.html#Update">Update Tool
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000000" size="3"> dialog box: when thinning via the
</font><font face="Arial" color="#000000" size="3"><em>Update Tool
</em></font><font face="Arial" color="#000000" size="3"> we are
</font><font face="Arial" color="#000000" size="3"><em>permanently
</em></font><font face="Arial" color="#000000" size="3"> discarding samples as the MCMC simulation runs, whereas here we have already generated (and stored) a suitable number of (posterior) samples and may wish to discard some of them only temporarily. Thus, setting
</font><font face="Arial" color="#000000" size="3"><em>k
</em></font><font face="Arial" color="#000000" size="3"> > 1 here will not have any impact on the storage (memory) requirements of processing long runs; if you wish to reduce the number of samples actually stored (to free-up memory) you should thin via the
</font><font face="Arial" color="#000000" size="3"><em>Update Tool
</em></font><font face="Arial" color="#000000" size="3">.<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>chains . to .:
</em></strong></font><font face="Arial" color="#000100" size="3">can be used to select the chains which contribute to the statistics being calculated.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>clear:
</em></strong></font><font face="Arial" color="#000100" size="3"> removes the stored values of the variable from computer memory.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>set:
</em></strong></font><font face="Arial" color="#000100" size="3"> must be used to start recording a chain of values for the variable.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>stats:
</em></strong></font><font face="Arial" color="#000100" size="3"> produces summary statistics for the variable, pooling over the chains selected. The required percentiles can be selected using the
</font><font face="Arial" color="#000100" size="3"><em>percentile
</em></font><font face="Arial" color="#000100" size="3"> selection box. The quantity reported in the MC error column gives an estimate of s / N
</font><font face="Arial" color="#000100" size="3"><sup>1/2
</sup></font><font face="Arial" color="#000100" size="3">, the Monte Carlo standard error of the mean. The batch means method outlined by Roberts (1996; p.50) is used to estimate s.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>density:
</em></strong></font><font face="Arial" color="#000100" size="3"> plots a smoothed kernel density estimate for the variable if it is continuous or a histogram if it is discrete.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em><a id="SamplesDialogCODA">coda:</a>
</em></strong></font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#000100" size="3">produces an ascii representation of the monitored values suitable for use in the
</font><font face="Arial" color="#000100" size="3"><em>CODA
</em></font><font face="Arial" color="#000100" size="3"> R/Splus diagnostic package. A window for each chain is produced, corresponding to the .out files of
</font><font face="Arial" color="#000100" size="3"><em>CODA
</em></font><font face="Arial" color="#000100" size="3">, showing the iteration number and value (to four significant figures). There is also a window containing a description of which lines of the .out file correspond to which variable - this corresponds to the
</font><font face="Arial" color="#000100" size="3"><em>CODA
</em></font><font face="Arial" color="#000100" size="3"> .ind file. These can be named accordingly and saved as text files for further use. (Care may be required to stop the Windows system adding a .txt extension when saving: enclosing the required file name in quotes should prevent this.)<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>trace:
</em></strong></font><font face="Arial" color="#000100" size="3"> plots the variable value against iteration number. This trace is dynamic, being redrawn each time the screen is redrawn.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>jump:
</em></strong></font><font face="Arial" color="#000100" size="3"> plots the mean square jumping distance of nodes with updaters averaged over batches of 100 iterations. This is related to the lag one auto-correlation.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em><a id="SamplesDialogBGRDiag">bgr diag:</a>
</em></strong></font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#000100" size="3">calculates the Gelman-Rubin statistic, as modified by Brooks and Gelman (1998). The basic idea is to generate multiple chains starting at over-dispersed initial values, and assess convergence by comparing within- and between-chain variability over the second half of those chains. We denote the number of chains generated by M and the length of each chain by 2T. We take as a measure of posterior variability the width of the 100(1
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3">)% credible interval for the parameter of interest (in OpenBUGS,
</font><font face="Symbol" color="#000100" size="3">a
</font><font face="Arial" color="#000100" size="3"> = 0.2). From the final T iterations we calculate the empirical credible interval for each chain. We then calculate the average width of the intervals across the M chains and denote this by W. Finally, we calculate the width B of the empirical credible interval based on all MT samples pooled together. The ratio R = B / W of pooled to average interval widths should be greater than 1 if the starting values are suitably overdispersed; it wil [...]
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">1000. Calculating R over the final halves of iterations 1
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">100, 1
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">200, 1
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">300, ..., 1
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3">1000, say, will give a clear picture of the convergence of R to 1 (assuming the total number of iterations is sufficiently large). If we plot against the starting iteration of each range (51, 101, 151, ..., 501), then we can immediately read off the approximate point of convergence, e.g.<br><br><img src="inferencemenu2.bmp" alt="[inferencemenu2]"><br>OpenBUGS automatically chooses the number of iterations between the ends of successive ra [...]
</font><font face="Symbol" color="#000100" size="3">-
</font><font face="Arial" color="#000100" size="3"> this is simply so that they can be seen clearly on the same scale as R. Brooks and Gelman (1998) stress the importance of ensuring not only that R has converged to 1 but also that B and W have converged to stability. This strategy works because both the length of the chains used in the calculation and the start-iteration are always increasing. Hence we are guaranteed to eventually (with an increasing sample size) discard any burn-in iter [...]
</font><font face="Arial" color="#000100" size="3">(see
</font><font face="Arial" color="#0000FF" size="3"><a href="../Manuals/WinBUGSGraphics.html#GeneralProperties">OpenBUGS Graphics</a>
</font><font face="Arial" color="#000100" size="3">).<br>
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>history:
</em></strong></font><font face="Arial" color="#000100" size="3"> plots out a complete trace for the variable.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>accept:
</em></strong></font><font face="Arial" color="#000100" size="3"> plots the fraction of iterations a node with an updater changes its value over batches of 100 iterations. <br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>quantiles:
</em></strong></font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#000100" size="3">plots out the running mean with running 95% confidence intervals against iteration number.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>auto cor:
</em></strong></font><font face="Arial" color="#000100" size="3"> plots the autocorrelation function of the variable out to lag 100. <br><br>See
</font><font face="Courier New" color="#0000FF" size="3"> OpenBUGS Graphics</a>
</font><font face="Arial" color="#000100" size="3"> for details of how to customize these plots.<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Compare">Compare...</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">[top]</a>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Select
</font><font face="Arial" color="#000100" size="3"><em>Compare...
</em></font><font face="Arial" color="#000100" size="3"> from the
</font><font face="Arial" color="#000100" size="3"><em>Inference
</em></font><font face="Arial" color="#000100" size="3"> menu to open the
</font><font face="Arial" color="#000100" size="3"><em>Comparison Tool
</em></font><font face="Arial" color="#000100" size="3"> dialog box. This is designed to facilitate comparison of elements of a vector of nodes (with respect to their posterior distributions).<br><br>
</font><font face="Arial" color="#000100" size="2"><br> <img src="inferencemenu3.bmp" alt="[inferencemenu3]"><br><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>node:
</em></strong></font><font face="Arial" color="#000100" size="3"> defines the vector of nodes to be compared with each other. As the comparisons are with respect to posterior distributions,
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> must be a monitored variable.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>other:
</em></strong></font><font face="Arial" color="#000100" size="3"> where appropriate,
</font><font face="Arial" color="#000100" size="3"><em>other
</em></font><font face="Arial" color="#000100" size="3"> defines a vector of reference points to be plotted alongside each element of
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> (on the same scale), for example,
</font><font face="Arial" color="#000100" size="3"><em>other
</em></font><font face="Arial" color="#000100" size="3"> may be the observed data in a
</font><font face="Arial" color="#000100" size="3"><em>model fit
</em></font><font face="Arial" color="#000100" size="3"> plot (see below). The elements of
</font><font face="Arial" color="#000100" size="3"><em>other
</em></font><font face="Arial" color="#000100" size="3"> may be either monitored variables, in which case the posterior mean is plotted, or they may be observed/known.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>axis:
</em></strong></font><font face="Arial" color="#000100" size="3"> where appropriate,
</font><font face="Arial" color="#000100" size="3"><em>axis
</em></font><font face="Arial" color="#000100" size="3"> defines a set of values against which the elements of
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> (and
</font><font face="Arial" color="#000100" size="3"><em>other
</em></font><font face="Arial" color="#000100" size="3">) should be plotted. Each element of
</font><font face="Arial" color="#000100" size="3"><em>axis
</em></font><font face="Arial" color="#000100" size="3"> must be either known/observed or, alternatively, a monitored variable, in which case the posterior mean is used.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>Note:
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><em>other
</em></font><font face="Arial" color="#000100" size="3">, and
</font><font face="Arial" color="#000100" size="3"><em>axis
</em></font><font face="Arial" color="#000100" size="3"> should all have the same number of elements!<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>beg
</em></strong></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><strong><em>end:
</em></strong></font><font face="Arial" color="#000100" size="3"> are used to select the subset of stored samples from which the desired plot should be derived.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>box plot:
</em></strong></font><font face="Arial" color="#000100" size="3"> this command button produces a single plot in which the posterior distributions of all elements of
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> are summarised side by side. For example,<br><br>
</font><font face="Arial" color="#000100" size="2"><br><img src="inferencemenu4.bmp" alt="[inferencemenu4]"><br><br>
</font><font face="Arial" color="#000100" size="3">By default, the distributions are plotted in order of the corresponding variable's index in
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> and are also labeled with that index. Boxes represent inter-quartile ranges and the solid black line at the (approximate) centre of each box is the mean; the arms of each box extend to cover the central 95 per cent of the distribution - their ends correspond, therefore, to the 2.5% and 97.5% quantiles. (Note that this representation differs somewhat from the traditional.)<br><br>(The default value of the baseline shown on the plot i [...]
</font><font face="Arial" color="#000100" size="3"><em>Comparison Tool
</em></font><font face="Arial" color="#000100" size="3">. This can be used to interact with the plot and change the way in which it is displayed, for example, it is possible to rank the distributions by their means or medians and/or plot them on a logarithmic scale. <br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>caterpillar:
</em></strong></font><font face="Arial" color="#000100" size="3"> a "caterpillar" plot is conceptually very similar to a box plot. The only significant differences are that the inter-quartile ranges are not shown and the default scale axis is now the x-axis - each distribution is summarised by a horizontal line representing the 95% interval and a dot to show where the mean is. (Again, the default baseline - in red - is the global mean of the posterior means.) Due to their greate [...]
</font><font face="Arial" color="#000100" size="3"><strong><em>density strips:
</em></strong></font><font face="Arial" color="#000100" size="3">A density strip is similar to a box plot, but more informative. Instead of just summary statistics, it represents the entire posterior distribution through shading. A density estimate of the distribution is computed, as described in
</font><font face="Arial" color="#0000FF" size="3"><u><a href="../Manuals/WinBUGSGraphics.html#DensityPlot">Density plot</a>
</u></font><font face="Arial" color="#000100" size="3">, and the darkness of the strip at each point is defined as proportional to the estimated density. For a discussion of this shading technique see
</font><font face="Arial" color="#0000FF" size="3"><u><a href="../Manuals/References.html#DenstripPaper">Jackson (2008)</a>
</u></font><font face="Arial" color="#000100" size="3">.<br><br><img src="inferencemenu5.bmp" alt="[inferencemenu5]">
</font><font face="Arial" color="#000100" size="3"><strong><em><br>model fit:
</em></strong></font><font face="Arial" color="#000100" size="3"> the elements of
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> (and
</font><font face="Arial" color="#000100" size="3"><em>other
</em></font><font face="Arial" color="#000100" size="3"> if specified) are treated as a time-series, defined by (increasing values of) the elements of
</font><font face="Arial" color="#000100" size="3"><em>axis
</em></font><font face="Arial" color="#000100" size="3">. The posterior distribution of each element of
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> is summarised by the 2.5%, 50% and 97.5% quantiles. Each of these quantities is joined to its direct neighbours (as defined by
</font><font face="Arial" color="#000100" size="3"><em>axis
</em></font><font face="Arial" color="#000100" size="3">) by straight lines (solid red in the case of the median and dashed blue for the 95% posterior interval) to form a piecewise linear curve - the 'model fit'. In cases where
</font><font face="Arial" color="#000100" size="3"><em>other
</em></font><font face="Arial" color="#000100" size="3"> is specified, its values are also plotted, using black dots, against the corresponding values of
</font><font face="Arial" color="#000100" size="3"><em>axis
</em></font><font face="Arial" color="#000100" size="3">, e.g.<br><br>
</font><font face="Arial" color="#000100" size="2"><br> <img src="inferencemenu6.bmp" alt="[inferencemenu6]"><br><br>
</font><font face="Arial" color="#000100" size="3">Where appropriate, either or both axes can be changed to a logarithmic scale via a property editor<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>scatterplot:
</em></strong></font><font face="Arial" color="#000100" size="3"> by default, the posterior means of
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> are plotted (using blue dots) against the corresponding values of
</font><font face="Arial" color="#000100" size="3"><em>axis
</em></font><font face="Arial" color="#000100" size="3">and an exponentially weighted smoother is fitted. <br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Correlations">Correlations...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">[top]</a>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br><br> <img src="inferencemenu7.bmp" alt="[inferencemenu7]">
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="3"><br><br>This non-modal dialog box is used to plot out the relationship between the simulated values of selected variables, which must have been monitored.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>nodes
</em></strong></font><font face="Arial" color="#000100" size="3">: scalars or arrays may be entered in each box, and all combinations of variables entered in the two boxes are selected. If a single array is given, all pairwise correlations will be plotted.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>scatter:
</em></strong></font><font face="Arial" color="#000100" size="3"> produces a scatter plot of the individual simulated values.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>matrix:
</em></strong></font><font face="Arial" color="#000100" size="3"> produces a matrix summary of the cross-correlations.
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><strong><em><br>print
</em></strong></font><font face="Arial" color="#000000" size="3">: opens a new window containing the coefficients for all possible correlations among the selected variables.<br><br>The calculations may take some time.
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Summary">
</strong></font><font face="Courier New" color="#000100" size="5">Summary...
</font><font face="Arial" color="#000100" size="2">.</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">[top]</a>
</font><font face="Arial" color="#000100" size="2"><strong><br><br> <img src="inferencemenu8.bmp" alt="[inferencemenu8]">
</strong></font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><br>This non modal dialog box is used to
</font><font face="Arial" color="#000000" size="3"> calculate running means, standard deviations and quantiles. Th
</font><font face="Arial" color="#000100" size="3">e commands in this dialog are less powerful and general than those in the
</font><font face="Arial" color="#000100" size="3"><em> Sample Monitor Too
</em></font><font face="Arial" color="#000100" size="3">l, but they also require much less storage (an important consideration when many variables and/or long runs are of interest).<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>node:
</em></strong></font><font face="Arial" color="#000100" size="3"> The variable of interest must be typed in this text field.
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3"><strong><em><br>set
</em></strong></font><font face="Arial" color="#000100" size="3">: starts recording the running totals for
</font><font face="Arial" color="#000100" size="3"><em> nod
</em></font><font face="Arial" color="#000100" size="3">e.<br>
</font><font face="Arial" color="#000000" size="3"><strong><em><br>stats
</em></strong></font><font face="Arial" color="#000000" size="3"><strong>:
</strong></font><font face="Arial" color="#000000" size="3"> displays the running means, standard deviations, and 2.5%, 50% (median) and 97.5% quantiles for
</font><font face="Arial" color="#000000" size="3"><em> nod
</em></font><font face="Arial" color="#000000" size="3">e.
</font><font face="Arial" color="#000000" size="3"><strong> Note that these running quantiles are calculated via an approximate algorithm
</strong></font><font face="Arial" color="#000000" size="3">(see
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Manuals/References.html#RunningQuantilesReference">here
</font><font face="Arial" color="#000000" size="3"></a> for details)
</font><font face="Arial" color="#000000" size="3"><strong> and should therefore be used with caution
</strong></font><font face="Arial" color="#000000" size="3">.
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>means
</em></strong></font><font face="Arial" color="#000100" size="3">: displays the running means for
</font><font face="Arial" color="#000100" size="3"><em> nod
</em></font><font face="Arial" color="#000100" size="3">e in a comma delimited form. This can be useful for passing the results to other statistical or display packages.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>clear:
</em></strong></font><font face="Arial" color="#000100" size="3"> removes the running totals for
</font><font face="Arial" color="#000100" size="3"><em> nod
</em></font><font face="Arial" color="#000100" size="3">e.<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Rank">
</strong></font><font face="Courier New" color="#000100" size="5">Rank...
</font><font face="Arial" color="#000100" size="2">.</a>
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">[top]</a>
</font><font face="Arial" color="#000100" size="2"><br><br> <img src="inferencemenu9.bmp" alt="[inferencemenu9]"><br>
</font><font face="Arial" color="#000100" size="3"><br><br>This non-modal dialog box is used to store and display the ranks of the simulated values in an array.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>node
</em></strong></font><font face="Arial" color="#000100" size="3"><em>:
</em></font><font face="Arial" color="#000100" size="3"> the variable to be ranked must be typed in this text field (must be an array).<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>set
</em></strong></font><font face="Arial" color="#000100" size="3">: starts building running histograms to represent the rank of each component of
</font><font face="Arial" color="#000100" size="3"><em> nod
</em></font><font face="Arial" color="#000100" size="3">e. An amount of storage proportional to the square of the number of components of
</font><font face="Arial" color="#000100" size="3"><em> nod
</em></font><font face="Arial" color="#000100" size="3">e is allocated. Even when
</font><font face="Arial" color="#000100" size="3"><em> nod
</em></font><font face="Arial" color="#000100" size="3">e has thousands of components this can require less storage than calculating the ranks explicitly in the model specification and storing their samples, and it is also much quicker.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>stats
</em></strong></font><font face="Arial" color="#000100" size="3"><strong>:
</strong></font><font face="Arial" color="#000100" size="3"> summarises the distribution of the ranks of each component of the variable
</font><font face="Arial" color="#000100" size="3"><em> nod
</em></font><font face="Arial" color="#000100" size="3">e. The quantiles highlighted in the percentile selection box are displayed.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>histogram
</em></strong></font><font face="Arial" color="#000100" size="3"><strong>:
</strong></font><font face="Arial" color="#000100" size="3"> displays the empirical distribution of the simulated rank of each component of the variable
</font><font face="Arial" color="#000100" size="3"><em> nod
</em></font><font face="Arial" color="#000100" size="3">e.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>clear
</em></strong></font><font face="Arial" color="#000100" size="3">: removes the running histograms for
</font><font face="Arial" color="#000100" size="3"><em> nod
</em></font><font face="Arial" color="#000100" size="3">e.<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="DIC">
</strong></font><font face="Courier New" color="#000100" size="5">DIC...
</font><font face="Arial" color="#000100" size="2">.</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="#Contents">[top]</a>
</font><font face="Arial" color="#000100" size="2"><br><br><br> <img src="inferencemenu10.bmp" alt="[inferencemenu10]">
</font><font face="Arial" color="#FF00FF" size="2"><br>
</font><font face="Arial" color="#FF00FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>The
</font><font face="Arial" color="#000000" size="3"><em> DIC Too
</em></font><font face="Arial" color="#000000" size="3">l dialog box is used to evaluate the
</font><font face="Arial" color="#000000" size="3"><em> Deviance Information Criterio
</em></font><font face="Arial" color="#000000" size="3">n (DIC;
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Manuals/References.html#DICPaper">Spiegelhalter et al., 2002</a>
</font><font face="Arial" color="#000000" size="3">) and related statistics
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3">- these can be used to assess model complexity and compare different models. Most of the
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Volumeii.html">examples
</font><font face="Arial" color="#000000" size="3"></a> packaged with
</font><font face="Arial" color="#000000" size="3"><em> OpenBUG
</em></font><font face="Arial" color="#000000" size="3">S contain an example of their usage.<br>
</font><font face="Arial" color="#000000" size="3"><strong><br>It is important to note that DIC assumes the posterior mean to be a good estimate of the stochastic parameters. If this is not so, say because of extreme skewness or even bimodality, then DIC may not be appropriate. There are also circumstances, such as with mixture models, in which OpenBUGS will not permit the calculation of DIC and so the menu option is grayed out. Please see the OpenBUGS web-page for current restrictions:
</strong></font><font face="Arial" color="#FF0000" size="3"><strong><br><br>
</strong></font><font face="Arial" color="#000000" size="3">https://openbugs.info<br>
</font><font face="Arial" color="#000000" size="3"><strong><em><br>set
</em></strong></font><font face="Arial" color="#000000" size="3">: starts calculating DIC and related statistics - the user should ensure that convergence has been achieved before pressing
</font><font face="Arial" color="#000000" size="3"><em> se
</em></font><font face="Arial" color="#000000" size="3">t as all subsequent iterations will be used in the calculation.<br>
</font><font face="Arial" color="#000000" size="3"><strong><em><br>clear
</em></strong></font><font face="Arial" color="#000000" size="3">: if a DIC calculation has been started (via
</font><font face="Arial" color="#000000" size="3"><em> se
</em></font><font face="Arial" color="#000000" size="3">t) this will clear it from memory, so that it may be restarted later.<br>
</font><font face="Arial" color="#000000" size="3"><strong><em><br>stats
</em></strong></font><font face="Arial" color="#000000" size="3">: displays the calculated statistics, as described below; see
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/References.html#DICPaper">Spiegelhalter et al. (2002)
</font><font face="Arial" color="#000000" size="3"></a> for full details; the section
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/Tricks.html">Advanced Use of the BUGS Language</a>
</font><font face="Arial" color="#000000" size="3"> also contains some comments on the use of DIC.<br><br>The stats button generates the following statistics:<br>
</font><font face="Arial" color="#000000" size="3"><strong><br>Dbar
</strong></font><font face="Arial" color="#000000" size="3">: this is the posterior mean of the deviance, which is exactly the same as if the node 'deviance' had been monitored (see
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#DevianceDefinition">here</a>
</font><font face="Arial" color="#000000" size="3">). This deviance is defined as -2 * log(likelihood): 'likelihood' is defined as p(y |
</font><font face="Arial" color="#000000" size="3"><em> thet
</em></font><font face="Arial" color="#000000" size="3">a), where
</font><font face="Arial" color="#000000" size="3"><em>
</em></font><font face="Arial" color="#000000" size="3">y comprises all stochastic nodes given values (i.e. data), and
</font><font face="Arial" color="#000000" size="3"><em> thet
</em></font><font face="Arial" color="#000000" size="3">a comprises the
</font><font face="Arial" color="#000000" size="3"><em> stochastic parent
</em></font><font face="Arial" color="#000000" size="3">s of
</font><font face="Arial" color="#000000" size="3"><em>
</em></font><font face="Arial" color="#000000" size="3">y - 'stochastic parents' are the stochastic nodes upon which the distribution of
</font><font face="Arial" color="#000000" size="3"><em>
</em></font><font face="Arial" color="#000000" size="3">y depends, when collapsing over all logical relationships.<br>
</font><font face="Arial" color="#000000" size="3"><strong><br>Dhat
</strong></font><font face="Arial" color="#000000" size="3">: this is a point estimate of the deviance (-2 * log(likelihood)) obtained by substituting in the posterior means
</font><font face="Arial" color="#000000" size="3"><em> theta.ba
</em></font><font face="Arial" color="#000000" size="3">r of
</font><font face="Arial" color="#000000" size="3"><em> thet
</em></font><font face="Arial" color="#000000" size="3">a: thus Dhat = -2 * log(p(y |
</font><font face="Arial" color="#000000" size="3"><em>theta.ba
</em></font><font face="Arial" color="#000000" size="3">r))
</font><font face="Arial" color="#000000" size="3"><em>.
</em></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><strong><br>pD
</strong></font><font face="Arial" color="#000000" size="3">: this is 'the effective number of parameters', and is given by
</font><font face="Arial" color="#000000" size="3"><strong> pD = Dbar - Dha
</strong></font><font face="Arial" color="#000000" size="3">t. Thus pD is the posterior mean of the deviance minus the deviance of the posterior means.<br>
</font><font face="Arial" color="#000000" size="3"><strong><br>DIC
</strong></font><font face="Arial" color="#000000" size="3">: this is the 'Deviance Information Criterion', and is given by
</font><font face="Arial" color="#000000" size="3"><strong> DIC = Dbar + pD
</strong></font><font face="Arial" color="#000000" size="3">or
</font><font face="Arial" color="#000000" size="3"><strong><br>DIC = Dhat + 2 * pD
</strong></font><font face="Arial" color="#000000" size="3">. The model with the smallest DIC is estimated to be the model that would best predict a replicate dataset of the same structure as that currently observed
</font><font face="Arial" color="#000000" size="3"><strong>.
</strong></font><font face="Arial" color="#000000" size="3"><br><br>
</font>
</p>
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<html>
<head>
<title>InfoMenu</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="infomenu0.bmp" alt="[infomenu0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">The Info Menu
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#GeneralProperties">General properties</a><br> <a href="#OpenLog">Open Log</a><br> <a href="#ClearLog">Clear Log</a><br> <a href="#NodeInfo">Node info...</a><br> <a href="#Uninitnodes">Uninitialized nodes</a><br> <a href="#Updatersbyname">Updaters by name</a><br> <a h [...]
</font><font face="Arial" color="#000100" size="2"><br><a id="GeneralProperties">
</font><font face="Courier New" color="#000100" size="5">General properties
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">This menu allows the user to obtain more information about how the software is working.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="OpenLog">
</font><font face="Courier New" color="#000100" size="5">Open Log</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">This option opens a log window to which error and status information is written.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="ClearLog">
</font><font face="Courier New" color="#000100" size="5">Clear Log
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">This option clears all the information displayed in the log window.<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="NodeInfo">Node info...</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2"> <img src="infomenu1.bmp" alt="[infomenu1]"><br><br>
</font><font face="Arial" color="#000100" size="3">This dialog box allows information about particular nodes in the model to be obtained. The model must be compiled before this dialog can be used. <br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>node:
</em></strong></font><font face="Arial" color="#000100" size="3"> the name of the node for which information is required should be typed here or selected from the drop down list.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>values:
</em></strong></font><font face="Arial" color="#000100" size="3"> displays the current value of the node (for each chain).<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>methods:
</em></strong></font><font face="Arial" color="#000100" size="3"> displays the type of updater used to sample from the node (if appropriate).<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>type:
</em></strong></font><font face="Arial" color="#000100" size="3"> displays the type used to represent the node.<br><br>As an example of using this dialog compile the Seeds model and then type the node name alpha0 into the node field.<br><br>
</font><font face="Arial" color="#000000" size="3">Clicking the value button opens a window displaying<br><br> <img src="infomenu2.bmp" alt="[infomenu2]"><br> <br>The model has been compiled with one chain and the current value of the alpha0 variable is 0.0<br><br>Clicking on the methods button opens a window displaying<br><br> <img [...]
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Uninitnodes">
</font><font face="Courier New" color="#000100" size="5">Uninitialized nodes
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">Shows nodes in the compiled model that have not been initialized yet. A new window is opened for each chain. <br><br>Again consider the Seeds example, compile the model and load the initial value file and then selected the Uninitialized node option, a window will open containing<br><br> <img src="infomenu5.bmp" alt="[infomenu5]"><br> [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Updatersbyname">
</font><font face="Courier New" color="#000100" size="5">Updaters by name
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">List the nodes which have associated updaters in alphabetical order with their updater algorithm. For block updating algorithms the first component in the block is shown followed by the other components of the block in angle brackets. Note for block updaters the first component might not be the node with the first name alphabetically.<br><br>For the Seeds example this option opens a window containing<br><br> & [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Updatersbydepth">
</font><font face="Courier New" color="#000100" size="5">Updaters by depth
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">List the nodes which have associated updaters in the reverse topological order to which they occur in the graphical model with their updater algorithm. Nodes in the model which are forward sampled have a negative depth. For block updating algorithms the first component in the block is shown followed by the other components of the block in angle brackets. Note for block updaters the first component might not be the node with the first name [...]
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Modules">
</font><font face="Courier New" color="#000100" size="5">Modules
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Displays all the modules (dynamic link libraries) in use. A typical window produced by this option would look like<br><br><img src="infomenu8.bmp" alt="[infomenu8]"><br><br>The modules are arranged in a directed acyclic graph where Clients gives the number of children each module has. Version is the current version of the module, Maintainer is the person who maintains the model (some times this is unknown), Compiled was the date when the [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font>
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<html>
<head>
<title>Introduction</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="introduction0.bmp" alt="[introduction0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Introduction
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#IntroductionThisManual">Introduction to OpenBUGS</a><br> <a href="#IntroductionAdviceForNewUsers">Advice for new users</a><br> <a href="#IntroductionMCMCMethods">MCMC methods</a><br>
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#0000FF" size="4">
</font><font face="Arial" color="#0000FF" size="4"><u><br>
</u></font><font face="Arial" color="#0000FF" size="2"><u><br>
</u></font><font face="Courier New" color="#000100" size="5"><a id="IntroductionThisManual">Introduction to OpenBUGS
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>This manual describes the
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> software - a program for Bayesian analysis of complex statistical models using Markov chain Monte Carlo (MCMC) techniques.
</font><font face="Arial" color="#000100" size="3"><strong>
</strong></font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> allows models to be described using the
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language, or as
</font><font face="Arial" color="#000100" size="3"><em>Doodles
</em></font><font face="Arial" color="#000100" size="3"> (graphical representations of models) which can, if desired, be translated to a text-based description. The
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language is more flexible than the Doodles graphical representation.
</font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong>Users are advised that this manual only concerns the syntax and functionality of
</strong></font><font face="Arial" color="#000100" size="3"><strong><em>OpenBUGS
</em></strong></font><font face="Arial" color="#000100" size="3"><strong>, and does not deal with issues of Bayesian reasoning, prior distributions, statistical modelling, monitoring convergence, and so on.
</strong></font><font face="Arial" color="#000100" size="3">If you are new to MCMC, you are strongly advised to use this software in conjunction with a course in which the strengths and weaknesses of this procedure are described. Please note the disclaimer at the beginning of this manual.<br><br>There is a large literature on Bayesian analysis and MCMC methods. For further reading, see, for example, Carlin and Louis (1996), Gelman et al (1995), Gilks, Richardson and Spiegelhalter (1996): [...]
</font><font face="Arial" color="#000100" size="3"><em>Classic
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> manual, 'Topics in Modelling', discusses 'non-informative' priors, model criticism, ranking, measurement error, conditional likelihoods, parameterisation, spatial models and so on, while the
</font><font face="Arial" color="#000100" size="3"><em>CODA
</em></font><font face="Arial" color="#000100" size="3"> documentation considers convergence diagnostics. Congdon (2001) shows how to analyse a very wide range of models using
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3">. The
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> website provides additional links to sites of interest, some of which provide extensive examples and tutorial material.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="IntroductionAdviceForNewUsers">
</font><font face="Courier New" color="#000100" size="5">Advice for new users
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>If you are using
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> for the first time, the following stages might be reasonable:<br><br>1. Step through the
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/Tutorial.html">simple worked example
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> in the tutorial.<br><br>2. Try other examples provided with this release (see
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Examples/Volumei.html">Examples Volume 1
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000000" size="3">,
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Volumeii.html">Examples Volume 2
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Volumeiii.html">Examples Volume 3
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">)<br><br>3. Edit the
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language of an example model to fit an example of your own.<br><br>
</font><font face="Arial" color="#000000" size="3">If you are interested in using Doodles:<br><br>
</font><font face="Arial" color="#000100" size="3">4. Try editing an existing Doodle (e.g. from
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Volumei.html">Examples Volume 1
</font><font face="Arial" color="#000100" size="3"></a>), perhaps to fit a problem of your own.<br><br>5. Try constructing a Doodle from scratch.<br><br>Note that there are many features in the
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language that cannot be expressed with Doodles. If you wish to proceed to serious, non-educational use, you may want to dispense with
</font><font face="Arial" color="#000100" size="3"><em>DoodleBUGS
</em></font><font face="Arial" color="#000100" size="3"> entirely, or just use it for initially setting up a simplified model that can be elaborated later using the
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language. Unfortunately we do not have a program to back-translate from a text-based model description to a Doodle!<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="IntroductionMCMCMethods">
</font><font face="Courier New" color="#000100" size="5">MCMC methods</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>Users should already be aware of the background to Bayesian Markov Chain Monte Carlo (MCMC) methods: see for example Gilks
</font><font face="Arial" color="#000100" size="3"><em>et al
</em></font><font face="Arial" color="#000100" size="3"> (1996). Having specified the model as a full joint distribution on all quantities, whether parameters or observables, we wish to sample values of the unknown parameters from their conditional (posterior) distribution given those stochastic nodes (see model specification section) that have been observed. OpenBUGS uses three families of MCMC algorithms: Gibbs, Metropolis Hasting and slice sampling.<br><br>The basic idea behind the Gib [...]
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> tries to block update groups of nodes that are likely to correlated based on the structure of the model. If
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> is unable to set up block updaters for some nodes in the model, it simulates the remaining nodes using single site updating. This can make convergence very slow and the program very inefficient for models with strongly related parameters.<br><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font>
</p>
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<html>
<head>
<title>Manual</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="manual0.bmp" alt="[manual0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">OpenBUGS User Manual
</font><font face="Arial" color="#000100" size="6"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="4"> Version 3.2.3 March 2014
</font><font face="Arial" color="#000100" size="2"><br><br><br><br>
</font><font face="Arial" color="#000100" size="3"> David Spiegelhalter
</font><font face="Arial" color="#000100" size="1"><sup>1
</sup></font><font face="Arial" color="#000100" size="3"> Andrew Thomas
</font><font face="Arial" color="#000100" size="1"><sup>2
</sup></font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">Nicky Best
</font><font face="Arial" color="#000100" size="1"><sup>3
</sup></font><font face="Arial" color="#000100" size="3">Dave Lunn
</font><font face="Arial" color="#000100" size="1"><sup>1
</sup></font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="1"><sup>1
</sup></font><font face="Arial" color="#000100" size="3">MRC Biostatistics Unit,
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="1"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">Dept of Mathematics & Statistics,<br> Institute of Public Health, University of St Andrews<br> Robinson Way, St Andrews<br> Cambridge CB2 2SR, UK Scotland
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1"><sup>3
</sup></font><font face="Arial" color="#000100" size="3">Department of Epidemiology & Public Health,<br> Imperial College School of Medicine,<br> Norfolk Place,<br> London W2 1PG, UK<br><br> e-mail:<br> bugs at mrc-bsu.cam.ac.uk [general]<br> helsinkiant at gmail.com [ [...]
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#000100" size="3"><strong>This manual describes how to use the OpenBUGS software. It starts with general sections on setting up statistical models in OpenBUGS and using Markov Chain Monte Carlo sampling for statistical inference. Then the idea of compound documents and the many menu options of the Windows interface to OpenBUGS are described in detail.<br><br><br>The OpenBUGS software is Open Source
</strong></font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/GNU-Licence.html">please click here to read the legal bit</a>
</font><font face="Arial" color="#000100" size="3"><br><br>Potential users are reminded to be extremely careful if using this program for serious statistical analysis. We have tested the program on quite a wide set of examples, but be particularly careful with types of model that are currently not featured. If there is a problem,
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> might just crash, which is not very good, but it might well carry on and produce answers that are wrong, which is even worse. Please let us know of any successes or failures.<br><br>
</font><font face="Arial" color="#FF0000" size="5"><strong>Beware: MCMC sampling can be dangerous!
</strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#0000FF" size="2"><br>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/Contents.html">
</font><font face="Courier New" color="#0000FF" size="6">Contents
</font><font face="Courier New" color="#0000FF" size="3"></a>
</font>
</p>
</body>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ManualsMenu</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="manualsmenu0.bmp" alt="[manualsmenu0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Manuals Menu
</font><font face="Arial" color="#000100" size="6"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="3">This menu gives access to the various manuals describing the use of the OpenBUGS software. The first group of options opens the contents pages of the manuals as hyper-text documents. Clicking on the blue links will open further windows displaying the contents of the manuals. The second group of options prints a copy of the manuals. If a physical printer is the default printer the result is a paper. If the default printer is set t [...]
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ModelMenu</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="modelmenu0.bmp" alt="[modelmenu0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">The Model Menu
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#GeneralProperties">General properties</a><br> <a href="#Specification">Specification...</a><br> <a href="#Update">Update...</a><br> <a href="#SaveState">Save State</a><br> <a href="#Seed">Random number generator...</a><br> <a href="#Script">Script</a><br> <a href="#Prettyprinting"> [...]
</font><font face="Arial" color="#0000FF" size="4">
</font><font face="Arial" color="#000100" size="2"><br><a id="GeneralProperties">
</font><font face="Courier New" color="#000100" size="5">General properties</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The commands in this menu either apply to the whole statistical model or open dialog boxes. <br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="Specification">
</font><font face="Courier New" color="#000100" size="5">Specification...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br><br> <img src="modelmenu1.bmp" alt="[modelmenu1]"><br><br>
</font><font face="Arial" color="#000100" size="3"><br>This non-modal dialog box acts on the focus view (the window with its title bar highlighted).<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>check model
</em></strong></font><font face="Arial" color="#000100" size="3">: If the focus view contains text,
</font><font face="Arial" color="#000100" size="3"><em> OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> assumes the model is specified in the
</font><font face="Arial" color="#000100" size="3"><em> BUG
</em></font><font face="Arial" color="#000100" size="3">S language. The
</font><font face="Arial" color="#000100" size="3"><em> check model
</em></font><font face="Arial" color="#000100" size="3"> button parses the
</font><font face="Arial" color="#000100" size="3"><em> BUG
</em></font><font face="Arial" color="#000100" size="3">S language description of the statistical model. If a syntax error is detected the cursor is placed where the error was found and a description of the error is
</font><font face="Arial" color="#000000" size="3"> given on the status line (lower left corner of screen). If no syntax errors are found, the message
</font><font face="Arial" color="#004080" size="3">"model is syntactically correct"
</font><font face="Arial" color="#000000" size="3"> should appear in the status line. If
</font><font face="Arial" color="#000100" size="3">text is highlighted, parsing starts from the first character highlighted
</font><font face="Arial" color="#000100" size="3"><em>(
</em></font><font face="Arial" color="#000100" size="3">i.e. highlight the word
</font><font face="Courier New" color="#000100" size="3">model
</font><font face="Arial" color="#000100" size="3">), otherwise parsing starts at the top of the window even if the cursor is currently in a different location..<br><br>If the focus view is a
</font><font face="Arial" color="#000100" size="3"><em>Doodle
</em></font><font face="Arial" color="#000100" size="3"> or contains a selected
</font><font face="Arial" color="#000100" size="3"><em> Doodle (i.e.
</em></font><font face="Arial" color="#000100" size="3"> the Doodle has been selected and is surrounded by a hairy border
</font><font face="Arial" color="#000100" size="3"><em>), OpenBUG
</em></font><font face="Arial" color="#000100" size="3">S assumes the model has been specified graphically. If a syntax error is detected the node where the error was found is highlighted and a description of the error is given on the status line.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>load data:
</em></strong></font><font face="Arial" color="#000100" size="3"> The
</font><font face="Arial" color="#000100" size="3"><em> load dat
</em></font><font face="Arial" color="#000100" size="3">a button acts on the focus view; it will be grayed out unless the focus view contains text and a syntactically correct model has been checked.<br><br>Data can be identified in two ways:<br><br>1) if the data are in a separate document, the window containing that document needs to be the focus view when the
</font><font face="Arial" color="#000100" size="3"><em> load dat
</em></font><font face="Arial" color="#000100" size="3">a command is used;<br>2) if the data are specified as part of a document, the first character of the data (either the word
</font><font face="Courier New" color="#000100" size="3">list
</font><font face="Arial" color="#000100" size="3"> if in S-Plus format, or the first array name if in rectangular format) must be highlighted and the data will be read starting with the first highlighted character.<br><br>See
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/ModelSpecification.html#FormattingOfData">Formatting of data</a>
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000100" size="3">for details of how the data should be formatted.
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>Any syntax errors or data inconsistencies are displayed in the status line. Corrections can be made to the data without returning to th
</font><font face="Arial" color="#000100" size="3"><em>e check mode
</em></font><font face="Arial" color="#000100" size="3">l stage. When the data have been loaded successfully,
</font><font face="Arial" color="#004080" size="3">"Data Loaded"
</font><font face="Arial" color="#000100" size="3"> should appear in the status line.<br><br>The
</font><font face="Arial" color="#000100" size="3"><em> load dat
</em></font><font face="Arial" color="#000100" size="3">a button becomes active once a model has been successfully checked, and ceases to be active once the model has been successfully compiled.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>num of chains:
</em></strong></font><font face="Arial" color="#000100" size="3"> The number of chains to be simulated can be entered into the text entry field next to the caption
</font><font face="Arial" color="#000100" size="3"><em> num of chains
</em></font><font face="Arial" color="#000100" size="3">. This field can be typed in after the model has been checked and before the model has been compiled. By default, one chain is simulated.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>compile:
</em></strong></font><font face="Arial" color="#000100" size="3"> The
</font><font face="Arial" color="#000100" size="3"><em> compil
</em></font><font face="Arial" color="#000100" size="3">e button builds the data structures needed to carry out MCMC sampling. The model is checked for completeness and consistency with the data. Any inconsistencies or errors are displayed on the status line.<br><br>A node called 'deviance' is automatically created which calculates minus twice the log-likelihood at each iteration, up to a constant. This node can be used like any other node in the graphical model.<br><br>This command becom [...]
</font><font face="Arial" color="#004080" size="3">model compiled
</font><font face="Arial" color="#000100" size="3">' should appear in the status line. <br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>load inits:
</em></strong></font><font face="Arial" color="#000100" size="3"> The
</font><font face="Arial" color="#000100" size="3"><em> load init
</em></font><font face="Arial" color="#000100" size="3">s button acts on the focus view; it will be grayed out unless the focus view contains text. The initial values will be loaded for the chain indicated in the text entry field to the right of the caption
</font><font face="Arial" color="#000100" size="3"><em> for chai
</em></font><font face="Arial" color="#000100" size="3">n. The value of this text field can be edited to load initial values for any of the chains.<br><br>Initial values are specified in exactly the same way as data files. If some of the elements in an array are known (say because they are constraints in a parameterisation), those elements should be specified as missing (NA) in the initial values file.<br><br>This command becomes active once the model has been successfully compiled, and c [...]
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#004080" size="3">"initial values loaded: model initialized"
</font><font face="Arial" color="#000100" size="3">. Otherwise the status line will show the message
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#004080" size="3">"initial values loaded but this or another chain contain uninitialized variables"
</font><font face="Arial" color="#000100" size="3">. The second message can have several meanings:<br><br>a) If only one chain is simulated it means that the chain contains some nodes that have not been initialized yet.<br>b) If several chains are to be simulated it could mean that no initial values have been loaded for one of the chains.<br><br>In either case further initial values can be loaded, or the
</font><font face="Arial" color="#000100" size="3"><em> gen init
</em></font><font face="Arial" color="#000100" size="3">s button can be pressed to generate initial values for
</font><font face="Arial" color="#000100" size="3"><em> all
</em></font><font face="Arial" color="#000100" size="3"> the uninitialized nodes in
</font><font face="Arial" color="#000100" size="3"><em> all
</em></font><font face="Arial" color="#000100" size="3"> the simulated chains. See the 'gen inits' section below for a description of how the values are generated.<br><br>Generally it is recommended to load initial values for all fixed effect nodes (founder nodes with no parents) for all chains, initial values for random effects can be generated using the
</font><font face="Arial" color="#000100" size="3"><em> gen init
</em></font><font face="Arial" color="#000100" size="3">s button.<br><br>The
</font><font face="Arial" color="#000100" size="3"><em> load init
</em></font><font face="Arial" color="#000100" size="3">s button can still be executed once the MCMC sampling has been started. It will have the effect of starting the sampler out on a new trajectory. A modal warning message will appear if the command is used in this context.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>gen inits:
</em></strong></font><font face="Arial" color="#000100" size="3"> The
</font><font face="Arial" color="#000100" size="3"><em> gen init
</em></font><font face="Arial" color="#000100" size="3">s button attempts to generate initial values by sampling either from the prior or from an approximation to the prior. In the case of discrete variables a check is made that a configuration of zero probability is not generated. This command can generate extreme values if any of the priors are very vague. If the command is successful the message
</font><font face="Arial" color="#004080" size="3">"initial values generated: model initialized"
</font><font face="Arial" color="#000100" size="3"> is displayed otherwise the message
</font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#004080" size="3">"could not generate initial values"
</font><font face="Arial" color="#000000" size="3"> is displayed
</font><font face="Arial" color="#000100" size="3">.<br><br>The
</font><font face="Arial" color="#000100" size="3"><em> gen init
</em></font><font face="Arial" color="#000100" size="3">s button becomes active once the model has been successfully compiled, and will cease to be active once the model has been initialized.<br><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="Update">
</strong></font><font face="Courier New" color="#000100" size="5">Update...
</font><font face="Arial" color="#000100" size="3">.</a>
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="3"><br> <img src="modelmenu2.bmp" alt="[modelmenu2]"><br><br>This menu will become active after the model has been compiled and initialized. It has the following fields that accept user input:
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3"><strong><em><br>updates
</em></strong></font><font face="Arial" color="#000100" size="3">:
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">The number of MCMC samples to save. Thus,
</font><font face="Arial" color="#000100" size="3"><em>update
</em></font><font face="Arial" color="#000100" size="3">s *
</font><font face="Arial" color="#000100" size="3"><em> thin
</em></font><font face="Arial" color="#000100" size="3"> MCMC updates will be carried out.
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3"><strong><em><br>refresh
</em></strong></font><font face="Arial" color="#000100" size="3">: The number of updates divided by
</font><font face="Arial" color="#000100" size="3"><em> thin
</em></font><font face="Arial" color="#000100" size="3"> between redrawing the screen.<br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>thin
</em></strong></font><font face="Arial" color="#000100" size="3">: The samples from every
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">k
</font><font face="Arial" color="#000100" size="3"><sup>th
</sup></font><font face="Arial" color="#000100" size="3"> iteration will be used for inference, where
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">k is the value of
</font><font face="Arial" color="#000100" size="3"><em> thin
</em></font><font face="Arial" color="#000100" size="3">. Setting
</font><font face="Arial" color="#000100" size="3"><em> k
</em></font><font face="Arial" color="#000100" size="3"> > 1 can help to reduce the autocorrelation in the sample, but there is no real advantage in thinning except to reduce storage requirements.
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000000" size="3"><strong><em><br>
</em></strong></font><font face="Arial" color="#000100" size="3"><strong><em>over relax
</em></strong></font><font face="Arial" color="#000100" size="3">: Click on this box (a tick will then appear) to select an over-relaxed form of MCMC (Neal, 1998) which will be executed where possible. This generates multiple samples at each iteration and then selects one that is negatively correlated with the current value. The time per iteration will be increased, but the within-chain correlations should be reduced and hence fewer iterations may be necessary. However, this method is not [...]
</font><font face="Arial" color="#000100" size="3"><strong><em><br>
</em></strong></font><font face="Arial" color="#000000" size="3">Click on the
</font><font face="Arial" color="#000000" size="3"><strong><em>update button
</em></strong></font><font face="Arial" color="#000000" size="3"> to start updating the model. Clicking on
</font><font face="Arial" color="#000000" size="3"><em>
</em></font><font face="Arial" color="#000000" size="3">the update button
</font><font face="Arial" color="#000000" size="3"><strong><em>
</em></strong></font><font face="Arial" color="#000000" size="3">during sampling will pause the simulation after the current block of iterations, as defined by
</font><font face="Arial" color="#000000" size="3"><em> refres
</em></font><font face="Arial" color="#000000" size="3">h, has been completed; the number of updates required can then be changed if needed. Clicking on the update button again will restart the simulation. This button becomes active when the model has been successfully compiled and given initial values.<br>
</font><font face="Arial" color="#000000" size="3"><strong><em><br>
</em></strong></font><font face="Arial" color="#000000" size="3">The
</font><font face="Arial" color="#000000" size="3"><strong><em>iteration
</em></strong></font><font face="Arial" color="#000000" size="3"> field displays the total number of MCMC updates divided by
</font><font face="Arial" color="#000000" size="3"><em>thin
</em></font><font face="Arial" color="#000000" size="3"> that have been carried out.
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>
</em></strong></font><font face="Arial" color="#000100" size="3">The
</font><font face="Arial" color="#000100" size="3"><strong><em>adapting
</em></strong></font><font face="Arial" color="#000100" size="3">box will be ticked while the Metropolis or slice-sampling MCMC algorithm is in its initial tuning phase where some optimization parameters are tuned.
</font><font face="Arial" color="#000000" size="3">The Metropolis and slice-sampling algorithms have adaptive phases of 4000 and 500 iterations respectively which will be discarded from all statistics. For details on how to change these default settings please see the <a href="#Updateroptions">
</font><font face="Arial" color="#0000FF" size="3">Updater Options
</font><font face="Arial" color="#000000" size="3"></a> section
</font><font face="Arial" color="#0000FF" size="3">.<br><br>
</font><font face="Arial" color="#000100" size="3">When there are multiple chains, a single update is generated for each chain and then the cycle is repeated for the requested number of updates. Random numbers are currently generated from a single random number sequence shared across the chains. When thin>1, thinned updates are drawn from the first chain, then thinned updates are generated from the second chain, and so on. However if thin=1, and the monitored samples are thinned via
</font><font face="Arial" color="#000100" size="3"><em>Inference > Samples
</em></font><font face="Arial" color="#000100" size="3">, the output<br>will be different, since we are then looping over chains within each iteration.
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="SaveState">
</strong></font><font face="Courier New" color="#000100" size="5">Save State</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br>The current state of all the stochastic variables in the model are displayed in S-Plus format with a separate window for each chain. These can be used as an initial value file for future runs.
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Seed">
</strong></font><font face="Courier New" color="#000100" size="5">Random number generator...
</font><font face="Arial" color="#000100" size="2">.</a>
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="2"><br><br> <img src="modelmenu3.bmp" alt="[modelmenu3]"><br><br>
</font><font face="Arial" color="#000100" size="3">Opens a non-modal dialog box, which is available only after compilation is completed and before any updates have been performed. The state can be changed after initial values are generated but before updates have been performed, however, this is not recommended.<br><br>The internal state of the random number generator can be set to one of 14 predefined states using the up down arrows. Each predefined state is 10
</font><font face="Arial" color="#000100" size="1"><sup>12
</sup></font><font face="Arial" color="#000100" size="3"> draws apart to avoid overlap in random number sequences.
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#FF00FF" size="3"><br>
</font><font face="Arial" color="#FF00FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Script">
</font><font face="Courier New" color="#000100" size="5">Script
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3">The Script menu item is used to execute "batch scripts" from the GUI-mode. If the focus-view contains a series of
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> batch-mode commands, then selecting the script menu item from the
</font><font face="Arial" color="#000000" size="3"><em>Model
</em></font><font face="Arial" color="#000000" size="3"> menu will cause the script to be executed. A subset of the script commands can be executed by highlighting them. Highlighting part of a batch command will likely produce an error. The script menu item allows batch mode execution to be mixed with GUI execution so batch scripts can be created incrementally and some repetitive tasks under the GUI (e.g., specifying variables to be monitored) can be automated during the model building/te [...]
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/Scripts.html">Scripts and Batch-mode
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000000" size="3"> for more details. <br><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Prettyprinting">
</font><font face="Courier New" color="#000100" size="5">Pretty print</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">Opens a new window containing the
</font><font face="Arial" color="#000000" size="3"><em>BUGS
</em></font><font face="Arial" color="#000000" size="3"> language code describing the currently checked model. The model can be specified in the
</font><font face="Arial" color="#000000" size="3"><em>BUGS
</em></font><font face="Arial" color="#000000" size="3"> language or as a
</font><font face="Arial" color="#000000" size="3"><em>Doodle
</em></font><font face="Arial" color="#000000" size="3">. Any comments in the original
</font><font face="Arial" color="#000000" size="3"><em>BUGS
</em></font><font face="Arial" color="#000000" size="3"> language description will be lost. The
</font><font face="Arial" color="#000000" size="3"><em>BUGS
</em></font><font face="Arial" color="#000000" size="3"> langguage code will be formatted in a standardized form.<br><br>For example if the model described by this Doodle is checked the pretty print option will open a windows containing the BUGS language code below<br><img src="modelmenu4.bmp" alt="[modelmenu4]"><br><br>
</font><font face="Arial" color="#000100" size="1"> <img src="modelmenu5.bmp" alt="[modelmenu5]">
</font><font face="Arial" color="#000000" size="3"><br><br><br>
</font><font face="Arial" color="#000100" size="2"><a id="Latexprinting">
</font><font face="Courier New" color="#000100" size="5">Latex
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>Opens a new window containing Latex code describing the currently checked model. The model can be specified in the
</font><font face="Arial" color="#000000" size="3"><em>BUGS
</em></font><font face="Arial" color="#000000" size="3"> language or as a
</font><font face="Arial" color="#000000" size="3"><em>Doodle
</em></font><font face="Arial" color="#000000" size="3">. Any comments in the original
</font><font face="Arial" color="#000000" size="3"><em>BUGS
</em></font><font face="Arial" color="#000000" size="3"> language description will be lost. <br><br>For example, if the following model is checked then the latex option will produce:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for (i in 1:K) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for (j in 1:n) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">Y[i, j] ~ dnorm(eta[i, j], tau.C)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">eta[i, j] <- phi[i, 1] / (1 + phi[i, 2] * exp(phi[i, 3] * x[j]))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">phi[i, 1] <- exp(theta[i, 1])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">phi[i, 2] <- exp(theta[i, 2]) - 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">phi[i, 3] <- -exp(theta[i, 3])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for (k in 1:3) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">theta[i, k] ~ dnorm(mu[k], tau[k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">tau.C ~ dgamma(1.0E-3, 1.0E-3)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">sigma.C <- 1 / sqrt(tau.C)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">varC <- 1 / tau.C<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for (k in 1:3) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">mu[k] ~ dnorm(0, 1.0E-4)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">tau[k] ~ dgamma(1.0E-3, 1.0E-3)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">sigma[k] <- 1 / sqrt(tau[k])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br> <img src="modelmenu6.bmp" alt="[modelmenu6]"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3">Processing the latex code gives
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"><img src="modelmenu7.bmp" alt="[modelmenu7]"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><a id="IOoptions">
</font><font face="Courier New" color="#000100" size="5">Input / Output options...</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br> <img src="modelmenu8.bmp" alt="[modelmenu8]"><br> <br>The model specification tool takes input from the focus window when the Input options is set to window, or from a file menu prompt when the Input option is set to file.<br><br>
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> will either produce output in windows if the Output option is set to window, or produce output in the log window if the Output option is set to log.<br><br>The precision to which
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> displays output is controlled by the output precision field.<br><br><br>
</font><font face="Arial" color="#000100" size="2"><a id="Compileoptions">
</font><font face="Courier New" color="#000100" size="5">Compile options...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br> <br> <br>
</font><font face="Arial" color="#000000" size="3"><strong><em>compile logicals
</em></strong></font><font face="Arial" color="#000000" size="3">:
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> tries to write and compile new Component Pascal classes to represent logical nodes in the statistical model. This option, which can increase execution speed, is available only with GUI execution of OpenBUGS.exe, as it relies on run-time linking This option is not available with native linux execution or programs such as BRugs, which utilize OpenBUGS.so or OpenBUGS.dll.<br><br>
</font><font face="Arial" color="#000000" size="3"><strong><em>updater by method
</em></strong></font><font face="Arial" color="#000000" size="3">:
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> chooses update algorithms for the model in a "by method" order if this box is checked, otherwise updaters are chosen by order of node name.<br><br>
</font><font face="Arial" color="#000000" size="3"><strong><em>use chain graph
</em></strong></font><font face="Arial" color="#000000" size="3">:
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> tries to rewrite random effects in terms of a chain graph.<br><br>
</font><font face="Arial" color="#000000" size="3"><strong><em>trap on error
</em></strong></font><font face="Arial" color="#000000" size="3">: Causes
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> to display a "trap" window when an unidentified error occurs, instead of displaying a short message "Sorry, something went wrong..." in the status bar. Trap windows contain information intended to help programmers fix the source code of OpenBUGS. Therefore some experts may find them useful for identifying difficult errors, but most users will find them more confusing than the default message. <br><br><br>
</font><font face="Arial" color="#000100" size="2"><a id="Updateroptions">
</font><font face="Courier New" color="#000100" size="5">Updater options</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">Tabbed dialog box for controlling how
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> updates the model.<br><br>The
</font><font face="Arial" color="#000000" size="3"><em>updaters
</em></font><font face="Arial" color="#000000" size="3"> tab is used to influence which updater algorithms are used, while the
</font><font face="Arial" color="#000000" size="3"><em>parameters
</em></font><font face="Arial" color="#000000" size="3"> tab is used to adjust the default parameters of the chosen algorithms.<br><br>The updater (sampler) algorithms that OpenBUGS has available are displayed in the list box underneath "sampler". The radio button can be used to enable / disable the selected sampler. The radio buttons are only active before a model has been compiled. They control which algorithms
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> will consider using when the model is compiled. <br><br>Once the model has been compiled, it is possible to change the algorithm used for a node (or a block of nodes) by typing the name of the node (variable) in the text entry box underneath "change updater for", selecting a new updater algorithm from the list and clicking ok. You can see which updaters are being used for each node by clicking
</font><font face="Arial" color="#000000" size="3"><em>Info > Updaters (by name)
</em></font><font face="Arial" color="#000000" size="3"> from the menu bar. The info menu can also be checked after a change is requested to confirm the change was made. There is more information on the resulting list in the
</font><font face="Arial" color="#0000FF" size="3"><a href="../Manuals/InfoMenu.html#Updatersbyname">Info menu</a>
</font><font face="Arial" color="#000000" size="3"> manual page. To change the updater for a block of nodes (from Info>Updaters (by name), enter the name of the first node in the block. A block updater for a block of nodes can only be changed to another block updater for the block of nodes.<br><br><br> <img src="modelmenu10.bmp" alt="[modelmenu10]"><br> <br> [...]
</font><font face="Arial" color="#000000" size="3"><em>parameters
</em></font><font face="Arial" color="#000000" size="3"> tab of the dialog lists the actual updater algorithms used in sampling nodes in the compiled model. To change the default parameters of one of these updaters, select it from the list and then edit the appropriate fields. Clicking
</font><font face="Arial" color="#000000" size="3"><em>set
</em></font><font face="Arial" color="#000000" size="3"> will modify the sampling parameters for the duration of the current
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> session; the default parameters will be restored when
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> is restarted. Clicking
</font><font face="Arial" color="#000000" size="3"><em>save
</em></font><font face="Arial" color="#000000" size="3"> will make changes to the default parameters of the algorithm persistent across
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3">sessions. Changes to the default parameters can only be made after a model has been compiled.<br><br><br> <img src="modelmenu11.bmp" alt="[modelmenu11]"><br><br><br><br>
</font><font face="Arial" color="#000100" size="2"><a id="Externalize">
</font><font face="Courier New" color="#000100" size="5">Externalize
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This option writes out all the internal data structures that OpenBUGS has created for a compiled model . It provides a way of "saving" the model for future use. The user is prompted to enter a filestem name in a dialog box and a file called 'filestem.bug' is created in a folder called "Restart" in the OpenBUGSxxx program folder. If there were no errors when saving the compiled model, the message
</font><font face="Arial" color="#004080" size="3">"model externalized to file ok"
</font><font face="Arial" color="#000000" size="3"> is displayed in the status bar.<br><br>The output files can be very large; users should remove these files when they are no longer needed. Script commands (see
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/Scripts.html">Scripts and Batch-mode
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000000" size="3">) are a better method for creating re-producible results, especially if these results need to be sent to other users.<br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Internalize">Internalize
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This option reads in all the internal data structures that OpenBUGS needs to re-create an executing model from a file created by Externalize. It provides a way of "restarting" the model for further use. This option will open a window containing a BUGS language description of the restarted model and all the tool dialogs will be restored to the state when the model was last executed. If there were no errors when internalizing the [...]
</font><font face="Arial" color="#004080" size="3">"model internalized from file ok"
</font><font face="Arial" color="#000000" size="3"> is displayed in the status bar.<br>
</font>
</p>
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<head>
<title>ModelSpecification</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="modelspecification0.bmp" alt="[modelspecification0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">The BUGS Model Specification<br> Language
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"><br><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"> <br> <a href="#GraphicalModels">Graphical models</a><br> <a href="#GraphsAsAFormalLanguage">Graphs as a formal language</a><br> <a href="#TheBUGSLanguageStochasticNodes">Stochastic nodes</a><br> <a href="#LogicalNodes">Logical nodes</a><br> <a href="#ArraysAndIndexing">Arrays and indexin [...]
</font><font face="Arial" color="#0000FF" size="4"> <br>
</font><font face="Arial" color="#000100" size="2"><br><a id="GraphicalModels">
</font><font face="Courier New" color="#000100" size="5">Graphical models
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">We strongly recommend that the first step in any analysis should be the construction of a
</font><font face="Arial" color="#000100" size="3"><em>directed graphical model
</em></font><font face="Arial" color="#000100" size="3">. Briefly, this represents all quantities as nodes in a directed graph, in which arrows run to nodes from their direct influences (parents). The model represents the assumption that, given its parent nodes pa[
</font><font face="Arial" color="#000100" size="3"><em>v
</em></font><font face="Arial" color="#000100" size="3">], each node
</font><font face="Arial" color="#000100" size="3"><em>v
</em></font><font face="Arial" color="#000100" size="3"> is independent of all other nodes in the graph except descendants of
</font><font face="Arial" color="#000100" size="3"><em>v
</em></font><font face="Arial" color="#000100" size="3">, where descendant has the obvious definition.<br><br>Nodes in the graph are of three types.<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">1.
</font><font face="Arial" color="#000100" size="3"><em>Constants
</em></font><font face="Arial" color="#000100" size="3"> are fixed by the design of the study: they are always founder nodes (
</font><font face="Arial" color="#000100" size="3"><em>i.e.
</em></font><font face="Arial" color="#000100" size="3"> do not have parents), and are denoted as rectangles in the graph. <br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">2.
</font><font face="Arial" color="#000100" size="3"><em>Stochastic node
</em></font><font face="Arial" color="#000100" size="3">s are variables that are given a distribution, and are denoted as ellipses in the graph; they may be parents or children (or both). Stochastic nodes may be observed in which case they are
</font><font face="Arial" color="#000100" size="3"><em>data
</em></font><font face="Arial" color="#000100" size="3">, or may be unobserved and hence be
</font><font face="Arial" color="#000100" size="3"><em>parameters
</em></font><font face="Arial" color="#000100" size="3">, which may be unknown quantities underlying a model, observations on an individual case that are unobserved say due to censoring, or simply missing data.<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">3.
</font><font face="Arial" color="#000100" size="3"><em>Deterministic nodes
</em></font><font face="Arial" color="#000100" size="3"> are logical functions of other nodes.<br><br>Quantities are specified to be data by giving them values in a data declaration. Values for constants can also specified as data.<br><br>Directed links may be of two types: a thin solid arrow indicates a stochastic dependence while a thick hollow arrow indicates a logical function. An undirected dashed link may also be drawn to represent an upper or lower bound for a stochastic node.<br>< [...]
</font><font face="Arial" color="#000100" size="3"><em> <br>
</em></font><font face="Courier New" color="#000100" size="3">(i in 1:N).
</font><font face="Arial" color="#000100" size="3"><br><center>
</font><font face="Arial" color="#000100" size="2"><br><img src="modelspecification1.bmp" alt="[modelspecification1]"><br><br>
</font><font face="Arial" color="#000100" size="3"><br>A simple graphical model, where
</font><font face="Courier New" color="#000100" size="3">Y[i]
</font><font face="Arial" color="#000100" size="3"> depends on
</font><font face="Courier New" color="#000100" size="3">mu[i]
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Courier New" color="#000100" size="3">tau
</font><font face="Arial" color="#000100" size="3">, with
</font><font face="Courier New" color="#000100" size="3">mu[i]
</font><font face="Arial" color="#000100" size="3"><br>being a logical function of
</font><font face="Courier New" color="#000100" size="3">alpha
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Courier New" color="#000100" size="3">beta
</font><font face="Arial" color="#000100" size="3">.<br><br>
</font><font face="Arial" color="#000100" size="2"></center>
</font><font face="Arial" color="#000100" size="3"><br>The conditional independence assumptions represented by the graph mean that the full joint distribution of all quantities
</font><font face="Arial" color="#000100" size="3"><em>V
</em></font><font face="Arial" color="#000100" size="3"> has a simple factorisation in terms of the conditional distribution p(
</font><font face="Arial" color="#000100" size="3"><em>v
</em></font><font face="Arial" color="#000100" size="3">| parents[
</font><font face="Arial" color="#000100" size="3"><em>v
</em></font><font face="Arial" color="#000100" size="3">]) of each node given its parents, so that
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3">p(
</font><font face="Arial" color="#000100" size="3"><em>V
</em></font><font face="Arial" color="#000100" size="3">) =
</font><font face="Symbol" color="#000100" size="6"><sub>P
</sub></font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">p(
</font><font face="Arial" color="#000100" size="3"><em>v
</em></font><font face="Arial" color="#000100" size="3">| parents[
</font><font face="Arial" color="#000100" size="3"><em>v
</em></font><font face="Arial" color="#000100" size="3">])
</font><font face="Arial" color="#000100" size="3"><em> v
</em></font><font face="Arial" color="#000100" size="3"> in
</font><font face="Arial" color="#000100" size="3"><em>V
</em></font><font face="Arial" color="#000100" size="2"><br> <br>
</font><font face="Arial" color="#000100" size="3">The crucial idea is that we need only provide the parent-child distributions in order to fully specify the model, and
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3">then sorts out the necessary sampling methods directly from the expressed graphical structure.<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="GraphsAsAFormalLanguage">Graphs as a formal language
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">A special drawing tool
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/DoodleBUGS.html">DoodleBUGS
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> has been developed for specifying graphical models, which uses a hyper-diagram approach to add extra information to the graph to give a complete model specification. Each stochastic and logical node in the graph must be given a name using the conventions explained in
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/DoodleBUGS.html#CreatingANode">Creating a node
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">.<br><br><center>
</font><font face="Arial" color="#000100" size="2"><br>.<img src="modelspecification2.bmp" alt="[modelspecification2]"><br><br></center>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">The shaded node
</font><font face="Courier New" color="#000100" size="3">Y[i]
</font><font face="Arial" color="#000100" size="3"> is normally distributed with mean
</font><font face="Courier New" color="#000100" size="3">mu[i]
</font><font face="Arial" color="#000100" size="3"> and<br> precision
</font><font face="Courier New" color="#000100" size="3">tau
</font><font face="Arial" color="#000100" size="3">.
</font><font face="Arial" color="#000100" size="1"><br> <br><center>
</font><font face="Arial" color="#000100" size="2"><br><img src="modelspecification3.bmp" alt="[modelspecification3]">
</font><font face="Arial" color="#000100" size="1"><br></center>
</font><font face="Arial" color="#000100" size="2"> <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">The shaded node
</font><font face="Courier New" color="#000100" size="3">mu[i]
</font><font face="Arial" color="#000100" size="3"> is a logical function of
</font><font face="Courier New" color="#000100" size="3">alpha
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Courier New" color="#000100" size="3">beta
</font><font face="Arial" color="#000100" size="3">, and the<br> constants
</font><font face="Courier New" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="3">. (
</font><font face="Courier New" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="3"> is not required to be shown in the graph).<br> <br>The value function of a logical node contains all the necessary information to define the logical node.<br> <br>As an alternative to the Doodle representation, the model can be specified using the text-based
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language, headed by the model statement:<br><br>
</font><font face="Courier New" color="#000100" size="3"> model {<br>
</font><font face="Arial" color="#000100" size="3"><em> text-based description of graph in BUGS language
</em></font><font face="Courier New" color="#000100" size="3"><br> }
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2"> <br><a id="TheBUGSLanguageStochasticNodes">
</font><font face="Courier New" color="#000100" size="5">The BUGS language: stochastic nodes
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">In the text-based model description, stochastic nodes are represented by the node name followed by a tilda symbol followed by the distribution name followed by a comma-separated list of parents enclosed in brackets,
</font><font face="Arial" color="#000100" size="3"><em>e.g.<br><br>
</em></font><font face="Courier New" color="#000100" size="3"> x ~ dnorm(mu, tau)
</font><font face="Arial" color="#000100" size="3"><br> <br>The distributions that can be used in
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3">are described in
</font><font face="Courier New" color="#0000FF" size="3"><a href="#ContentsAI">Appendix I Distributions</a>
</font><font face="Arial" color="#000100" size="3">. The parameters of a distribution must be explicit nodes in the graph (scalar parameters can also be numerical constants) and so may not be expressions.<br><br>
</font><font face="Arial" color="#000100" size="2"><a id="ConstraintsOnUsingCertainDistributions">
</font><font face="Arial" color="#000100" size="3">Multivariate nodes must form contiguous elements in an array. Since the final element in an array changes fastest, such nodes must be defined as the final part of any array. For example, to define a set containing I multivariate normal variables of dimensional K as a single multidimensional array
</font><font face="Courier New" color="#000100" size="3">x[i, j]
</font><font face="Arial" color="#000100" size="3">, we could write:<br><br>
</font><font face="Courier New" color="#000100" size="3"> for (i in 1 : I) {<br> x[i, 1 : K] ~ dmnorm(mu[], tau[ , ])<br> }
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">Data defined by a multivariate distribution must not contain missing (unobserved) values. The only exception to this rule is the multivariate normal distribution. We realise this is an unfortunate restriction and we hope to relax it in the future. For multinomial data, it may be possible to get round this problem by re-expressing the multivariate likelihood as a sequence of conditional univariate binomial distributions or as Poisson distr [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Censoring is denoted using the notation
</font><font face="Courier New" color="#000100" size="3">C(lower, upper)
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><em>e.g.
</em></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Courier New" color="#000100" size="3"> x ~ dnorm(mu, tau)C(lower, upper)
</font><font face="Arial" color="#000100" size="3"><br> <br>would denote a quantity x from the normal distribution with parameters mu, tau, which had been observed to lie between lower and upper. Leaving either lower or upper blank corresponds to no limit, e.g. C(lower,) corresponds to an observation known to lie above lower. Whenever censoring is specified the censored node contributes a term to the full conditional d [...]
</font><font face="Arial" color="#000000" size="3">In general multivariate nodes can not be censored, the multivariate normal distribution is exempted from this restriction.
</font><font face="Arial" color="#FF00FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>Truncation is denoted by using the notation
</font><font face="Courier New" color="#000100" size="3">T(lower, upper),
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><em>eg
</em></font><font face="Arial" color="#000100" size="3">.<br><br>
</font><font face="Courier New" color="#000100" size="3"> x ~ dnorm(mu, tau)T(lower, upper)
</font><font face="Arial" color="#000100" size="3"><br> <br>would denote a quantity x from the modified normal distribution normalized by dividing by the integral of the distribution between limits lower and upper, which lies between lower and upper. Leaving either lower or upper blank corresponds to no limit, e.g. T(lower,) corresponds to an observation known to lie above lower. x can either be observed or unobserved. [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The precision matrices for multivariate normals must be positive definite. If a Wishart prior is not used for the precision matrix, then the elements of the precision matrix are updated univariately without any check of positive-definiteness. This will result in a crash
</font><font face="Arial" color="#000000" size="3">unless the precision matrix is parameterised appropriately.
</font><font face="Arial" color="#000000" size="3"><strong>This is the user's responsibility!
</strong></font><font face="Arial" color="#000000" size="3">Forming the precision matrix from the product of cholesky factors will ensure positive definiteness.<br><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="LogicalNodes">
</font><font face="Courier New" color="#000100" size="5">The BUGS language: logical nodes
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Logical nodes are represented by the node name followed by a left pointing arrow followed by a logical
</font><font face="Arial" color="#000100" size="2"><a id="expression">
</font><font face="Arial" color="#000100" size="3">expression
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Arial" color="#000100" size="3"> of its parent nodes e.g.<br><br>
</font><font face="Courier New" color="#000100" size="3"> mu[i] <- beta0 + beta1 * z1[i] + beta2 * z2[i] + b[i]
</font><font face="Arial" color="#000100" size="3"><br> <br>Logical expressions can be built using the following operators: plus (
</font><font face="Courier New" color="#000100" size="3">A + B
</font><font face="Arial" color="#000100" size="3">), multiplication (
</font><font face="Courier New" color="#000100" size="3">A * B
</font><font face="Arial" color="#000100" size="3">), minus (
</font><font face="Courier New" color="#000100" size="3">A - B
</font><font face="Arial" color="#000100" size="3">), division (
</font><font face="Courier New" color="#000100" size="3">A / B
</font><font face="Arial" color="#000100" size="3">) and unitary minus (
</font><font face="Courier New" color="#000100" size="3">-A
</font><font face="Arial" color="#000100" size="3">). The scalar valued functions in
</font><font face="Courier New" color="#0000FF" size="3"><a href="#ContentsAII">Appendix II Functions and Functionals</a>
</font><font face="Arial" color="#000100" size="3"> can also be used in logical expressions. A vector-valued logical function can only be used as the sole term on the right hand side of a vector-valued logical relation.<br><br>A link function can also be specified acting on the left hand side of a logical node
</font><font face="Arial" color="#000100" size="3"><em>e.g.
</em></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Courier New" color="#000100" size="3"> logit(mu[i]) <- beta0 + beta1 * z1[i] + beta2 * z2[i] + b[i]
</font><font face="Arial" color="#000100" size="3"><br><br>The following functions can be used on the left hand side of logical nodes as link functions:
</font><font face="Courier New" color="#000100" size="3">log
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Courier New" color="#000100" size="3">logit
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Courier New" color="#000100" size="3">cloglog
</font><font face="Arial" color="#000100" size="3">, and
</font><font face="Courier New" color="#000100" size="3">probit
</font><font face="Arial" color="#000100" size="3"> (where
</font><font face="Courier New" color="#000100" size="3">probit(x) <- y
</font><font face="Arial" color="#000100" size="3"> is equivalent to
</font><font face="Courier New" color="#000100" size="3">x <- phi(y)
</font><font face="Arial" color="#000100" size="3">).<br><br>A special logical node called "deviance" is created automatically by
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3">: It calculates -2 * log(likelihood), where 'likelihood' is the conditional probability of all data nodes given their stochastic parent nodes. This node can be monitored, and is used in the DIC tool - see
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/InferenceMenu.html#DIC">DIC...</a>
</font><font face="Arial" color="#000100" size="3"><br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="ArraysAndIndexing">Arrays and indexing
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Arrays are indexed by terms within square brackets. The four basic operators +, -, *, and / along with appropriate bracketing are allowed to calculate an integer function as an index, for example:<br><br>
</font><font face="Courier New" color="#000100" size="3"> Y[(i + j) * k, l]
</font><font face="Arial" color="#000100" size="3"><br><br>On the left-hand-side of a relation, an expression that always evaluates to a fixed value is allowed for an index, whether it is a constant or a function of data. On the right-hand-side the index can be a fixed value or a named node, which allows a straightforward formulation for mixture models in which the appropriate element of an array is 'picked' according to a random quantity (see
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#NestedIndexingAndMixtures">Nested indexing and mixtures</a>
</font><font face="Arial" color="#000100" size="3">). However, functions of unobserved nodes are not permitted to appear directly as an index term (intermediate deterministic nodes may be introduced if such functions are required).<br><br>The conventions broadly follow those of S-Plus:<br><br>
</font><font face="Courier New" color="#000100" size="3">n : m
</font><font face="Arial" color="#000100" size="3"> represents
</font><font face="Arial" color="#000100" size="3"><em>n
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><em>n
</em></font><font face="Arial" color="#000100" size="3"> + 1, ...,
</font><font face="Arial" color="#000100" size="3"><em>m
</em></font><font face="Arial" color="#000100" size="3">.<br>
</font><font face="Courier New" color="#000100" size="3">x[ ]
</font><font face="Arial" color="#000100" size="3"> represents all values of a vector
</font><font face="Arial" color="#000100" size="3"><em>x
</em></font><font face="Arial" color="#000100" size="3">.<br>
</font><font face="Courier New" color="#000100" size="3">y[, 3]
</font><font face="Arial" color="#000100" size="3"> indicates all values of the third column of a two-dimensional array
</font><font face="Arial" color="#000100" size="3"><em>y
</em></font><font face="Arial" color="#000100" size="3">.<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Multidimensional arrays are handled as one-dimensional arrays with a constructed index. Thus functions defined on arrays must be over equally spaced nodes within an array: for example
</font><font face="Courier New" color="#000100" size="3">sum(y[i, 1:4, k])
</font><font face="Arial" color="#000100" size="3">.<br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000000" size="3">When dealing with unbalanced or hierarchical data a number of different approaches are possible - see
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/Tricks.html#HandlingUnbalancedDatasets">Handling unbalanced datasets</a>.
</font><font face="Arial" color="#000000" size="3"> The ideas discussed in
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#NestedIndexingAndMixtures">Nested indexing and mixtures</a>
</font><font face="Arial" color="#000000" size="3"> may also be helpful in this respect.<br><br><br>
</font><font face="Arial" color="#000000" size="2"><a id="RepeatedStructures">
</font><font face="Courier New" color="#000100" size="5">Repeated structures
</font><font face="Arial" color="#000000" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]<br>
</font><font face="Arial" color="#FF0000" size="5"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3">Repeated structures are specified using a "for - loop". The syntax for this is:<br><br>
</font><font face="Courier New" color="#000100" size="3"> for (i in a : b) {
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><em> list of statements to be repeated for increasing values of loop-variable
</em></font><font face="Arial" color="#000000" size="3">i<br>
</font><font face="Courier New" color="#000100" size="3"> }
</font><font face="Arial" color="#000000" size="3"><br> <br>Note that a and b must either be explicit (such as
</font><font face="Courier New" color="#000100" size="3">for (i in 1:100)
</font><font face="Arial" color="#000000" size="3">) or supplied as data. Neither a nor b may be logical nodes (such as
</font><font face="Courier New" color="#000100" size="3">b <- 100
</font><font face="Arial" color="#000000" size="3">) or stochastic nodes - see
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/Tricks.html#WhereTheSizeOfASetIsARandomQuantity">here</a>
</font><font face="Arial" color="#000000" size="3">for a possible way to get round this.<br><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="DataTransformations">
</font><font face="Courier New" color="#000100" size="5">Data transformations
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Although transformations of data can always be carried out before using
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3">, it is convenient to be able to try various transformations of dependent variables within a model description. For example, we may wish to try both
</font><font face="Courier New" color="#000100" size="3"><em>y
</em></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Courier New" color="#000100" size="3"><em>sqrt(y)
</em></font><font face="Arial" color="#000100" size="3"> as dependent variables without creating a separate variable
</font><font face="Courier New" color="#000100" size="3"><em>z = sqrt(y)
</em></font><font face="Arial" color="#000100" size="3"> in the data file.<br><br>The BUGS language therefore permits the following type of structure to occur:<br><br>
</font><font face="Courier New" color="#000100" size="3"> for (i in 1:N) {<br> z[i] <- sqrt(y[i])<br> z[i] ~ dnorm(mu, tau)<br> }
</font><font face="Arial" color="#000100" size="3"><br><br>Strictly speaking, this goes against the declarative structure of the model specification, with the accompanying exhortation to construct a directed graph and then to make sure that each node appears once and only once on the left-hand side of a statement. However, a check has been built in so that, when finding a logical node which also features as a stochastic node (such as z above), a stochastic node is created with the calcula [...]
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Leuk.html">Leuk</a>
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Endo.html">Endo</a>
</font><font face="Arial" color="#000100" size="3"> examples.<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="NestedIndexingAndMixtures">Nested indexing and mixtures
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Nested indexing can be very effective. For example, suppose
</font><font face="Courier New" color="#000100" size="3">N
</font><font face="Arial" color="#000100" size="3"> individuals can each be in one of
</font><font face="Courier New" color="#000100" size="3">I
</font><font face="Arial" color="#000100" size="3"> groups, and
</font><font face="Courier New" color="#000100" size="3">g[1:N]
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">is a vector which contains the group membership. Then "group" coefficients
</font><font face="Courier New" color="#000100" size="3">beta[i]
</font><font face="Arial" color="#000100" size="3"> can be fitted using
</font><font face="Courier New" color="#000100" size="3">beta[g[j]]
</font><font face="Arial" color="#000100" size="3"> in a regression equation.<br><br>In the
</font><font face="Arial" color="#000100" size="3"><em>BUGS
</em></font><font face="Arial" color="#000100" size="3"> language, nested indexing can be used for the parameters of distributions: for example, the
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Examples/Eyes.html">Eyes</a>
</font><font face="Arial" color="#000100" size="3"> example concerns a normal mixture in which the
</font><font face="Arial" color="#000100" size="3"><em>i
</em></font><font face="Arial" color="#000100" size="3"><sup>th
</sup></font><font face="Arial" color="#000100" size="3"> case is in an unknown group
</font><font face="Arial" color="#000100" size="3"><em>T
</em></font><font face="Arial" color="#000100" size="3"><em><sub>i
</sub></em></font><font face="Arial" color="#000100" size="3"> which determines the mean
</font><font face="Arial" color="#000100" size="3"><em>l
</em></font><font face="Arial" color="#000100" size="3"><em><sub>T
</sub></em></font><font face="Arial" color="#000100" size="3"><em><sub>i
</sub></em></font><font face="Arial" color="#000100" size="3"> of the measurement
</font><font face="Arial" color="#000100" size="3"><em>y
</em></font><font face="Arial" color="#000100" size="3"><em><sub>i
</sub></em></font><font face="Arial" color="#000100" size="3">. Hence the model is<br><br>
</font><font face="Arial" color="#000100" size="3"><em> T
</em></font><font face="Arial" color="#000100" size="3"><em><sub>i
</sub></em></font><font face="Arial" color="#000100" size="3"> ~ Categorical(
</font><font face="Arial" color="#000100" size="3"><em>P
</em></font><font face="Arial" color="#000100" size="3">)<br>
</font><font face="Arial" color="#000100" size="3"><em> y
</em></font><font face="Arial" color="#000100" size="3"><em><sub>i
</sub></em></font><font face="Arial" color="#000100" size="3"> ~ Normal(
</font><font face="Symbol" color="#000100" size="3"><em>l
</em></font><font face="Arial" color="#000100" size="3"><em><sub>T
</sub></em></font><font face="Arial" color="#000100" size="3"><em><sub>i
</sub></em></font><font face="Arial" color="#000100" size="3"> ,
</font><font face="Symbol" color="#000100" size="3"><em>t
</em></font><font face="Arial" color="#000100" size="3"> )<br><br>which may be written in the BUGS language as<br><br>
</font><font face="Courier New" color="#000100" size="3"> for (i in 1:N) {<br> T[i] ~ dcat(P[])<br> y[i] ~ dnorm(lambda[T[i]], tau)<br> }
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><br>The mixture construct can also be applied to vector value parameters eg<br>
</font><font face="Courier New" color="#000100" size="3"><br> for (i in 1 : ns){<br> nbiops[i] <- sum(biopsies[i, ]) <br> true[i] ~ dcat(p[])<br> biopsies[i, 1 : 4] ~ dmulti(error[true[i], ], nbiops[i])<br> }<br>
</font><font face="Arial" color="#000100" size="3"> <br>Multiple (up to four) variable indices are allowed in setting up mixture models. eg<br><br>
</font><font face="Courier New" color="#000100" size="3"> dyspnoea ~ dcat(p.dyspnoea[either,bronchitis,1:2])<br> either <- max(tuberculosis,lung.cancer)<br> bronchitis ~ dcat(p.bronchitis[smoking,1:2])
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2"><a id="FormattingOfData">
</font><font face="Courier New" color="#000100" size="5">Formatting of data</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Data can be in an R/S-Plus format (used by R and S-Plus and most of the examples in OpenBUGS
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">) or, for data in arrays, in rectangular format.<br><br>Missing values are represented as
</font><font face="Courier New" color="#000100" size="3">NA
</font><font face="Arial" color="#000100" size="3">.<br><br>The whole array must be specified in the file - it is not possible just to specify selected components. Any parts of the array you do not want to specify must be filled with NAs.<br><br>All variables in a data file must be defined in a model, even if just left unattached to the rest of the model. <br><br>
</font><font face="Arial" color="#000100" size="3"><strong>R/<a id="FormattingOfDataSPlusFormat">S-Plus format:</a>
</strong></font><font face="Arial" color="#000100" size="3"> This allows scalars and arrays to be named and given values in a single structure headed by key-word list. There must be no space after list.<br><br>For example, in the Rats example, we need to specify a scalar
</font><font face="Courier New" color="#000100" size="3">xbar
</font><font face="Arial" color="#000100" size="3">, dimensions
</font><font face="Courier New" color="#000100" size="3">N
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Courier New" color="#000100" size="3">T
</font><font face="Arial" color="#000100" size="3">, a vector
</font><font face="Courier New" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="3"> and a two-dimensional array
</font><font face="Courier New" color="#000100" size="3">Y
</font><font face="Arial" color="#000100" size="3"> with 30 rows and 5 columns. This is achieved using the following format:<br><br>
</font><font face="Courier New" color="#000100" size="3"> list(<br> xbar=22, N=30, T=5,<br> x=c(8.0, 15.0, 22.0, 29.0, 36.0),<br> Y=structure(<br> &nb [...]
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> reads data into an array by filling the right-most index first, whereas the R/S-Plus program fills the left-most index first. Hence
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> reads the string of numbers
</font><font face="Courier New" color="#000100" size="3">c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10)
</font><font face="Arial" color="#000100" size="3"> into a 2 * 5 dimensional matrix in the order <br>
</font><font face="Courier New" color="#000100" size="3"> [i, j]th element of matrix value<br> [1, 1] 1<br> [1, 2] [...]
</font><font face="Arial" color="#000100" size="3"><br>whereas R/S-Plus read the same string of numbers in the order<br><br>
</font><font face="Courier New" color="#000100" size="3"> [i, j]th element of matrix value<br> [1, 1] 1<br> [2, 1] [...]
</font><font face="Arial" color="#000100" size="3"><br><br>Hence the ordering of the array dimensions must be reversed before using the R/S-Plus
</font><font face="Courier New" color="#000100" size="3">dput
</font><font face="Arial" color="#000100" size="3"> function to create a data file for input into
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3">.<br><br>For example, consider the 2 * 5 dimensional matrix<br><br>
</font><font face="Courier New" color="#000100" size="3"> 1 2 3 4 5<br> 6 7 8 9 10
</font><font face="Arial" color="#000100" size="3"><br><br>This must be stored in R/S-Plus as a 5 * 2 dimensional matrix:<br><br>
</font><font face="Courier New" color="#000100" size="3"> > M<br> [,1] [,2]<br> [1,] 1 6<br> [2,] 2 7<br> [3,] 3 8<br> [4,] 4 9<br> [5,] 5 10
</font><font face="Arial" color="#000100" size="3"><br><br>The R/S-Plus command<br><br>
</font><font face="Courier New" color="#000100" size="3"> > dput(list(M=M), file="matrix.dat")
</font><font face="Arial" color="#000100" size="3"><br><br>will then produce the following data file<br><br>
</font><font face="Courier New" color="#000100" size="3"> list(M=structure(.Data=c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10),<br> .Dim=c(5,2))
</font><font face="Arial" color="#000100" size="3"><br><br>Edit the
</font><font face="Courier New" color="#000100" size="3">.Dim
</font><font face="Arial" color="#000100" size="3"> statement in this file from
</font><font face="Courier New" color="#000100" size="3">.Dim=c(5,2)
</font><font face="Arial" color="#000100" size="3"> to
</font><font face="Courier New" color="#000100" size="3">.Dim=c(2,5)
</font><font face="Arial" color="#000100" size="3">. The file is now in the correct format to input the required 2 * 5 dimensional matrix into
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3">.<br><br>Now consider a 3 * 2 * 4 dimensional array<br><br>
</font><font face="Courier New" color="#000100" size="3"> 1 2 3 4<br> 5 6 7 8<br><br> 9 10 11 12<br> 13 14 15 16<br><br>   [...]
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This must be stored in R/S-Plus as the 4 * 2 * 3 dimensional array:<br>
</font><font face="Courier New" color="#000100" size="3"><br> > A<br> , , 1<br> [,1] [,2]<br> [1,] 1 5<br> [2,] 2 6<br> [3,] 3 7<br> [4,] 4 8<br><br> , , 2<br> [,1] [,2]<br>&n [...]
</font><font face="Arial" color="#000000" size="3"><br><br>The command<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"> > dput(list(A=A), file="array.dat")
</font><font face="Arial" color="#000100" size="3"><br><br>will then produce the following data file<br><br>
</font><font face="Courier New" color="#000100" size="3"> list(A=structure(.Data=c( 1, 2, 3, 4, 5, 6, 7, 8,<br> 9, 10, 11, 12, 13, 14, 15, 16,<br> & [...]
</font><font face="Arial" color="#000100" size="3"><br><br>Edit the
</font><font face="Courier New" color="#000100" size="3">.Dim
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3">statement in this file from
</font><font face="Courier New" color="#000100" size="3">.Dim=c(4,2,3)
</font><font face="Arial" color="#000000" size="3"> to
</font><font face="Courier New" color="#000100" size="3">.Dim=c(3,2,4)
</font><font face="Arial" color="#000000" size="3">. The file is now in the correct format to input the required 3 * 2 * 4 dimensional array into
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3">in the order
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Courier New" color="#000100" size="3"> [i, j, k]th element of matrix value<br> [1, 1, 1] 1<br> [1, 1, 2] &nb [...]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="FormattingOfDataRectangularFormat">Rectangular format:</a>
</strong></font><font face="Arial" color="#000100" size="3">The columns for data in rectangular format need to be headed by the array name. The arrays need to be of equal size, and the array names must have explicit brackets: for example:<br><br>
</font><font face="Courier New" color="#000100" size="3"> age[] sex[]<br> 26 0<br> 52 1<br> ...<br> 34 0<br> END
</font><font face="Arial" color="#000000" size="3"><br><br><a id="FormattingOfDataENDCommand">
</font><font face="Arial" color="#000000" size="3"><strong>Note that the file must end with an 'END' keyword, as shown above and below, and this must be followed by at least one blank line.
</strong></font><font face="Arial" color="#000000" size="3"></a><br><br>
</font><font face="Arial" color="#000100" size="3">Multi-dimensional arrays can be specified by explicit indexing: for example, the
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Examples/Ratsy.html">Ratsy</a>
</font><font face="Arial" color="#000100" size="3"> file begins<br><br>
</font><font face="Courier New" color="#000100" size="3"> Y[,1] Y[,2] Y[,3] Y[,4] Y[,5]<br> 151 199 246 283 320<br> 145 199 249 293 354<br> 147 [...]
</font><font face="Arial" color="#000000" size="3"><br><br>The first index position for any array must always be empty.<br>
</font><font face="Arial" color="#000100" size="3"><br>It is possible to load a mixture of rectangular and R/S-Plus format data files for the same model. For example, if data arrays are provided in a rectangular file, constants can be defined in a separate list statement (see also the
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Rats.html">Rats</a>
</font><font face="Arial" color="#000100" size="3">example with data files
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Ratsx.html">Ratsx
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Ratsy.html">Ratsy
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">).<br><br>(See
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/Tricks.html#HandlingUnbalancedDatasets">here
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> for details of how to handle unbalanced data.)<br><br>Note that programs exist for conversion of data from other packages: please see the OpenBUGS resources at <br><br> http://www.openbugs.info<br><br><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="modelspecification4.bmp" alt="[modelspecification4]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Arial" color="#000100" size="2"><a id="ContentsAI">
</font><font face="Arial" color="#000100" size="6"><strong><sup>Appendix I Distributions
</sup></strong></font><font face="Arial" color="#000100" size="2"></a><br><br>
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#DiscreteUnivariate">Discrete Univariate</a>
</strong></font><font face="Arial" color="#000100" size="4"> <br>
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#Bernoulli">Bernoulli</a><br> <a href="#Binomial">Binomial</a><br> <a href="#Categorical">Categorical</a><br> <a href="#NegativeBinomial">Negative Binomial</a><br> <a href="#Poisson">Poisson</a><br>
</font><font face="Arial" color="#000100" size="2"><a href="#Geometric">
</font><font face="Courier New" color="#0000FF" size="3">Geometric
</font><font face="Arial" color="#000100" size="2"></a><br> <a href="#Geometric0">
</font><font face="Courier New" color="#0000FF" size="3">Geometric (alternative)
</font><font face="Arial" color="#000100" size="2"></a></a>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#Hypergeometric">Non-central Hypergeometric</a><br>
</font><font face="Arial" color="#000100" size="4"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#ContinuousUnivariate">Continuous Univariate
</strong></font><font face="Arial" color="#000100" size="4"></a> <br>
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#Beta">Beta</a><br> <a href="#ChiSquared">Chi-squared</a><br> <a href="#DoubleExponential">Double Exponential</a><br> <a href="#Exponential">Exponential</a><br> <a href="#Flat">Flat</a><br> <a href="#Gamma">Gamma</a><br> <a href="#GeneralizedExtremeValue">Generalized Extreme Value</a><br>&nb [...]
</font><font face="Arial" color="#000100" size="4"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#DiscreteMultivariate">Discrete Multivariate
</strong></font><font face="Arial" color="#000100" size="4"></a> <br>
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#Multinomial">Multinomial</a>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="4"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="#ContinuousMultivariate">Continuous Multivariate</a>
</strong></font><font face="Arial" color="#000100" size="4"> <br>
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#Dirichlet">Dirichlet</a><br> <a href="#MultivariateNormal">Multivariate Normal</a><br> <a href="#MultivariateStudentT">Multivariate Student-t</a><br> <a href="#Wishart">Wishart</a><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="DiscreteUnivariate">
</strong></font><font face="Courier New" color="#000100" size="5">Discrete Univariate
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#ContentsAI">top appendix i</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><strong><a id="Bernoulli">Bernoulli</a>
</strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>r ~ dbern(p)
</sup></font><font face="Arial" color="#000100" size="3"> <img src="modelspecification5.bmp" alt="[modelspecification5]"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><strong><a id="Binomial">Binomial</a>
</strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>r ~ dbin(p, n)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification6.bmp" alt="[modelspecification6]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="Categorical">Categorical</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>r ~ dcat(p[])
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification7.bmp" alt="[modelspecification7]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="NegativeBinomial">Negative Binomial</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dnegbin(p, r)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification8.bmp" alt="[modelspecification8]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="Poisson">Poisson</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>r ~ dpois(lambda)
</sup></font><font face="Arial" color="#000100" size="3"> <img src="modelspecification9.bmp" alt="[modelspecification9]"><br><a id="Geometric">
</font><font face="Arial" color="#000000" size="3"><strong><a id="Poisson">Geometric</a></a>
</strong></font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Courier New" color="#000100" size="3">r ~ dgeom(p) <img src="modelspecification10.bmp" alt="[modelspecification10]">
</font><font face="Arial" color="#000100" size="3"><br><br><a id="Geometric0"><a id="Geometric">
</font><font face="Arial" color="#000000" size="3"><strong><a id="Poisson">Geometric (alternative form)</a></a></a>
</strong></font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Courier New" color="#000100" size="3">r ~ dgeom0(p) <img src="modelspecification11.bmp" alt="[modelspecification11]">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong><br><a id="Hypergeometric">Non-central Hypergeometric</a><br>
</strong></font><font face="Courier" color="#000100" size="3">x ~ dhyper(</a>n, m, N, psi)
</font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Courier" color="#000100" size="3"><sup> <img src="modelspecification12.bmp" alt="[modelspecification12]">
</sup></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="ContinuousUnivariate">
</strong></font><font face="Courier New" color="#000100" size="5">Continuous Univariate
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#ContentsAI">top appendix i</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><strong><a id="Beta">Beta</a>
</strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>p ~ dbeta(a, b)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification13.bmp" alt="[modelspecification13]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="ChiSquared">Chi-squared</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dchisqr(k)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification14.bmp" alt="[modelspecification14]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="DoubleExponential">Double Exponential</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ ddexp(mu, tau)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification15.bmp" alt="[modelspecification15]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="Exponential">Exponential</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dexp(lambda)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification16.bmp" alt="[modelspecification16]"><br><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="Flat">Flat</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dflat()
</sup></font><font face="Arial" color="#000000" size="3"><sup> constant value for all x; not a proper distribution
</sup></font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="Flat"><a id="Gamma">Gamma</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dgamma(r, mu)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification17.bmp" alt="[modelspecification17]"><br><br><a id="GeneralizedExtremeValue">
</font><font face="Arial" color="#000000" size="3"><strong>Generalized Extreme Value
</strong></font><font face="Arial" color="#000000" size="3"></a> <br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dgev(mu,sigma,eta)
</sup></font><font face="Arial" color="#000000" size="3"><img src="modelspecification18.bmp" alt="[modelspecification18]">
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="GeneralizedF">Generalized F</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ df(n,m,mu,tau)<br><img src="modelspecification19.bmp" alt="[modelspecification19]"><br>
</sup></font><font face="Arial" color="#000000" size="3"><sup>Reduces to the standard F for mu=0, tau=1.
</sup></font><font face="Courier New" color="#000100" size="3"><sup><br>
</sup></font><font face="Arial" color="#000000" size="3"><br><a id="GeneralizedGamma">
</font><font face="Arial" color="#000000" size="3"><strong>Generalized Gamma
</strong></font><font face="Arial" color="#000000" size="3"></a><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dggamma(r, mu, beta)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification20.bmp" alt="[modelspecification20]"><br><br>
</font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3"><a id="GeneralizedPareto">
</font><font face="Arial" color="#000000" size="3"><strong>Generalized Pareto
</strong></font><font face="Arial" color="#000000" size="3"></a>
</font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Courier New" color="#000100" size="3"><sup>x ~ dgpar(mu,sigma,eta)
</sup></font><font face="Arial" color="#000000" size="3"><sup>
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification21.bmp" alt="[modelspecification21]">
</font><font face="Arial" color="#000000" size="3"><strong><br><br><a id="llog">Generic
</strong></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000000" size="3"><strong><a id="Generic">LogLikelihood</a> distribution</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3">x ~dloglik(lambda)
</font><font face="Arial" color="#000000" size="3"> exp(lambda); NB does not depend on x. See
</font><font face="Courier New" color="#0000FF" size="3">
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Manuals/Tricks.html#GenericDistribution">Generic sampling distributions</a>.
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="LogNormal">Log-normal</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dlnorm(mu, tau)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification22.bmp" alt="[modelspecification22]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="Logistic">Logistic</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dlogis(mu, tau)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification23.bmp" alt="[modelspecification23]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="Normal">Normal</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dnorm(mu, tau)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification24.bmp" alt="[modelspecification24]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="Pareto">Pareto</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dpar(alpha, c)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification25.bmp" alt="[modelspecification25]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="StudentT">Student-t</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dt(mu, tau, k)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification26.bmp" alt="[modelspecification26]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="Uniform">Uniform</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dunif(a, b)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification27.bmp" alt="[modelspecification27]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="Weibull">Weibull</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x ~ dweib(v, lambda)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification28.bmp" alt="[modelspecification28]"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="DiscreteMultivariate">
</strong></font><font face="Courier New" color="#000100" size="5">Discrete Multivariate
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#ContentsAI">top appendix i</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3"><strong><a id="Multinomial">Multinomial</a>
</strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x[] ~ dmulti(p[], N)
</sup></font><font face="Arial" color="#000100" size="3"> <img src="modelspecification29.bmp" alt="[modelspecification29]"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="ContinuousMultivariate">
</strong></font><font face="Courier New" color="#000100" size="5">Continuous Multivariate
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#ContentsAI">top appendix i</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><strong><br><a id="Dirichlet">Dirichlet</a>
</strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>p[] ~ ddirich(alpha[])
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification30.bmp" alt="[modelspecification30]"><br>
</font><font face="Arial" color="#000000" size="3"><sup>May also be spelt
</sup></font><font face="Courier New" color="#000000" size="3"><sup>ddirch
</sup></font><font face="Arial" color="#000000" size="3"><sup> as in WinBUGS. <br>
</sup></font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="MultivariateNormal">Multivariate Normal</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x[] ~ dmnorm(mu[], T[,])
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification31.bmp" alt="[modelspecification31]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="MultivariateStudentT">Multivariate Student-t</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x[] ~ dmt(mu[], T[,], k)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification32.bmp" alt="[modelspecification32]"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><a id="Wishart">Wishart</a>
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>x[,] ~ dwish(R[,], k)
</sup></font><font face="Arial" color="#000000" size="3"> <img src="modelspecification33.bmp" alt="[modelspecification33]">
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br><br><br><img src="modelspecification34.bmp" alt="[modelspecification34]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Arial" color="#000100" size="2"><a id="ContentsAII">
</font><font face="Arial" color="#000100" size="6"><strong><sup>Appendix II Functions and Functionals
</sup></strong></font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Arial" color="#000100" size="3"><br>Function arguments represented by
</font><font face="Courier New" color="#000100" size="3"><strong>e
</strong></font><font face="Arial" color="#000100" size="3"> can be
</font><font face="Arial" color="#0000FF" size="2"><a href="#expression">
</font><font face="Arial" color="#0000FF" size="3">expressions
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Arial" color="#000100" size="3">, those by
</font><font face="Courier New" color="#000100" size="3"><strong>s
</strong></font><font face="Arial" color="#000100" size="3"> must be scalar-valued nodes in the graph and those represented by
</font><font face="Courier New" color="#000100" size="3"><strong>v
</strong></font><font face="Arial" color="#000100" size="3"> must be vector-valued nodes in a graph. Some function arguments must be stochastic nodes. Functionals are described using a similar notation to functions, the special notation
</font><font face="Courier New" color="#000100" size="3">F(x)
</font><font face="Arial" color="#000100" size="3"> is used to describe the function on which the functional acts. See example
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Functionals.html">Functionals
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> for details. Systems of ordinary differential equations and their solution can be described in the BUGS language by using the special
</font><font face="Courier New" color="#000100" size="3">D(x[1:n], t)
</font><font face="Arial" color="#000100" size="3"> notation. See example
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Sixcomp.html">ode</a>
</font><font face="Arial" color="#000100" size="3"> for details. <br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5">Scalar functions
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="5"><strong><u><br>
</u></strong></font><font face="Arial" color="#000100" size="1"><strong><u>
</u></strong></font><font face="Arial" color="#000100" size="1"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3">abs(e)
</font><font face="Arial" color="#000100" size="3"> absolute value of e, |e|<br><br>
</font><font face="Courier New" color="#000100" size="3">arccos(e)
</font><font face="Arial" color="#000100" size="3"> inverse cosine of e<br><br>
</font><font face="Courier New" color="#000100" size="3">arccosh(e)
</font><font face="Arial" color="#000100" size="3"> inverse hyperbolic cosine of e<br><br>
</font><font face="Courier New" color="#000100" size="3">arcsin(e)
</font><font face="Arial" color="#000100" size="3"> inverse sine of e<br><br>
</font><font face="Courier New" color="#000100" size="3">arcsinh(e)
</font><font face="Arial" color="#000100" size="3"> inverse hyperbolic sine of e<br><br>
</font><font face="Courier New" color="#000100" size="3">arctan(e)
</font><font face="Arial" color="#000100" size="3"> inverse tangent of e<br><br>
</font><font face="Courier New" color="#000100" size="3">arctanh(e)
</font><font face="Arial" color="#000100" size="3"> inverse hyperbolic tangent of e<br><br>
</font><font face="Courier New" color="#000100" size="3">cloglog(e)
</font><font face="Arial" color="#000100" size="3"> complementary log log of e, ln(-ln(1 -
</font><font face="Arial" color="#000100" size="3"><em>e
</em></font><font face="Arial" color="#000100" size="3">))<br><br>
</font><font face="Courier New" color="#000100" size="3">cos(e)
</font><font face="Arial" color="#000100" size="3"> cosine of e<br><br>
</font><font face="Courier New" color="#000100" size="3">cosh(e)
</font><font face="Arial" color="#000100" size="3"> hyperbolic cosine of e<br><br>
</font><font face="Courier New" color="#000100" size="3">cumulative(s1, s2)
</font><font face="Arial" color="#000100" size="3"> tail area of distribution of s1 up to the value of s2, s1 must be <br> stochastic, s1 and s2 can be the same<br><br>
</font><font face="Arial" color="#000000" size="3"><a id="CutFunction">
</font><font face="Courier New" color="#000100" size="3">cut(e)</a>
</font><font face="Arial" color="#000000" size="3"> cuts edges in the graph - see <br>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/Tricks.html#UseOfTheCutFunction">Use of the "cut" function
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#0000FF" size="3"><strong><br><br>
</strong></font><font face="Courier New" color="#000100" size="3">density(s1, s2)
</font><font face="Arial" color="#000000" size="3"> density of distribution of s1 at value of s2, s1 must be<br> a stochastic node supplied as data, s1 and s2 can be the same.<br>
</font><font face="Arial" color="#0000FF" size="3"><strong><br>
</strong></font><font face="Courier New" color="#000100" size="3">deviance(s1, s2)
</font><font face="Arial" color="#000000" size="3"> deviance of distribution of s1 at value of s2, s1 must be<br> a stochastic node supplied as data, s1 and s2 can be the same.<br><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Courier New" color="#000100" size="3">equals(e1, e2)
</font><font face="Arial" color="#000000" size="3"> 1 if
</font><font face="Arial" color="#000000" size="3"><em>value of e
</em></font><font face="Arial" color="#000000" size="3">1 equals value of
</font><font face="Arial" color="#000000" size="3"><em>e
</em></font><font face="Arial" color="#000000" size="3">2; 0 otherwise<br><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Courier New" color="#000100" size="3">exp(e)
</font><font face="Arial" color="#000100" size="3"> exp(
</font><font face="Arial" color="#000100" size="3"><em>e
</em></font><font face="Arial" color="#000100" size="3">)<br><br>
</font><font face="Courier New" color="#000100" size="3">gammap(s1, s2)
</font><font face="Arial" color="#000100" size="3"> partial (incomplete) gamma function, value of standard<br> gamma density with parameter s1 integrated up to s2<br><br>
</font><font face="Courier New" color="#000100" size="3">ilogit(e)
</font><font face="Arial" color="#000100" size="3"> exp(
</font><font face="Arial" color="#000100" size="3"><em>e)
</em></font><font face="Arial" color="#000100" size="3">/ (1 + exp(
</font><font face="Arial" color="#000100" size="3"><em>e
</em></font><font face="Arial" color="#000100" size="3">))<br>
</font><font face="Arial" color="#000000" size="2"><sub><br>
</sub></font><font face="Arial" color="#000100" size="3">
</font><font face="Courier New" color="#000100" size="3">icloglog(e)
</font><font face="Arial" color="#000100" size="3"> 1 - exp( - exp(
</font><font face="Arial" color="#000100" size="3"><em>e
</em></font><font face="Arial" color="#000100" size="3">))<br><br>
</font><font face="Arial" color="#000000" size="2"><sub>
</sub></font><font face="Courier New" color="#000100" size="3">integral(F(s), s1, s2, s3)<br>
</font><font face="Arial" color="#000000" size="3">definite integral of function F(s) between s = s1 and s = s2<br> to accuracy s3<br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3">log(e)
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">natural logarithm of e<br>
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Courier New" color="#000100" size="3">logfact(e)
</font><font face="Arial" color="#000100" size="3"> ln(
</font><font face="Arial" color="#000100" size="3"><em>e
</em></font><font face="Arial" color="#000100" size="3">!)<br><br>
</font><font face="Courier New" color="#000100" size="3">loggam(e)
</font><font face="Arial" color="#000100" size="3"> logarithm of gamma function of e<br><br>
</font><font face="Courier New" color="#000100" size="3">logit(e)
</font><font face="Arial" color="#000100" size="3"> ln(
</font><font face="Arial" color="#000100" size="3"><em>e
</em></font><font face="Arial" color="#000100" size="3">/ (1 -
</font><font face="Arial" color="#000100" size="3"><em>e
</em></font><font face="Arial" color="#000100" size="3">))<br><br>
</font><font face="Courier New" color="#000100" size="3">max(e1, e2)
</font><font face="Arial" color="#000100" size="3"> e1 if e1 > e2; e2 otherwise<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3">min(e1, e2)
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">e1 if e1 < e2; e2 otherwise<br><br>
</font><font face="Courier New" color="#000100" size="3">phi(e)
</font><font face="Arial" color="#000100" size="3"> standard normal cdf<br><br>
</font><font face="Arial" color="#000100" size="1"><sup>
</sup></font><font face="Courier New" color="#000100" size="3"><sup>post.p.value(s)
</sup></font><font face="Arial" color="#000100" size="3"><sup>
</sup></font><font face="Arial" color="#000100" size="3">s must be a stochastic node, returns one if a sample from <br> the prior is less than the value of s.<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3"><sup>pow(e1, e2)
</sup></font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3"><em>e
</em></font><font face="Arial" color="#000100" size="2">1
</font><font face="Arial" color="#000100" size="1"><em><sup>e
</sup></em></font><font face="Arial" color="#000100" size="1"><sup>2<br><br>
</sup></font><font face="Courier New" color="#000100" size="3"><sup>prior.p.value(s)
</sup></font><font face="Arial" color="#000100" size="3"><sup>
</sup></font><font face="Arial" color="#000100" size="3">s must be a stochastic node, returns one if a sample from <br> the prior after resampling its stochastic parents is less than<br> value of s.<br> <br>
</font><font face="Courier New" color="#000100" size="3">probit(e)
</font><font face="Arial" color="#000100" size="3"> inverse of
</font><font face="Courier New" color="#000100" size="3">phi(e)
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="1"><sup><br>
</sup></font><font face="Arial" color="#000100" size="3">
</font><font face="Courier New" color="#000100" size="3">replicate.post(s)
</font><font face="Arial" color="#000100" size="3"> replicate from distribution of s, s must be stochastic node <br><br>
</font><font face="Courier New" color="#000100" size="3">replicate.prior(s)
</font><font face="Arial" color="#000100" size="3"> replicate from distribution of s after replicating from it parents if<br> they are stochastic, s must be stochastic node <br>
</font><font face="Arial" color="#000100" size="2"><em><br>
</em></font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3">round(e)
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">nearest integer to e
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#000100" size="3">sin(e)
</font><font face="Arial" color="#000100" size="3"> sine of e<br><br>
</font><font face="Courier New" color="#000100" size="3">sinh(e)
</font><font face="Arial" color="#000100" size="3"> hyperbolic sine of e<br><br>
</font><font face="Arial" color="#000000" size="2"><sub>
</sub></font><font face="Courier New" color="#000100" size="3">solution(F(s), s1, s2, s3)
</font><font face="Arial" color="#000000" size="3"> <br> a solution of equation F(s) = 0 lying between s = s1 and s = s2<br> to accuracy s3, s1 and s2 must bracket a solution<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3"><sup>sqrt(e)
</sup></font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">e
</font><font face="Arial" color="#000100" size="1"><sup>1/2<br>
</sup></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3">step(e)
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">1 if
</font><font face="Arial" color="#000100" size="3"><em>e
</em></font><font face="Arial" color="#000100" size="3"> >= 0; 0 otherwise<br>
</font><font face="Arial" color="#000100" size="1"><sub><br>
</sub></font><font face="Courier New" color="#000100" size="3">tan(e)
</font><font face="Arial" color="#000100" size="3"> tangent of e<br><br>
</font><font face="Courier New" color="#000100" size="3">tanh(e)
</font><font face="Arial" color="#000100" size="3"> hyperbolic tangent of e<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3">trunc(e)
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">greatest integer less than or equal to e<br>
</font><font face="Arial" color="#000100" size="2"><em><br>
</em></font><font face="Arial" color="#000100" size="1"><strong><u><br>
</u></strong></font><font face="Courier New" color="#000100" size="5">Vector functions
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3"><sup>inprod(v1, v2)
</sup></font><font face="Arial" color="#000000" size="3"><sup>
</sup></font><font face="Arial" color="#000000" size="3"><sup>inner product of v1 and v2,
</sup></font><font face="Symbol" color="#000100" size="6"><sub>
</sub></font><font face="Symbol" color="#000100" size="6"><sup>S
</sup></font><font face="Arial" color="#000000" size="1"><sup>i
</sup></font><font face="Arial" color="#000000" size="3"><sup>v
</sup></font><font face="Arial" color="#000000" size="2"><sup>1
</sup></font><font face="Arial" color="#000000" size="1"><sup>i
</sup></font><font face="Arial" color="#000000" size="1"><sup>
</sup></font><font face="Arial" color="#000000" size="3"><sup>v
</sup></font><font face="Arial" color="#000000" size="2"><sup>2i<br>
</sup></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3"><a id="InterpLinFunction">interp.lin(e, v1, v2)<br>
</font><font face="Arial" color="#000000" size="3"> v
</font><font face="Arial" color="#000000" size="2">2
</font><font face="Arial" color="#000000" size="1"><sub>p
</sub></font><font face="Arial" color="#000000" size="2"> + (
</font><font face="Arial" color="#000000" size="3">v
</font><font face="Arial" color="#000000" size="2">2
</font><font face="Arial" color="#000000" size="1"><sub>p
</sub></font><font face="Arial" color="#000000" size="1"><sub>
</sub></font><font face="Arial" color="#000000" size="1"><sub>+
</sub></font><font face="Arial" color="#000000" size="1"><sub>
</sub></font><font face="Arial" color="#000000" size="1"><sub>1
</sub></font><font face="Arial" color="#000000" size="2"> -
</font><font face="Arial" color="#000000" size="3">v
</font><font face="Arial" color="#000000" size="2">2
</font><font face="Arial" color="#000000" size="1"><sub>p
</sub></font><font face="Arial" color="#000000" size="2">) * (
</font><font face="Arial" color="#000000" size="3">e - v
</font><font face="Arial" color="#000000" size="2">1
</font><font face="Arial" color="#000000" size="1"><sub>p
</sub></font><font face="Arial" color="#000000" size="2">) / (
</font><font face="Arial" color="#000000" size="3">v
</font><font face="Arial" color="#000000" size="2">1
</font><font face="Arial" color="#000000" size="1"><sub>p
</sub></font><font face="Arial" color="#000000" size="1"><sub>
</sub></font><font face="Arial" color="#000000" size="1"><sub>+
</sub></font><font face="Arial" color="#000000" size="1"><sub>
</sub></font><font face="Arial" color="#000000" size="1"><sub>1
</sub></font><font face="Arial" color="#000000" size="2"> -
</font><font face="Arial" color="#000000" size="3">v
</font><font face="Arial" color="#000000" size="2">1
</font><font face="Arial" color="#000000" size="1"><sub>p
</sub></font><font face="Arial" color="#000000" size="2">)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3">where the elements of
</font><font face="Arial" color="#000000" size="3"><em>v
</em></font><font face="Arial" color="#000000" size="2">1
</font><font face="Arial" color="#000000" size="3">are in ascending order<br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3"> and p is such that
</font><font face="Arial" color="#000000" size="3"><em>v
</em></font><font face="Arial" color="#000000" size="2">1
</font><font face="Arial" color="#000000" size="1"><sub>p
</sub></font><font face="Arial" color="#000000" size="2"> <
</font><font face="Arial" color="#000000" size="3"><em>e
</em></font><font face="Arial" color="#000000" size="2"> <
</font><font face="Arial" color="#000000" size="3"><em>v
</em></font><font face="Arial" color="#000000" size="2">1
</font><font face="Arial" color="#000000" size="1"><sub>p
</sub></font><font face="Arial" color="#000000" size="1"><sub>
</sub></font><font face="Arial" color="#000000" size="1"><sub>+
</sub></font><font face="Arial" color="#000000" size="1"><sub>
</sub></font><font face="Arial" color="#000000" size="1"><sub>1.<br> <br>
</sub></font><font face="Arial" color="#000000" size="3"><sub> Given function values in the vector v2 evaluated at the points in <br> v1, this estimates the function value at a new point e by simple <br> linear interpolation using the closest bounding pair of points.<br> For example, given the population in 1991,2001 and 2011, we<br> [...]
</sub></font><font face="Arial" color="#000000" size="1"><sub><br>
</sub></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#000100" size="3">inverse(v)
</font><font face="Arial" color="#000100" size="3"> inverse of symmetric positive-definite matrix v<br><br>
</font><font face="Courier New" color="#000100" size="3">logdet(v)
</font><font face="Arial" color="#000100" size="3"> log of determinant of v for symmetric positive-definite
</font><font face="Arial" color="#000100" size="3"><em>v<br><br>
</em></font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3"><sup>mean(v)
</sup></font><font face="Arial" color="#000100" size="2">
</font><font face="Symbol" color="#000100" size="6"><sub>S
</sub></font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">v
</font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="2"> /
</font><font face="Arial" color="#000100" size="3">n
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">n = dim(v)
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#000100" size="3">eigen.vals(v)
</font><font face="Arial" color="#000100" size="3"> eigenvalues of matrix v<br>
</font><font face="Arial" color="#000100" size="3"><sup><br>
</sup></font><font face="Courier New" color="#000100" size="3"><sup>ode(v1, v2, D(v3, s1), s2, s3)<br>
</sup></font><font face="Arial" color="#000100" size="3"><sup> solution of system of ordinary differential equations at grid <br> of points v2 given initial values v1 at time s2 solved<br> to accuracy s3. v3 is a vector of components of the system<br> of ode and s1 is the time variable.
</sup></font><font face="Arial" color="#000100" size="3"> See the PDF files in the
</font><font face="Courier New" color="#000100" size="3"><sup> <br> Diff/Docu
</sup></font><font face="Arial" color="#000100" size="3"><sup>directory of the OpenBUGS installation for <br> further details.
</sup></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Courier New" color="#000100" size="3">prod(v)
</font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="6"><sub>P
</sub></font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><em>v
</em></font><font face="Arial" color="#000100" size="1"><sub>i<br>
</sub></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"><sup>p.valueM(v)
</sup></font><font face="Arial" color="#000100" size="3"><sup>
</sup></font><font face="Arial" color="#000100" size="3">v must be a multivariate stochastic node, returns a vector of<br> ones and zeros depending on if a sample from the prior is less<br> than value of the corresponding component of v<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3">rank(v, s)
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">number of components of v
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">less than or equal to s
</font><font face="Arial" color="#000100" size="1"><sub><br>
</sub></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3"><sup>ranked(v, s)
</sup></font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">the
</font><font face="Arial" color="#000100" size="3"><em>s
</em></font><font face="Arial" color="#000100" size="1"><sup>th
</sup></font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">smallest component of v<br><br>
</font><font face="Courier New" color="#000100" size="3">replicate.postM(v)
</font><font face="Arial" color="#000100" size="3"> replicate from multivariate distribution of v, v must be stochastic<br> and multivariate<br><br>
</font><font face="Courier New" color="#000100" size="3">sd(v)
</font><font face="Arial" color="#000100" size="3"> standard deviation of components of
</font><font face="Arial" color="#000100" size="3"><em>v
</em></font><font face="Arial" color="#000100" size="3"> (n - 1 in denominator)<br>
</font><font face="Arial" color="#000100" size="3"><sup><br>
</sup></font><font face="Courier New" color="#000100" size="3"><sup>sort(v)
</sup></font><font face="Arial" color="#000100" size="3"><sup> vector v sorted in ascending order<br><br>
</sup></font><font face="Arial" color="#000100" size="1">
</font><font face="Courier New" color="#000100" size="3"><sup>sum(v)
</sup></font><font face="Arial" color="#000100" size="2">
</font><font face="Symbol" color="#000100" size="6"><sub>S
</sub></font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><em>v
</em></font><font face="Arial" color="#000100" size="1"><sub>i
</sub></font>
</p>
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<head>
<title>References</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="references0.bmp" alt="[references0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">References
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="2"><br><br><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><a id="CODARef">Best N G, Cowles M K and Vines S K (1997)</a>
</font><font face="Arial" color="#000100" size="2"><em>CODA: Convergence diagnosis and output analysis software for Gibbs sampling output, Version 0.4
</em></font><font face="Arial" color="#000100" size="2">. MRC Biostatistics Unit, Cambridge:<br>
</font><font face="Arial" color="#000100" size="3">http://www.mrc-bsu.cam.ac.uk/bugs/classic/coda04/readme.shtml
</font><font face="Arial" color="#000100" size="2"><br><br>Breslow N E and Clayton D G (1993) Approximate inference in generalized linear mixed models.
</font><font face="Arial" color="#000100" size="2"><em>Journal of the American Statistical Association
</em></font><font face="Arial" color="#000100" size="2">.
</font><font face="Arial" color="#000100" size="2"><strong>88
</strong></font><font face="Arial" color="#000100" size="2">, 9-25.<br><br>Brooks S P (1998) Markov chain Monte Carlo method and its application.
</font><font face="Arial" color="#000100" size="2"><em>The Statistician
</em></font><font face="Arial" color="#000100" size="2">.
</font><font face="Arial" color="#000100" size="2"><strong>47
</strong></font><font face="Arial" color="#000100" size="2">, 69-100.<br>
</font><font face="Arial" color="#000100" size="2"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><a id="BGRDiagPaper">Brooks S P and Gelman A (1998)</a> Alternative methods for monitoring convergence of iterative simulations.
</font><font face="Arial" color="#000100" size="2"><em>Journal of Computational and Graphical Statistics
</em></font><font face="Arial" color="#000100" size="2">.
</font><font face="Arial" color="#000100" size="2"><strong>7
</strong></font><font face="Arial" color="#000100" size="2">, 434-455.<br><br>Carlin B P
</font><font face="Arial" color="#000100" size="2"><strong>
</strong></font><font face="Arial" color="#000100" size="2">and Louis T A (1996)
</font><font face="Arial" color="#000100" size="2"><em> Bayes and Empirical Bayes Methods for Data Analysis
</em></font><font face="Arial" color="#000100" size="2">. Chapman and Hall, London, UK.<br><br>Congdon P (2001)
</font><font face="Arial" color="#000100" size="2"><em>Bayesian Statistical Modelling
</em></font><font face="Arial" color="#000100" size="2">. John Wiley & Sons, Chichester, UK.<br><br>Crowder M J (1978) Beta-binomial Anova for proportions.
</font><font face="Arial" color="#000100" size="2"><em>Applied Statistics
</em></font><font face="Arial" color="#000100" size="2">.
</font><font face="Arial" color="#000100" size="2"><strong>27
</strong></font><font face="Arial" color="#000100" size="2">, 34-37.<br><br><a id="Gamerman">Gamerman D (1997)</a> Sampling from the posterior distribution in generalized linear mixed models.
</font><font face="Arial" color="#000100" size="2"><em>Statistics and Computing
</em></font><font face="Arial" color="#000100" size="2">.
</font><font face="Arial" color="#000100" size="2"><strong>7
</strong></font><font face="Arial" color="#000100" size="2">, 57-68.<br><br>Gelman A, Carlin J C, Stern H and Rubin D B (1995)
</font><font face="Arial" color="#000100" size="2"><em>Bayesian Data Analysis.
</em></font><font face="Arial" color="#000100" size="2"> Chapman and Hall, New York.<br><br>Gilks W (1992) Derivative-free adaptive rejection sampling for Gibbs sampling. In
</font><font face="Arial" color="#000100" size="2"><em> Bayesian Statistics 4
</em></font><font face="Arial" color="#000100" size="2">, (J M Bernardo, J O Berger, A P Dawid, and A F M Smith, eds), Oxford University Press, UK, pp. 641-665.<br><br>Gilks W R, Richardson S and Spiegelhalter D J (Eds.) (1996)
</font><font face="Arial" color="#000100" size="2"><em>Markov chain Monte Carlo in Practice
</em></font><font face="Arial" color="#000100" size="2">. Chapman and Hall, London, UK.<br><br>
</font><font face="Arial" color="#000100" size="2"><a id="DenstripPaper">Jackson C H (2008)</a> Displaying uncertainty with shading.
</font><font face="Arial" color="#000100" size="2"><em>The American Statistician.
</em></font><font face="Arial" color="#000100" size="2"><strong>62
</strong></font><font face="Arial" color="#000100" size="2">, 340-347.<br>
</font><font face="Arial" color="#000100" size="2"><br>Neal R (1997) Markov chain Monte Carlo methods based on 'slicing' the density function.
</font><font face="Arial" color="#000100" size="2"><em>Technical Report 9722
</em></font><font face="Arial" color="#000100" size="2">, Department of Statistics, University of Toronto, Canada:<br>
</font><font face="Arial" color="#000100" size="3">http://www.cs.utoronto.ca/~radford/publications.html
</font><font face="Arial" color="#000100" size="2"><br><br>Neal R (1998) Suppressing random walks in Markov chain Monte Carlo using ordered over-relaxation. In
</font><font face="Arial" color="#000100" size="2"><em>Learning in Graphical Models
</em></font><font face="Arial" color="#000100" size="2">, (M I Jordan, ed). Kluwer Academic Publishers, Dordrecht, pp. 205-230.<br>
</font><font face="Arial" color="#000100" size="3">http://www.cs.utoronto.ca/~radford/publications.html
</font><font face="Arial" color="#000100" size="2"><strong><br><br>
</strong></font><font face="Arial" color="#000100" size="2">Roberts G O (1996). Markov chain concepts related to sampling algorithms. In W R Gilks, S Richardson and D J Spiegelhalter (Eds.)
</font><font face="Arial" color="#000100" size="2"><em>Markov chain Monte Carlo in Practice
</em></font><font face="Arial" color="#000100" size="2">. Chapman and Hall, London, UK.<br><br><a id="DICPaper">Spiegelhalter D J, Best N G, Carlin B P and van der Linde A (2002)</a> Bayesian measures of model complexity and fit (with discussion).
</font><font face="Arial" color="#000100" size="2"><em>J. Roy. Statist. Soc. B
</em></font><font face="Arial" color="#000100" size="2">.
</font><font face="Arial" color="#000100" size="2"><strong>64
</strong></font><font face="Arial" color="#000100" size="2">, 583-640.<br><br><a id="RunningQuantilesReference">Tierney L (1983)</a> A space-efficient recursive procedure for estimating a quantile of an unknown distribution.
</font><font face="Arial" color="#000100" size="2"><em>SIAM J. Sci. Stat. Comput
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</strong></font><font face="Arial" color="#000100" size="2">, 706-711.<br><br>
</font>
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<html>
<head>
<title>Scripts</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="scripts0.bmp" alt="[scripts0]">
</font><font face="Courier New" color="#000100" size="6">Scripts and Batch-mode
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Scripting">Scripting</a>
</font><font face="Arial" color="#FF0000" size="5"><em><br><br>
</em></font><font face="Arial" color="#000100" size="3">As an alternative to the menu / dialog box interface, scripting commands has been created that can 1) automate routine analyses, 2) create reproducible analyses, and 3) produce batch execution for simulation studies, etc. The scripting commands work in effect by writing values into fields and clicking on buttons in relevant dialog boxes. It is possible to combine use of scripting with the menu / dialog box interface.<br><br>The scrip [...]
</font><font face="Arial" color="#0000FF" size="3">(
</font><font face="Times New Roman" color="#0000FF" size="3"></a><a href="#ScriptCommands">Script Commands</a>
</font><font face="Arial" color="#0000FF" size="3">)
</font><font face="Arial" color="#000100" size="3"> can be used so that full path names are not required for all file names. The linux shell commands
</font><font face="Arial" color="#0000FF" size="3">(<a href="#LinuxScript">
</font><font face="Times New Roman" color="#0000FF" size="3">Linux execution</a>)
</font><font face="Times New Roman" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">offer an alternative approach for path names in linux.<br><br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="GUIScript">Executing script commands from the GUI</a>
</font><font face="Courier New" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">A set of script commands can be executed from the GUI by selecting the window that contains them, and then selecting Script from the Model menu. All commands in the window are executed, unless some commands are highlighted, in which case only the highlighted commands are executed (a partially highlighted command will produce an error). The contents of a window with script commands does not have to be saved before it is executed. Input fil [...]
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> format (.odc) or text format, in which case it must have a .txt extension.<br><br>After execution of script commands, GUI menu selections can be used to view changed settings. If a dialog box was already open when a script was executed, it may need to be closed and re-opened to ensure that its contents are refreshed. Execution of script and GUI commands can be mixed, allowing automation of tasks such as summary setting for models wi [...]
</font><font face="Courier New" color="#000100" size="5"><a id="WindowsScript">Batch-mode in Windows</a>
</font><font face="Arial" color="#FF0000" size="5"><em><br><br>
</em></font><font face="Arial" color="#000100" size="3">OpenBUGS can execute a file of script commands in Batch-mode from a programming shell using the following syntax:<br>
</font><font face="Arial" color="#FF0000" size="5"><em><br>
</em></font><font face="Arial" color="#000000" size="3">"FULLPATH/OpenBUGS.exe" /PAR "FULLPATH/ScriptName.txt" /HEADLESS<br><br>It is important to add modelQuit('yes') at the end of the script file so OpenBUGS will stop execution and return control to the initiating shell when the script commands are complete. It is also important to include a modelDisplay('log') at the beginning of the script file, and modelSaveLog('filename.odc') before modelQuit as this is the only [...]
</font><font face="Arial" color="#000100" size="3">Input files (including the script) may be in either native
</font><font face="Arial" color="#000100" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000100" size="3"> format (.odc) or text format. Text format requires a .txt extension.<br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="LinuxScript">Batch-mode in Linux</a><br><br>
</font><font face="Arial" color="#000100" size="3">OpenBUGS can be executed from the Linux OS on Intel-based machines in a native format that yields results that exactly agree with those from the Windows OS on the same hardware. The GUI, and graphical output (e.g., history plots) depend on Windows-specific code, however, and are not available with Linux execution.<br>
</font><font face="Courier New" color="#000100" size="5"><br>
</font><font face="Arial" color="#000100" size="3">A bash shell script called OpenBUGS is included in the standard Linux distribution in the /bin sub-directory. Once this directory is added to a user's path, the OpenBUGS command behaves like a standard Linux program. Typing OpenBUGS without inputs starts the program in interactive mode with screen I/O. To exit the program type "modelQuit()". To execute a script file, script.txt, in batch mode with output to file log.txt:<br><br> [...]
</font><font face="Arial" color="#000100" size="3"><strong>modelSetWD("/path/to/dir/")
</strong></font><font face="Arial" color="#000100" size="3">can be specified to reset the working directory to /path/to/dir
</font><font face="Arial" color="#000100" size="3"><strong>.
</strong></font><font face="Arial" color="#000100" size="3"><br><br>Additional options can be found by typing OpenBUGS --help.<br><br>Input files must be in ASCII format. The log file (ASCII format) is always written to standard output with Linux execution, so the modelSaveLog command is disabled during Linux execution. <br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="ScriptCommands">The scripting commands</a><br>
</font><font face="Arial" color="#000100" size="3"><br>Script commands and a brief synopsis of their menu/dialog box equivalent are supplied below. The script command and corresponding menu name are in bold. The menu names are followed by their associated menu options or dialog box and potential user inputs. You can find detailed descriptions of the menu/dialog box options in the corresponding Manual entries for the
</font><font face="Arial" color="#0000FF" size="3"><a href="../Manuals/ModelMenu.html">Model menu</a>,
</font><font face="Arial" color="#000100" size="3"> <a href="../Manuals/InferenceMenu.html">
</font><font face="Arial" color="#0000FF" size="3">Inference menu
</font><font face="Arial" color="#000100" size="3"></a>, <a href="../Manuals/InfoMenu.html">
</font><font face="Arial" color="#0000FF" size="3">Info menu
</font><font face="Arial" color="#000100" size="3"></a> and <a href="../Manuals/FileMenu.html">
</font><font face="Arial" color="#0000FF" size="3">File menu</a>
</font><font face="Arial" color="#000100" size="3">.<br><br>Script commands have two input types: character strings and integers. If a string argument contains non-alpha-numeric characters (including space but excluding the period) the string must be enclosed in quotes. Arguments that are required to be supplied by the user are shown in
</font><font face="Arial" color="#0000FF" size="3"><em>blue italics
</em></font><font face="Arial" color="#000100" size="3">; optional arguments are displayed in plain text. Optional arguments will be set to default values if they are omitted.<br><br>If the menu/dialog box equivalent of the specified script command would normally be grayed out because of inappropriate timing, for example, then the script command will not execute and an error message will be produced instead.<br><br>Commands that are preceded by an
</font><font face="Arial" color="#000000" size="3">asterisk (*)
</font><font face="Arial" color="#000100" size="3">, are not available with Linux execution.<br><br>The translations between commands in the script language and the underlying Component Pascal procedures implementing them in OpenBUGS are in the file Bugs/Mod/Script.odc in the OpenBUGS program directory. Explanations of the commands and their inputs are in the documentation for the menu items.<br><br><br>
</font><font face="Courier New" color="#000000" size="3"><strong><u> Script_command_description
</u></strong></font><font face="Arial" color="#000000" size="3"><strong>
</strong></font><font face="Courier New" color="#000000" size="3"><strong><u>Menu_/_dialog_box_equivalent
</u></strong></font><font face="Arial" color="#000100" size="3"><strong><br> <br> modelGetWD()
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> None
</strong></font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3">Returns
</font><font face="Arial" color="#0000FF" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">the default path for file name input<br><br>
</font><font face="Arial" color="#000100" size="3"><strong> modelSetWD(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> None
</strong></font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = Full default path for file name input<br>
</font><font face="Arial" color="#000100" size="3"><strong><br> modelCheck(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Specification... >
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = (full path to) Model file<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>modelData(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Specification... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = (full path to) Data file<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>modelCompile(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>int
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Specification... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- int
</em></font><font face="Arial" color="#000100" size="3"> = number of chains<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>modelInits(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000000" size="3">int
</font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Specification... > <br>
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = (full path to) Inits file<br> - int = for chain (default=1)<br>
</font><font face="Arial" color="#000000" size="3">The initial values for each chain must be in separate files.
</font><font face="Arial" color="#000100" size="3"><br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>modelGenInits()
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Specification... >
</font><font face="Arial" color="#000100" size="3"><u><br><br> _____________________________________________________________________<br> <br>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>modelUpdate(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>int0
</em></font><font face="Arial" color="#000100" size="3">, int1, int2, string
</font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Update...> <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- int0
</em></font><font face="Arial" color="#000100" size="3"> = updates<br> - int1 = thin. Thinning in this way will discard the samples (c.f. the samplesThin() command)<br> - int2 = frequency of refreshing the display in the Windows interface<br> - string = "T" or "F" for over relax<br> _____________________________________________________________________<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>modelSaveState(
</strong></font><font face="Arial" color="#000100" size="3">string
</font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Save State<br> - string = fileStem<br>
</font><font face="Arial" color="#000000" size="3">Note that the string must be specified for Linux execution.
</font><font face="Arial" color="#000100" size="3"><br> _____________________________________________________________________<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>modelGetRN()
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> RN generator...<br> Returns the starting (preset) state of the random number generator<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>modelSetRN(
</strong></font><font face="Arial" color="#000100" size="3">int
</font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> RN generator...<br> Set the starting (preset) state of the random number generator to 'int'. This must be an <br> integer from 1 to 14 inclusive. <br> _____________________________________________________________________
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="3"><strong>modelDisplay(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Input/Output options...<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = 'window' or 'log'<br> <br>
</font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3"><strong>modelPrecision(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>int
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Input/Output options...<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- int
</em></font><font face="Arial" color="#000100" size="3"> = number of significant digits for output<br> _____________________________________________________________________<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>modelDisable(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Updater options...<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = name of updater to disable<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>modelEnable(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Updater options...<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = name of updater to enable<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>modelSetAP(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#0000FF" size="3"><em>int
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model>
</strong></font><font face="Arial" color="#000100" size="3">Updater options...<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = name of sampler<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- int
</em></font><font face="Arial" color="#000100" size="3"> = number of iterations in the adaptive phase
</font><font face="Arial" color="#FF0000" size="3">
</font><font face="Arial" color="#000100" size="3"><br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>modelSetIts(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#0000FF" size="3"><em>int
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Updater options...<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = name of sampler <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- int
</em></font><font face="Arial" color="#000100" size="3"> = number of iterations<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>modelSetOR(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#0000FF" size="3"><em>int
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Updater options...<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = name of sampler<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- int
</em></font><font face="Arial" color="#000100" size="3"> = number of samples to generate for over-relaxed MCMC<br> _____________________________________________________________________ <br>
</font><font face="Arial" color="#000100" size="3"><strong>modelExternalize(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Externalize<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = file name, including the extension. The extension is conventionally ".bug" for externalized OpenBUGS models.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>modelInternalize(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Model
</strong></font><font face="Arial" color="#000100" size="3">> Internalize<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = file name, including extension. <br>
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>modelQuit(
</strong></font><font face="Arial" color="#000100" size="3">string
</font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> File
</strong></font><font face="Arial" color="#000100" size="3"> > Exit<br> - string = 'y' or 'yes' to quick without a dialog box opening before exiting<br> If string is omitted, a dialog box appears before exit.<br> <br> *
</font><font face="Arial" color="#000100" size="3"><strong>modelSaveLog(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> File
</strong></font><font face="Arial" color="#000100" size="3">> Save As... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = file name
</font><font face="Arial" color="#000100" size="3"><u><br>
</u></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3">If the file ends with ".txt" the log window is saved to a text file (with all graphics, fonts, etc., stripped out).<br>
</font><font face="Arial" color="#000100" size="3">_____________________________________________________________________<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>samplesSet(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Samples... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node to set<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>samplesClear(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Samples... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node to clear<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>samplesBeg(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>int
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3"> > Samples...<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- int
</em></font><font face="Arial" color="#000100" size="3"> = beginning update to define subset of the stored sample for analysis<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>samplesEnd(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>int
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3"> > Samples... <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- int
</em></font><font face="Arial" color="#000100" size="3"> = ending update to define subset of the stored sample for analysis<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>samplesFirstChain(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>int
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3"> > Samples...<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- int
</em></font><font face="Arial" color="#000100" size="3"> = select beginning of range of chains which contribute to statistics being calculated<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>samplesLastChain(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>int
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3"> > Samples... <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- int
</em></font><font face="Arial" color="#000100" size="3"> = select end of range of chains which contribute to statistics being calculated
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3"> <br>
</font><font face="Arial" color="#000100" size="3"><strong>samplesThin(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>int
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3"> > Samples...<br>
</font><font face="Arial" color="#0000FF" size="3"><em>- int
</em></font><font face="Arial" color="#000100" size="3"> = thin. Every
</font><font face="Arial" color="#000100" size="3"><em>int
</em></font><font face="Arial" color="#000100" size="3"><sup>th
</sup></font><font face="Arial" color="#000100" size="3"> sample is used for inference. Does not impact storage<br> requirements.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>samplesStats(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Samples... > <br> -
</font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to calculate sample statistics. Can use '*' for all set nodes.<br> <br> *
</font><font face="Arial" color="#000100" size="3"><strong>samplesDensity(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Samples... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to generate density plot. Can use '*' for all set nodes.<br> <br> *
</font><font face="Arial" color="#000100" size="3"><strong>samplesAutoC(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3"> > Samples... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to generate autocorrelation plot. Can use '*' for all set nodes.<br> <br> *
</font><font face="Arial" color="#000100" size="3"><strong>samplesTrace(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>Inference
</strong></font><font face="Arial" color="#000100" size="3">> Samples... > <br>
</font><font face="Arial" color="#0000FF" size="3">-
</font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to generate trace plot. Can use '*' for all set nodes.<br> <br> *
</font><font face="Arial" color="#000100" size="3"><strong>samplesHistory(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Samples... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to generate history plot. Can use '*' for all set nodes.<br> <br> *
</font><font face="Arial" color="#000100" size="3"><strong>samplesQuantiles(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Samples... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to generate quantiles plot. Can use '*' for all set nodes.<br> <br> *
</font><font face="Arial" color="#000100" size="3"><strong>samplesBgr(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Samples... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to generate Brooks-Gelman-Rubin diagnostics. <br> Can use '*' for all set nodes.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>samplesCoda(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string0
</em></font><font face="Arial" color="#000100" size="3">, string1
</font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Samples... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string0
</em></font><font face="Arial" color="#000100" size="3"> = node for which to save all monitored values in plain text files, formatted for <br> use in the
</font><font face="Courier New" color="#000100" size="3">coda
</font><font face="Arial" color="#000100" size="3"> package for R. Can use '*' for all set nodes.<br> - string1 = 'fileStem'<br><br> There will be one file for each parallel chain, named as
</font><font face="Courier New" color="#000100" size="3">fileStemCODAchain1.txt, fileStemCODAchain2.txt
</font><font face="Arial" color="#000100" size="3"> and so on, and a file
</font><font face="Courier New" color="#000100" size="3"> fileStemCODAindex.txt
</font><font face="Arial" color="#000100" size="3"> <br> indexing the row numbers corresponding to each node.
</font><font face="Arial" color="#000100" size="3"><em><br> ______________________________________________________________<br> <br>
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>summarySet(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Summary... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to calculate running mean, standard deviation and quantiles<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>summaryStats(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Summary... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to display approximate running summary statistics<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>summaryMean(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Summary... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to display running mean in comma delimited form<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>summaryClear(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>Inference
</strong></font><font face="Arial" color="#000100" size="3">> Summary... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node to remove the running summary statistics<br> _____________________________________________________________________<br>
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>ranksSet(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Rank... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node to be ranked (must be an array)
</font><font face="Arial" color="#000100" size="3"><em><br>
</em></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong>ranksStats(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Rank... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to summarize the simulated ranks of the components<br> <br> *
</font><font face="Arial" color="#000100" size="3"><strong>ranksHistogram(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Rank... > <br>
</font><font face="Arial" color="#000100" size="3"><em>-
</em></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to display a histogram of the simulated ranks of the components<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>ranksClear(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> Rank... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to clear the running summary
</font><font face="Arial" color="#000100" size="3"><em><br> _____________________________________________________________________<br> <br>
</em></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong>dicSet()
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> DIC... ><br> Start calculating DIC and related statistics<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>dicClear()
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">> DIC... > <br> Clear DIC calculations from memory<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>dicStats()
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Inference
</strong></font><font face="Arial" color="#000100" size="3">>DIC... > <br> Display DIC, Dbar, Dhat, and pD<br> _____________________________________________________________________<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>infoNodeValues(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Info
</strong></font><font face="Arial" color="#000100" size="3">> Node info... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which to display the current value(s)<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>infoNodeMethods(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Info
</strong></font><font face="Arial" color="#000100" size="3">> Node info... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which you want to see the type of updater used to sample from<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>infoNodeTypes(
</strong></font><font face="Arial" color="#0000FF" size="3"><em>string
</em></font><font face="Arial" color="#000100" size="3"><strong>)
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Info
</strong></font><font face="Arial" color="#000100" size="3">> Node info... > <br>
</font><font face="Arial" color="#0000FF" size="3"><em>- string
</em></font><font face="Arial" color="#000100" size="3"> = node for which you want to see the node type<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>infoMemory()
</strong></font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3"><strong> Info
</strong></font><font face="Arial" color="#000100" size="3">> Memory<br> Show the amount of memory allocated<br> _____________________________________________________________________<br> <br>
</font><font face="Arial" color="#000000" size="3">*
</font><font face="Arial" color="#000000" size="3"><strong>infoUnitializedUpdaters()
</strong></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000000" size="3"><strong> Info
</strong></font><font face="Arial" color="#000000" size="3">> Uninitialized Nodes<br> Shows nodes in the compiled model that have not been initialized yet.<br> <br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3"><strong>infoUpdatersbyName()
</strong></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000000" size="3"><strong> Info
</strong></font><font face="Arial" color="#000000" size="3">> Updaters(by name)<br> List the nodes with their associated updater algorithm in alphabetical order .<br> <br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000000" size="3"><strong>infoUpdatersbyDepth()
</strong></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000000" size="3"><strong> Info
</strong></font><font face="Arial" color="#000000" size="3">> Updaters(by depth)<br> List the nodes with their associated updater algorithm in the reverse topological order to <br> which they occur in the graphical model.<br> _____________________________________________________________________<br> <br>
</font><font face="Arial" color="#000000" size="3"><strong>infoModules()
</strong></font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000000" size="3"><strong> Info
</strong></font><font face="Arial" color="#000000" size="3">> Modules<br>
</font><font face="Arial" color="#000100" size="3">Displays all the modules (dynamic link libraries) in use.
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#FF0000" size="3"><em><br>
</em></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#000100" size="5"><br><a id="Example">Example</a>
</font><font face="Arial" color="#FF0000" size="5"><em><br>
</em></font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3">The script code below shows the steps you might use to reproduce the Rats example. To execute, highlight the entire script (or one line at a time) and select
</font><font face="Arial" color="#000100" size="3"><strong>Model
</strong></font><font face="Arial" color="#000100" size="3"> > Script.
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Courier New" color="#000100" size="3"># Check model syntax<br>modelCheck('C:/Program Files/OpenBUGS/Examples/Ratsmodel.txt')<br><br># Load data<br>modelData('C:/Program Files/OpenBUGS/Examples/Ratsdata.txt')<br><br># Compile with one chain<br>modelCompile(1)<br><br># Load inital values for first chain<br>modelInits('C:/Program Files/OpenBUGS/Examples/Ratsinits.txt',1)<br><br># Start with 1000 update burn-in<br>modelUpdate(1000)<br><br># Set nodes of interest<br>samplesS [...]
</font>
</p>
</body>
</html>
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+++ b/doc/Manuals/TextMenu.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>TextMenu</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="textmenu0.bmp" alt="[textmenu0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">The Text Menu
</font><font face="Arial" color="#000100" size="6"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#GeneralProperties">General properties</a><br> <a href="#Find/Replace">Find/Replace...</a><br> <a href="#FindAgain">Find Again</a><br> <a href="#FindPrevious">Find Previous</a><br> <a href="#FindFirst">Find First</a><br> <a href="#FindLast">Find Last</a><br> <a href="#ShiftLeft [...]
</font><font face="Courier New" color="#000100" size="5"> <br> <br>
</font><font face="Arial" color="#000100" size="2"><a id="GeneralProperties">
</font><font face="Courier New" color="#000100" size="5">General properties
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The commands in this menu provide tools for searching for and replacing text and inserting special formatting options into the text.<br><br><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Find/Replace">
</strong></font><font face="Courier New" color="#000100" size="5">Find/Replace...</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This command is used to find and replace text. It causes a non modal dialog box to pop up.<br>
</font><font face="Arial" color="#0000FF" size="3"><br> <img src="textmenu1.bmp" alt="[textmenu1]"><br> <br>
</font><font face="Arial" color="#000000" size="3">The 'Find' field contains the text to be searched for. If a stretch of text is highlighted before this dialog is opened this will appear in the 'Find' field. The 'Repl.' field is the text that will be substituted for the text in the 'Find' field if the 'Replace', 'Repl. & Find' or 'Repl. All In Sel.' buttons are clicked. 'Repl. & Find' will also find the next occurrence of the 'Find' text. 'Repl. All In Sel.' will replace all occu [...]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="FindAgain">
</strong></font><font face="Courier New" color="#000100" size="5">Find Again
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This command finds the next occurrence of a highlighted piece of text in the document.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="FindPrevious">
</strong></font><font face="Courier New" color="#000100" size="5">Find Previous
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This command finds the previous occurrence of a highlighted piece of text in the document.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="FindFirst">Find First
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This command finds the first occurence of a highlighted piece of text in the document.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="FindLast">
</strong></font><font face="Courier New" color="#000100" size="5">Find Last
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This command finds the last occurence of a highlighted piece of text in the document.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="ShiftLeft">
</strong></font><font face="Courier New" color="#000100" size="5">Shift Left</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This command shifts the highlighted text one tab stop to the left.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="ShiftRight">
</strong></font><font face="Courier New" color="#000100" size="5">Shift Right</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This command shifts the highlighted text one tab stop to the right.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="InsertParagraph">Insert Paragraph
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="InsertRuler">
</strong></font><font face="Courier New" color="#000100" size="5">Insert Ruler</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This command inserts a ruler at the caret position of the text document.<br>
</font><font face="Arial" color="#0000FF" size="3"><br> <img src="textmenu2.bmp" alt="[textmenu2]"><br> <br>
</font><font face="Arial" color="#000000" size="3">The ruler controls the formatting of the text below the ruler until another ruler is encountered. Tab stops can be added to the ruler by clicking with the mouse in the white region below the grey shaded bar. The tab stop shows up as a black inverted triangle. The position of the tab stop can be changed by dragging it with the mouse. To remove a tab stop drag it all the way to the extreme left edge of the ruler. <br><br>The buttons above t [...]
</font><font face="Courier New" color="#000100" size="5"><a id="InsertSoftHyphen">Insert-Soft-Hyphen
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="InsertNonBrkHyphen">Insert Non-Brk-Hyphen
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This command inserts a hyphen that will not split over a line break.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="InsertNonBrkSpace">Insert Non-Brk-Space
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This command inserts a space that will not split over a line break. It is useful if you want to underline a stretch of text containing spaces.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="InsertDigitSpace">Insert Digit Space
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This command inserts a space that has the same width as a digit (0..9).<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Show/HideMarks">
</strong></font><font face="Courier New" color="#000100" size="5">Show/Hide Marks
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">This command toggles between making special formatting controls visible in the text or making them invisible. Seeing the formatting controls is particularly useful when creating targets and links. See the
</font><font face="Arial" color="#0000FF" size="3"><a href="../Manuals/ToolsMenu.html">Tools menu</a>
</font><font face="Arial" color="#000000" size="3"> for a description on how to do this.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="MakeDefaultAttributes">Make Default Attributes
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="MakeDefaultRuler">Make Default Ruler
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="4"><br>
</font>
</p>
</body>
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diff --git a/doc/Manuals/TipsTroubleshooting.html b/doc/Manuals/TipsTroubleshooting.html
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@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>TipsTroubleshooting</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="tipstroubleshooting0.bmp" alt="[tipstroubleshooting0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Tips and Troubleshooting
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#RestrictionsWhenModelling">Restrictions when modelling</a><br> <a href="#SomeErrorMessages">Some error messages</a><br> <a href="#TrapMessages">Trap windows</a><br> <a href="#TheProgramHangs">The program hangs</a><br> <a href="#SpeedingUpSampling">Speeding up sampling</a><br> &nb [...]
</font><font face="Arial" color="#000100" size="2"><br><br><a id="RestrictionsWhenModelling">
</font><font face="Courier New" color="#000100" size="5">Restrictions when modelling
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Restrictions have been stated throughout this manual. A summary list is as follows:<br>
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3">a) Each stochastic and logical node must appear once and only once on the left-hand-side of an expression. The only exception is when carrying out a data transformation (see
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Manuals/ModelSpecification.html#DataTransformations">Data transformations</a>
</font><font face="Arial" color="#000100" size="3">).
</font><font face="Arial" color="#000000" size="3">This means, for example, that it is generally not possible to give a distribution to a quantity that is specified as a logical function of an unknown parameter.<br>
</font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">b) Truncated sampling distributions cannot be handled using the C(.,.) construct - see
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Manuals/ModelSpecification.html#TheBUGSLanguageStochasticNodes">BUGS language: stochastic nodes</a>.
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#FF0000" size="3"><br>
</font><font face="Arial" color="#000000" size="3">c) Multivariate distributions: Wishart distributions may only be used as conjugate priors and must have known parameters; multivariate normal and Student-t distributions can be used anywhere in the graph (i.e. as prior or likelihood) and there are no restrictions regarding their parameters. See
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/ModelSpecification.html#TheBUGSLanguageStochasticNodes">BUGS language: stochastic nodes
</font><font face="Arial" color="#0000FF" size="3"></a>.<br>
</font><font face="Arial" color="#000000" size="3"><br>d) Logical nodes cannot be given data or initial values. This means, for example, that it is not possible to
</font><font face="Arial" color="#000100" size="3">model observed data that is the sum of two random variables. (See
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Manuals/ModelSpecification.html#LogicalNodes">Logical nodes
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">.)<br><br>
</font><font face="Arial" color="#000100" size="2"><br><br><a id="SomeErrorMessages">
</font><font face="Courier New" color="#000100" size="5">Some error messages
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">In general OpenBUGS tries to give informative, easily understood error messages when there is a problem with the model specification, the data or initial values, or if problems occur with the sampling algorithms. However sometimes numerical problems occur with the sampling algorithms, when this happens a trap message is produced providing a detailed trace back to where the error occurs. <br><br>When an error occurs in the syntax of the mo [...]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">a)
</font><font face="Arial" color="#000100" size="3"><strong>'expected variable name'
</strong></font><font face="Arial" color="#000100" size="3">indicates an inappropriate variable name, for example a variable name in a data set is not a variable name in the model.<br><br>b)
</font><font face="Arial" color="#000100" size="3"><strong>'linear predictor in probit regression too large'
</strong></font><font face="Arial" color="#000100" size="3">indicates numerical overflow. See possible solutions below for Trap 'undefined real result'.<br><br>
</font><font face="Arial" color="#000000" size="3">c)
</font><font face="Arial" color="#000000" size="3"><strong>'logical expression too complex'
</strong></font><font face="Arial" color="#000000" size="3"> - a logical node is defined in terms of too many parameters/constants or too many operators: try introducing further logical nodes to represent parts of the overall calculation; for example, a1 + a2 + a3 + b1 + b2 + b3 could be written as A + B where A and B are the simpler logical expressions a1 + a2 + a3 and b1 + b2 + b3, respectively. Note that linear predictors with many terms should be formulated by 'vectorizing' parameters [...]
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/ModelSpecification.html#LogicalNodes">Logical nodes
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000000" size="3">).<br><br>
</font><font face="Arial" color="#000100" size="3">d)
</font><font face="Arial" color="#000100" size="3"><strong>'invalid or unexpected token scanned' -
</strong></font><font face="Arial" color="#000100" size="3">the parser has encountered an unexpected symbol, for example if using a Doodle check that the
</font><font face="Arial" color="#000100" size="3"><em>value
</em></font><font face="Arial" color="#000100" size="3"> field of a logical node has been completed.<br><br>e)
</font><font face="Arial" color="#000100" size="3"><strong>'unable to choose update method'
</strong></font><font face="Arial" color="#000100" size="3">indicates that a restriction in the program has been violated - see
</font><font face="Courier New" color="#0000FF" size="3"><a href="#RestrictionsWhenModelling">Restrictions when modelling</a>
</font><font face="Arial" color="#000100" size="3"> above.<br><br>f)
</font><font face="Arial" color="#000100" size="3"><strong>'undefined variable'
</strong></font><font face="Arial" color="#000100" size="3">- undefined variables are allowed in the model so long as they are not used on the right hand side of a relation.<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3">g)
</font><font face="Arial" color="#000000" size="3"><strong>'index out of range'
</strong></font><font face="Arial" color="#000000" size="3"> - usually indicates that a loop-index goes beyond the size of a vector (or matrix dimension).
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>In rare cases
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> is unable to find a suitable sampling algorithm for a node in the model. The error message
</font><font face="Arial" color="#000000" size="3"><strong>'Unable to choose update method for node x'
</strong></font><font face="Arial" color="#000000" size="3">will be displayed where x is the node for which
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3"> can not find an update method.<br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="TrapMessages">
</font><font face="Courier New" color="#000100" size="5">Trap windows
</font><font face="Arial" color="#000000" size="3"></a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">Trap windows occur when a problem with the BUGS software is detected by the run time system. The run time system is a small piece of software that watches the main program (OpenBUGS) and reports if some illegal action occurs. The first line of the trap windows gives a description of the type of illegal action detected by the run time system. Note that a trap window is different form an error message. It can be thought of as an error in th [...]
</font><font face="Arial" color="#000100" size="1">fields
</font><font face="Arial" color="#000100" size="3"> give information about structured variables. <br><br>A section of a typical trap widow is shown below (in this case
</font><font face="Arial" color="#000100" size="1"><strong>TRAP 0
</strong></font><font face="Arial" color="#000100" size="3"> is a special, deliberate -that is programmed - error).<br><br> <img src="tipstroubleshooting3.bmp" alt="[tipstroubleshooting3]"><br><br><br>Some common illegal actions detected by the run time system are:<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">a)
</font><font face="Arial" color="#000100" size="3"><strong>'undefined real result'
</strong></font><font face="Arial" color="#000100" size="3">indicates numerical overflow. Possible reasons include:<br>- initial values generated from a 'vague' prior distribution may be numerically extreme - specify appropriate initial values;<br>- numerically impossible values such as log of a non-positive number - check, for example, that no zero expectations have been given when Poisson modelling;<br>- numerical difficulties in sampling. Possible solutions include:<br>- better initial [...]
</font><font face="Arial" color="#000100" size="3"><strong>'index array out of range' -
</strong></font><font face="Arial" color="#000100" size="3">possible reasons include:<br>- attempting to assign values beyond the declared length of an array;<br><br>c)
</font><font face="Arial" color="#000100" size="3"><strong>'stack overflow'
</strong></font><font face="Arial" color="#000100" size="3">can occur if there is a recursive definition of a logical node.<br><br>d)
</font><font face="Arial" color="#000100" size="3"><strong>'NIL dereference (read)'
</strong></font><font face="Arial" color="#000100" size="3">can occur at compilation in some circumstances when an inappropriate transformation is made, for example an array into a scalar.<br><br>e)
</font><font face="Arial" color="#000100" size="3"><strong>argument of sqrt must not be negative
</strong></font><font face="Helvetica" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">the square root of a negative number has been taken, this occurs if the precision matrix of a multivariate normal is not positive definite.
</font><font face="Helvetica" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="2"><strong><br>
</strong></font><font face="Courier New" color="#000100" size="5"><a id="TheProgramHangs">The program hangs</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">This could be due to:<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">a) a problem that seems to happen with NT - rebooting is a crude way out;<br>b) interference with other programs running - try to run WinBUGS on its own;<br>c) a particularly ill-posed model - try the approaches listed above under Trap messages.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="SpeedingUpSampling">
</font><font face="Courier New" color="#000100" size="5">Speeding up sampling
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The key is to reduce function evaluations by expressing the model in as concise a form as possible. For example, take advantage of the functions provided and use nested indexing wherever possible. Look at the packaged examples and others provided on users' web sites.<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="ImprovingConvergence">Improving convergence
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Possible solutions include:
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3">a) better parameterisation to improve orthogonality of joint posterior;<br>b) standardisation of covariates to have mean 0 and standard deviation 1;<br>c) use of ordered over-relaxation.<br>
</font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="3">For other problems, try the FAQ pages of the web site (http://openbugs.info).
</font><font face="Arial" color="#000100" size="2"><strong><br>
</strong></font>
</p>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ToolsMenu</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="toolsmenu0.bmp" alt="[toolsmenu0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">The Tools Menu
</font><font face="Arial" color="#000100" size="6"><strong><br>
</strong></font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#GeneralProperties">General properties</a><br> <a href="#DocumentSize">Document Size...</a><br> <a href="#InsertOLE">Insert OLE Object...</a><br> <a href="#InsertHeader">Insert Header</a><br> <a href="#CreateLink">Create Link</a><br> <a href="#CreateTarget">Create Target</a><br> [...]
</font><font face="Arial" color="#000100" size="5"><strong> <br> <br>
</strong></font><font face="Arial" color="#000100" size="2"><a id="GeneralProperties">
</font><font face="Courier New" color="#000100" size="5">General properties
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The commands in this menu provide various miscelaneous tools.<br><br>
</font><font face="Arial" color="#0000FF" size="4"><br><a id="DocumentSize">
</font><font face="Courier New" color="#000100" size="5">Document Size...</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br> <img src="toolsmenu1.bmp" alt="[toolsmenu1]"><br> <br> <br>
</font><font face="Courier New" color="#000100" size="5"><a id="InsertOLE">Insert OLE Object
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command opens a modal dialog box allowing an OLE object to be inserted into a document at the caret position.<br>
</font><font face="Arial" color="#0000FF" size="3"><br> <img src="toolsmenu2.bmp" alt="[toolsmenu2]"><br> <br> <br>
</font><font face="Courier New" color="#000100" size="5"><a id="InsertHeader">Insert Header</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command inserts a header into the document which becomes visible when the document is printed.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="CreateLink">Create Link</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command turns the highlighted text into a hyper text link if possible. The highlighted text must have a form like <Dialog.Bleep>
</font><font face="Arial" color="#0000FF" size="3">Bleep
</font><font face="Arial" color="#000100" size="3"><> which gives the following link <img src="toolsmenu3.bmp" alt="[toolsmenu3]">. <br><br>Typical links are <br><br><StdLinks.ShowTarget('Contents')>
</font><font face="Arial" color="#0000FF" size="3">top
</font><font face="Arial" color="#000100" size="3"><> <br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><StdCmds.OpenBrowser('Manuals/ToolsMenu', 'Tools Menu')>
</font><font face="Arial" color="#0000FF" size="3">Tools Menu
</font><font face="Arial" color="#000100" size="3"><><br><br>If the 'Show Marks' command from the Edit menu is choosen links show up as angled hollow arrows.To return the link into text form hold the control key down and click into one of these arrows.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="CreateTarget">
</font><font face="Courier New" color="#000100" size="5">Create Target</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command turns the highlighted text into a target that can be jumped to. The highlighted text should have a form like
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000100" size="3"><ExpandAll>Expand All<>.<br><br>If the 'Show Marks' command from the Edit menu is choosen links show up as hollow circles.To return the target into text form hold the control key down and click into one of these circles.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="CreateFold">
</font><font face="Courier New" color="#000100" size="5">Create Fold
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command turns the highlighted text into a fold enclosed between hollow (open) arrows. Clicking on either of the arrows will close the fold (the arrows become solid black), the caret is then placed between the arrows and text can be typed into the closed fold. Clicking on the black arrow will open the fold again.<br><br>The text in the open fold<br><br><img src="toolsmenu4.bmp" alt="[toolsmenu4]"><br><br>The text in the closed fold<br [...]
</font><font face="Arial" color="#0000FF" size="3"><br><a id="ExpandAll">
</font><font face="Courier New" color="#000100" size="5">Expand All</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command opens all the closed folds in the document.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="CollapseAll">
</font><font face="Courier New" color="#000100" size="5">Collapse All</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command closes all the open folds in the document.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Fold">
</font><font face="Courier New" color="#000100" size="5">Fold...</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br> <img src="toolsmenu6.bmp" alt="[toolsmenu6]"><br> <br> <br><a id="EncodeDocument">
</font><font face="Courier New" color="#000100" size="5">Encode Document
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command encodes a document into ascii characters. The encoded version of the document is opened in a new window. The encoded document can be sent by email.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="EncodeSelection">
</font><font face="Courier New" color="#000100" size="5">Encode Selection
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command encodes a highlighted section of a document into ascii characters. The encoded section of the document is opened in a new window.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="EncodeFile">
</font><font face="Courier New" color="#000100" size="5">Encode File...
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command encodes a file into ascii characters. The encoded version of the file is opened in a new window. A standard file open dialig pops up for choosing which file to encode<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="EncodeFileList">
</font><font face="Courier New" color="#000100" size="5">Encode File List</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command encodes a list of files into a document containg only ascii charcters. The document is opened in a new window. The list of files to be enco´ded must be highlighted in the document in the top window.<br><br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="Decode">
</font><font face="Courier New" color="#000100" size="5">Decode
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command decodes an encoded document, file or list of files.<br>
</font><font face="Arial" color="#0000FF" size="3"><br><a id="AboutEncodedMaterial">
</font><font face="Courier New" color="#000100" size="5">About Encoded Material</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000100" size="3">This command gives information about what is encoded.
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font>
</p>
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diff --git a/doc/Manuals/Tricks.html b/doc/Manuals/Tricks.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Tricks</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="tricks0.bmp" alt="[tricks0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Advanced Use of the BUGS<br> Language
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#GenericDistribution">Generic sampling distribution</a><br> <a href="#SpecifyingANewPriorDistribution">Specifying a new prior distribution</a><br> <a href="#UsingPDAndDIC">Using pD and DIC</a><br> <a href="#MixturesOfModelsOfDifferentComplexity">Mixtures of models of different comple [...]
</font><font face="Arial" color="#000100" size="2"><br><br><a id="GenericDistribution">
</font><font face="Courier New" color="#000100" size="5">Generic sampling distribution
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Suppose we wish to use a sampling distribution that is not included in the standard distributions (see
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/ModelSpecification.html#ContentsAI">Appendix I Distributions
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">), in which an
</font><font face="Arial" color="#000000" size="3">observation x[i] contributes a likelihood term L[i]
</font><font face="Arial" color="#000100" size="3">(a function of x[i]).
</font><font face="Arial" color="#000000" size="3">We may use the 'loglik' distribution dloglik, for a dummy observed variable:<br><br> dummy[i] <- 0<br> dummy[i] ~dloglik(logLike[i])<br> <br>where logLike[i] is the contribution to the log-likelihood for the ith observation. The dloglik function implements the 'zero poisson' method utilized in WinBUGS.<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3">This is illustrated in the example below in which a normal likelihood is constructed and the results are compared to the standard formulation.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for (i in 1:7) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">dummy[i] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">dummy[i] ~ dloglik(logLike[i]) # likelihood is exp(logLike[i])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> # log(likelihood)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">logLike[i] <- -log(sigma) - 0.5 * pow((x[i]
</font><font face="Symbol" color="#000000" size="3">-
</font><font face="Arial" color="#000000" size="3"> mu) / sigma, 2) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">mu ~ dunif(-10, 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">sigma ~ dunif(0, 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3"><strong>or
</strong></font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># check using normal distribution<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for (i in 1:7) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> x[i] ~ dnorm(mu, prec)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">prec <- 1 / (sigma * sigma)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">mu ~ dunif(-10, 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">sigma ~ dunif(0, 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Data:<br>
</strong></font><font face="Arial" color="#000100" size="3">list(x = c(-1, -0.3, 0.1, 0.2, 0.7, 1.2, 1.7))<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Initial values:<br>
</strong></font><font face="Arial" color="#000000" size="3">list(sigma = 1, mu = 0)<br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Results:
</strong></font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> mu 0.3763 0.447 0.01203 -0.5436 0.3789 1.302 1001 9000<br> sigma 1.145 0.4368 0.01743 0.6113 1.047 2.263 1001 9000<br><br>or<br><br>
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> mu 0.3642 0.494 0.004657 -0.6213 0.3663 1.342 1001 9000<br> sigma 1.208 0.5572 0.01174 0.6299 1.083 2.486 1001 9000<br><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="SpecifyingANewPriorDistribution">
</font><font face="Courier New" color="#000100" size="5">Specifying a new prior distribution
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3">For a parameter
</font><font face="Arial" color="#000000" size="3"><em>theta
</em></font><font face="Arial" color="#000000" size="3">, if we want to use a prior distribution
</font><font face="Arial" color="#000100" size="3">not included in the standard distributions (see
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/ModelSpecification.html#ContentsAI">Appendix I Distributions
</font><font face="Arial" color="#0000FF" size="3"></a>)
</font><font face="Arial" color="#000000" size="3"> , then we can use the 'dloglik' distribution (see above) for the prior specification. A single dummy observation contributes the appropriate term to the likelihood for
</font><font face="Arial" color="#000000" size="3"><em>theta
</em></font><font face="Arial" color="#000000" size="3">; and when it is combined with a 'flat' prior for
</font><font face="Arial" color="#000000" size="3"><em>theta,
</em></font><font face="Arial" color="#000000" size="3"> the correct distribution results:<br><br>
</font><font face="Arial" color="#000100" size="3"> theta ~ dflat()<br> dummy ~dloglik(logLike)<br> logLike <- log(
</font><font face="Arial" color="#000000" size="3"><em>desired prior for theta
</em></font><font face="Arial" color="#000000" size="3">)
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>This is illustrated by the below example in which a normal prior is constructed and the results are compared to the standard formulation. It is important to note that this method will cause the theta variable to be sampled using the metropolis algorithm and may lead to poor convergence and a high Monte Carlo error.
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for (i in 1:7) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">x[i] ~ dnorm(mu, prec)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">dummy <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">dummy ~ dloglik(phi) # likelihood is exp(phi)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">phi <- -0.5 * pow(mu, 2) # log(N(0, 1))<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">mu ~ dflat() # 'flat' prior<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">prec <- 1 / (sigma * sigma)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">sigma ~ dunif(0, 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br>or<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">for (i in 1:7) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">x[i] ~ dnorm(mu, prec)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br> mu ~ dnorm(0, 1) # 'known' normal prior<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">prec <- 1 / (sigma * sigma)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">sigma ~ dunif(0, 10)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Data:<br>
</strong></font><font face="Arial" color="#000100" size="3"> list(x = c(-1, -0.3, 0.1, 0.2, 0.7, 1.2, 1.7))<br><br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Initial values:<br>
</strong></font><font face="Arial" color="#000100" size="3"> list(sigma = 1, mu = 0)<br> <br>
</font><font face="Arial" color="#0000FF" size="3"><strong>Results:
</strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> mu 0.2859 0.4108 0.008778 -0.5574 0.3002 1.08 1001 9000<br> sigma 1.162 0.4721 0.008885 0.6178 1.05 2.359 1001 9000<br> & [...]
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> mu 0.2973 0.4043 0.003525 -0.5499 0.3112 1.07 1 10000<br> sigma 1.166 0.4785 0.007654 0.6234 1.059 2.315 1 10000<br><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><a id="UsingPDAndDIC">
</font><font face="Courier New" color="#000100" size="5">Using pD and DIC
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3">Here we make a number of observations regarding the use of DIC and pD
</font><font face="Arial" color="#000100" size="3">-
</font><font face="Arial" color="#000000" size="3"> for a full discussion see
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Manuals/References.html#DICPaper">Spiegelhalter et al. (2002)</a>:
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3">1) DIC is intended as a generalisation of Akaike's Information Criterion (AIC). For non-hierarchical models, pD should be approximately the true number of parameters.<br><br>2) Slightly different values of Dhat (and hence pD and DIC) can be obtained depending on the parameterisation used for the prior distribution. For example, consider the precision
</font><font face="Arial" color="#000000" size="3"><em>tau
</em></font><font face="Arial" color="#000000" size="3"> (1 / variance) of a normal distribution. The two priors<br>
</font><font face="Arial" color="#000100" size="3"><br> tau ~ dgamma(0.001, 0.001)
</font><font face="Arial" color="#000000" size="3"> and<br>
</font><font face="Arial" color="#000100" size="3"> log.tau ~ dunif(-10, 10); log(tau) <- log.tau
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000000" size="3">are essentially identical but will give slightly different results for Dhat. The first prior distribution has stochastic parent
</font><font face="Arial" color="#000000" size="3"><em>tau
</em></font><font face="Arial" color="#000000" size="3"> and hence the posterior mean of
</font><font face="Arial" color="#000000" size="3"><em>tau
</em></font><font face="Arial" color="#000000" size="3"> is substituted in Dhat, while in the second parameterisation the stochastic parent is
</font><font face="Arial" color="#000000" size="3"><em>log.tau
</em></font><font face="Arial" color="#000000" size="3"> and hence the posterior mean of log(
</font><font face="Arial" color="#000000" size="3"><em>tau
</em></font><font face="Arial" color="#000000" size="3">) is substituted in Dhat.<br><br>3) For sampling distributions that are log-concave in their stochastic parents, pD is guaranteed to be positive (provided the simulation has converged). However, we have obtained negative pD's in the following situations:
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#000000" size="3">i) with non-log-concave likelihoods (e.g. Student-t distributions) when there is substantial conflict between prior and data;<br>ii) when the posterior distribution for a parameter is symmetric and bimodal, and so the posterior mean is a very poor summary statistic and gives a very large deviance.
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#000000" size="3">4) No MC error is available on the DIC. MC error on Dbar can be obtained by monitoring deviance and is generally quite small. The primary concern is to ensure convergence of Dbar
</font><font face="Arial" color="#000100" size="3">-
</font><font face="Arial" color="#000000" size="3"> it is therefore worthwhile checking the stability of Dbar over a long chain.<br><br>5) The minimum DIC estimates the model that will make the best short-term predictions, in the same spirit as Akaike's criterion. However, if the difference in DIC is, say, less than 5, and the models make very different inferences, then it could be misleading just to report the model with the lowest DIC.<br><br>6) DICs are comparable only over models with [...]
</font><font face="Arial" color="#000000" size="3"><strong>It is important to note that the calculation of DIC will be disallowed for certain models. <br>
</strong></font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#000100" size="2"><a id="MixturesOfModelsOfDifferentComplexity">
</font><font face="Courier New" color="#000100" size="5">Mixtures of models of different complexity
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3">Suppose we assume that each observation, or group of observations, is from one of a set of distributions, where the members of the set have different complexity. For example, we may think data for each person's growth curve comes from either a linear or quadratic line. We might think we would require 'reversible jump' techniques, but this is not the case as we are really only considering a single mixture model as a sampling distribution. [...]
</font><font face="Arial" color="#000000" size="3"><em>OpenBUGS
</em></font><font face="Arial" color="#000000" size="3">, using a set of simulated data.<br><br>Suppose that for each i: x[i] ~ N(mu, 1) with probability p; and x[i] ~ N(0, 1) otherwise (i.e. with probability 1 - p). We generate 100 observations with p = 0.4 and mu = 3 as follows. We forward sample
</font><font face="Arial" color="#000000" size="3"><em>once
</em></font><font face="Arial" color="#000000" size="3"> from the model below by compiling the code and then using the 'gen inits' facility. The simulated data can then be obtained by selecting
</font><font face="Arial" color="#000000" size="3"><em>Save State
</em></font><font face="Arial" color="#000000" size="3"> from the
</font><font face="Arial" color="#000000" size="3"><em>Model
</em></font><font face="Arial" color="#000000" size="3"> menu.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> mu <- 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> p <- 0.4<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> m[1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> m[2] <- mu<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1 : 100) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> group[i] ~ dbern(p)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> index[i] <- group[i] + 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> y[i] ~ dnorm(m[index[i]], 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br>We may observe the underlying mixture distribution by monitoring any one of the y[i]'s over a number of additional sampling cycles. For example, the following kernel density plot was obtained after monitoring y[1] for 1000 iterations:<br><br>
</font><font face="Arial" color="#000100" size="2"><br> <img src="tricks1.bmp" alt="[tricks1]">
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="2">T
</font><font face="Arial" color="#000000" size="3">o analyse the simulated data we use the following code:<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> mu ~ dunif(-5, 5)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> p ~ dunif(0, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> m[1] <- 0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> m[2] <- mu<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1:100) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> group[i] ~ dbern(p)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> index[i] <- group[i] + 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> y[i] ~ dnorm(m[index[i]], 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}<br><br>After 101000 iterations (with a burn-in of 1000) we have good agreement with the 'true' values:<br><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> mu 3.058 0.2071 0.001288 2.655 3.056 3.472 1001 100000<br> p 0.4243 0.05985 3.718E-4 0.3098 0.4232 0.5438 1001 100000<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="5">Initial values
</font><font face="Arial" color="#000000" size="3">:<br>
</font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3"> list(mu = 0, p = 0.5)<br><br>
</font><font face="Arial" color="#0000FF" size="5">Simulated data:
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000000" size="2">list(<br>y = c(<br>2.401893189187883,0.2400077667887621,-0.1556589480882761,-0.8457182007723154,0.37008097263224,<br>3.586009960655263,1.598955590680827,3.826518138558907,-0.9630895329522409,0.6951468806412424,<br>3.129328672725175,0.01025316168135796,0.4887298480200992,0.3865632519840305,-0.2697534502300845,<br>-1.18891944058751,4.654771935717583,0.8063807170988319,-0.9867060769784521,0.9154433557950319,<br>-0.5419217214549653,3 [...]
</font><font face="Arial" color="#000000" size="3"><br>Naturally, the standard warnings about mixture distributions apply, in that convergence may be poor and careful parameterisation may be necessary to avoid some of the components becoming empty.<br><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="WhereTheSizeOfASetIsARandomQuantity">Where the size of a set is a random quantity
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3">Suppose the size of a set is a random quantity: this naturally occurs in 'changepoint' problems where observations up to an unknown changepoint K come from one model, and after K come from another. Note that we
</font><font face="Arial" color="#000000" size="3"><strong>cannot
</strong></font><font face="Arial" color="#000000" size="3"> use the construction<br><br>
</font><font face="Arial" color="#000100" size="3"> for (i in 1:K) {<br> y[i] ~
</font><font face="Arial" color="#000000" size="3"><em>model 1
</em></font><font face="Arial" color="#000100" size="3"><br> }<br> for (i in (K + 1):N) {<br> y[i] ~
</font><font face="Arial" color="#000000" size="3"><em>model 2
</em></font><font face="Arial" color="#000100" size="3"><br> }<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">since the index for a loop cannot be a random quantity. Instead we can use the step function to set up an indicator as to which set each observation belongs to:<br><br>
</font><font face="Arial" color="#000100" size="3"> for (i in 1:N) {<br> ind[i] <- 1 + step(i - K - 0.01)
</font><font face="Arial" color="#000000" size="3"> # will be 1 for all i <= K, 2 otherwise
</font><font face="Arial" color="#000100" size="3"><br> y[i] ~
</font><font face="Arial" color="#000000" size="3"><em>model
</em></font><font face="Arial" color="#000100" size="3">ind[i]<br> }<br>
</font><font face="Arial" color="#000000" size="3"><br>This is illustrated by the problem of adding up terms in a series of unknown length.<br><br>Suppose we want to find the distribution of the sum of the first K integers, where K is a random quantity. We shall assume K has a uniform distribution on 1 to 10. <br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> model <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1:10) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> p[i] <- 1 / 10 # set up prior for K<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> x[i] <- i # set up array of integers<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> K ~ dcat(p[]) # sample K from its prior<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1:10) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"># determine which of the x[i]'s are to be summed<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> xtosum[i] <- x[i] * step(K - i + 0.01) <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> s <- sum(xtosum[])<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br><br>
</font><font face="Arial" color="#000100" size="2"><br> <img src="tricks2.bmp" alt="[tricks2]">
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="AssessingSensitivityToPriorAssumptions">Assessing sensitivity to prior assumptions
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3">One way to do this is to repeat the analysis under different prior assumptions, but within the same simulation in order to aid direct comparison of results. Assuming the consequences of K prior distributions are to be compared:<br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3">a) replicate the dataset K times within the model code;<br>b) set up a loop to repeat the analysis for each prior, holding results in arrays;<br>c) compare results using the
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/InferenceMenu.html#Compare">'compare'</a>
</font><font face="Arial" color="#000000" size="3">facility.
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#000000" size="3">The example
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Examples/Magnesium.html">
</font><font face="Arial" color="#0000FF" size="3">prior-sensitivity</a>
</font><font face="Arial" color="#000000" size="3"> explores six different suggestions for priors on the random-effects variance in a meta-analysis.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="ModellingUnknownDenominators">
</font><font face="Courier New" color="#000100" size="5">Modelling unknown denominators</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3">Suppose we have an unknown Binomial denominator for which we wish to express a prior distribution. It can be given a Poisson prior but this makes it difficult to express a reasonably uniform distribution. Alternatively a continuous distribution could be specified and then the 'round' function used. For example, suppose we are told that a fair coin has come up heads 10 times
</font><font face="Arial" color="#000100" size="3">-
</font><font face="Arial" color="#000000" size="3"> how many times has it been tossed?<br><br>
</font><font face="Arial" color="#000100" size="3"> model {<br> r <- 10<br> p <- 0.5<br> r ~ dbin(p, n)<br> [...]
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><strong> node mean sd MC error 2.5% median 97.5% start sample<br>
</strong></font><font face="Arial" color="#000100" size="3"> n 21.08 4.794 0.07906 13.0 21.0 32.0 1001 5000<br> n.cont 21.08 4.804 0.07932 13.31 20.6 32.0 1001 5000<br> <br>
</font><font face="Arial" color="#000000" size="3">Assuming a uniform prior for the number of tosses, we can be 95% sure that the coin has been tossed between 13 and 32 times.
</font><font face="Arial" color="#000100" size="3">A discrete prior on the integers could also have been used in this context.<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="HandlingUnbalancedDatasets">Handling unbalanced datasets
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3">Suppose we observe the following data on three individuals:<br><br> Person 1: 13.2<br> Person 2: 12.3 , 14.1<br> Person 3: 11.0, 9.7, 10.3, 9.6<br> <br>There are three different ways of entering such 'ragged' data into WinBUGS:<br><br>
</font><font face="Arial" color="#000000" size="3"><strong>1. Fill-to-rectangular:
</strong></font><font face="Arial" color="#000000" size="3"> Here the data is 'padded out' by explicitly including the missing data, i.e.<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y[,1] y[,2] y[,3] y[,4]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> 13.2 NA NA NA<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> 12.3 14.1 NA NA<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> 11.0 9.7 10.3 9.6<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> END<br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3">or list(y = structure(.Data = c(13.2, NA, NA, NA, 12.3, 14.1, NA, NA, 11.0, 9.7, 10.3, 9.6), .<br>Dim = c(3, 4)).<br><br>A model such as
</font><font face="Arial" color="#000100" size="3">y[i, j] ~ dnorm(mu[i], 1)
</font><font face="Arial" color="#000000" size="3"> can then be fitted. This approach is inefficient unless one explicitly wishes to estimate the missing data.<br><br>
</font><font face="Arial" color="#000000" size="3"><strong>2. Nested indexing:
</strong></font><font face="Arial" color="#000000" size="3"> Here the data are stored in a single array and the associated person is recorded as a factor, i.e.<br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y[] person[]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> 13.2 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> 12.3 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> 14.1 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> 11.0 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> 9.7 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> 10.3 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> 9.6 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> END<br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3">or list(y = c(13.2, 12.3, 14.1, 11.0, 9.7, 10.3, 9.6), person = c(1, 2, 2, 3, 3, 3, 3)).<br><br>A model such as
</font><font face="Arial" color="#000100" size="3">y[k] ~ dnorm(mu[person[k]], 1)
</font><font face="Arial" color="#000000" size="3"> can then be fitted. This seems an efficient and clear way to handle the problem.<br><br>
</font><font face="Arial" color="#000000" size="3"><strong>3. Offset:
</strong></font><font face="Arial" color="#000000" size="3">Here an 'offset' array holds the position in the data array at which each
</font><font face="Arial" color="#000100" size="3">person's data starts. For example, the data might be
</font><font face="Arial" color="#000000" size="3"><br><br>list(y = c(13.2, 12.3, 14.1, 11.0, 9.7, 10.3, 9.6), offset = c(1, 2, 4, 8))<br><br>and lead to a model containing the code<br>
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in offset[i]:(offset[i + 1] - 1)) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y[k] ~ dnorm(mu[i], 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br><br>The danger with this method is that it relies on getting the offsets correct and they are difficult to check. <br><br>The three methods are illustrated in the small example below.<br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><strong>Fill-to-rectangular:<br>
</strong></font><font face="Arial" color="#000100" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1:3) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[i] ~ dunif(0, 100)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (j in 1:4) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y[i, j] ~ dnorm(mu[i], 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">y[, 1] y[, 2] y[, 3] y[, 4]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">13.2 NA NA NA<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">12.3 14.1 NA NA<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">11.0 9.7 10.3 9.6<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">END<br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="2">list(y = structure(.Data = c(13.2, NA, NA, NA, 12.3, 14.1, NA, NA, 11.0, 9.7, 10.3, 9.6), .Dim = c(3, 4))<br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong>Nested indexing:<br>
</strong></font><font face="Arial" color="#0000FF" size="3"><strong><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">model <br> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (i in 1:3) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> mu[i] ~ dunif(0, 100)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> for (k in 1:7) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y[k] ~ dnorm(mu[person[k]], 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3">}
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">y[] person[]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">13.2 1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">12.3 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">14.1 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">11.0 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">9.7 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">10.3 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">9.6 3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2">END<br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000100" size="2">list(y = c(13.2, 12.3, 14.1, 11.0, 9.7, 10.3, 9.6), person = c(1, 2, 2, 3, 3, 3, 3))<br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><strong>Offset:<br><br>
</strong></font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">model {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (i in 1:3) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> mu[i] ~ dunif(0, 100)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> for (k in offset[i]:(offset[i + 1] - 1)) {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> y[k] ~ dnorm(mu[i], 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3"> }<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="3">}
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">y[]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">13.2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">12.3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">14.1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">11.0<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">9.7<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">10.3<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">9.6<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">END<br><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">offset[]<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">1<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">4<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">8<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2">END<br><br>list(y = c(13.2, 12.3, 14.1, 11.0, 9.7, 10.3, 9.6), offset = c(1, 2, 4, 8))<br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="UseOfTheCutFunction">Use of the "cut" function
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000000" size="3">Suppose we observe some data that we do not wish to contribute to the parameter estimation and yet we wish to consider as part of the model. This might happen, for example:<br><br>a) when we wish to make predictions on some individuals on whom we have observed some partial data that we do not wish to use for parameter estimation;<br>b) when we want to use data to learn about some parameters and not others;<br>c) when we want evidence from [...]
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> model <br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> {<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y <- 2<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> y ~ dnorm(theta.cut, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta.cut <- cut(theta)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> theta ~ dnorm(0, 1)<br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="3"> }<br>
</font><font face="Arial" color="#000000" size="2"><br>
</font>
</p>
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<title>Tutorial</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="tutorial0.bmp" alt="[tutorial0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">Tutorial
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#Introduction">Introduction</a><br> <a href="#SpecifyingAModelInTheBUGSLanguage">Specifying a model in the BUGS language</a><br> <a href="#RunningAModelInWinBUGS">Running a model in WinBUGS</a><br> <a href="#MonitoringParameterValues">Monitoring parameter values</a><br> <a hre [...]
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Introduction">
</strong></font><font face="Courier New" color="#000100" size="5">Introduction
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">This tutorial is designed to provide new users with a step-by-step guide to running an analysis in OpenBUGS. It is not intended to be prescriptive, but rather to introduce you to the main tools needed to run an MCMC simulation in OpenBUGS, and give some guidance on appropriate usage of the software.<br><br>The
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Seeds.html">Seeds
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> example from Volume I of the OpenBUGS examples will be used throughout this tutorial. This example is taken from Table 3 of Crowder (1978) and concerns the proportion of seeds that germinated on each of 21 plates arranged according to a 2 by 2 factorial layout by seed and type of root extract. The data are shown below, where r
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> and n
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> are the number of germinated and the total number of seeds on the i
</font><font face="Arial" color="#000100" size="3"><sup>th
</sup></font><font face="Arial" color="#000100" size="3"> plate, i = 1, ..., N. These data are also analysed by, for example, Breslow and Clayton (1993).<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><em> seed O. aegyptiaco 75 seed O. aegyptiaco 73
</em></font><font face="Arial" color="#000100" size="2"><br> Bean Cucumber Bean Cucumber<br> r n r/n r n r/n r n r/n r n r/n<br>&nb [...]
</font><font face="Arial" color="#000100" size="2"><sup>
</sup></font><font face="Arial" color="#000100" size="2"><sup> 10 13 0.77
</sup></font><font face="Arial" color="#000100" size="2"><sup>
</sup></font><font face="Arial" color="#0000FF" size="2"><strong><sup><br>
</sup></strong></font><font face="Arial" color="#0000FF" size="2"><strong>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The model is essentially a random effects logistic regression, allowing for over-dispersion. If p
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> is the probability of germination on the i
</font><font face="Arial" color="#000100" size="3"><sup>th
</sup></font><font face="Arial" color="#000100" size="3"> plate, we assume<br><br> r
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Binomial(p
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, n
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)<br> <br> logit(p
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">) = a
</font><font face="Arial" color="#000100" size="3"><sub>0
</sub></font><font face="Arial" color="#000100" size="3"> + a
</font><font face="Arial" color="#000100" size="3"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="3"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3"> + a
</font><font face="Arial" color="#000100" size="3"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="3"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3"> + a
</font><font face="Arial" color="#000100" size="3"><sub>12
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="3"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="3"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3"> + b
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><br> <br> b
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> ~ Normal(0,
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3">)<br> <br>where x
</font><font face="Arial" color="#000100" size="3"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3"> and x
</font><font face="Arial" color="#000100" size="3"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3"> are the seed type and root extract of the i
</font><font face="Arial" color="#000100" size="3"><sup>th
</sup></font><font face="Arial" color="#000100" size="3"> plate, and an interaction term a
</font><font face="Arial" color="#000100" size="3"><sub>12
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="3"><sub>1i
</sub></font><font face="Arial" color="#000100" size="3">x
</font><font face="Arial" color="#000100" size="3"><sub>2i
</sub></font><font face="Arial" color="#000100" size="3"> is included.
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="SpecifyingAModelInTheBUGSLanguage">Specifying a model in the BUGS language
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The BUGS language allows a concise expression of the model, using the 'twiddles' symbol ~ to denote stochastic (probabilistic) relationships, and the left arrow ('<' sign followed by '-' sign) to denote deterministic (logical) relationships. The stochastic parameters a
</font><font face="Arial" color="#000100" size="3"><sub>0
</sub></font><font face="Arial" color="#000100" size="3">, a
</font><font face="Arial" color="#000100" size="3"><sub>1
</sub></font><font face="Arial" color="#000100" size="3">, a
</font><font face="Arial" color="#000100" size="3"><sub>2
</sub></font><font face="Arial" color="#000100" size="3">, a
</font><font face="Arial" color="#000100" size="3"><sub>12
</sub></font><font face="Arial" color="#000100" size="3">, and
</font><font face="Symbol" color="#000100" size="3">t
</font><font face="Arial" color="#000100" size="3"> are given proper but minimally informative prior distributions, while the logical expression for sigma allows the standard deviation (of the random effects distribution) to be estimated.
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br> model <br> {<br> for (i in 1:N) {<br> r[i] ~ dbin(p[i], n[i])<br> b[i] ~ dnorm(0, tau)<br> logit(p[i]) <- alpha0 + alpha1 * x1[i] + alpha2 * x2[i]<br> &n [...]
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/ModelSpecification.html">Model Specification
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> ,
</font><font face="Arial" color="#0000FF" size="3"><a href="../Manuals/ModelSpecification.html#ContentsAI">
</font><font face="Courier New" color="#0000FF" size="3">Appendix I Distributions
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">and
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/ModelSpecification.html#ContentsAII">Appendix II Functions and functionals
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">. See also the on-line examples:
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Examples/Volumei.html">Volume I</a>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Volumeii.html">Volume II</a>
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Volumeiii.html">Volume III
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">. An alternative way of specifying a model in OpenBUGS is to use the graphical interface known as
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Manuals/DoodleBUGS.html">DoodleBUGS</a>.
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><a id="RunningAModelInWinBUGS">
</font><font face="Courier New" color="#000100" size="5">Running a model in OpenBUGS
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The OpenBUGS software uses
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/CompoundDocuments.html">compound documents
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">, which comprise various different types of information (formatted text, tables, formulae, plots, graphs, etc.) displayed in a single window and stored in a single file. This means that it is possible to run the model for the "seeds" example directly from this tutorial document, since the model code can be made 'live' just by highlighting it. However, it is more usual when creating your own models to have the model code and data [...]
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Seedsmodel.html">here
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000000" size="3">).
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><strong>Step 1<br>
</strong></font><font face="Arial" color="#000100" size="3">Open the Seedsmodel file as follows:<br><br>* Point to
</font><font face="Arial" color="#FF0000" size="3"><u>F
</u></font><font face="Arial" color="#FF0000" size="3">ile
</font><font face="Arial" color="#000100" size="3"> on the tool bar and click once with the left mouse button (LMB).<br>* Highlight the
</font><font face="Arial" color="#FF0000" size="3"><u>O
</u></font><font face="Arial" color="#FF0000" size="3">pen...
</font><font face="Arial" color="#000100" size="3"> option and click once with LMB.<br>* Select the Examples directory and double-click on the Seeds file to open.<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><strong>Step 2
</strong></font><font face="Arial" color="#000100" size="3"><br>To run the model, we first need to check that the model description does fully define a probability model:<br><br>* Point to
</font><font face="Arial" color="#FF0000" size="3"><u>M
</u></font><font face="Arial" color="#FF0000" size="3">odel
</font><font face="Arial" color="#000100" size="3"> on the tool bar and click once with LMB.<br>* Highlight the
</font><font face="Arial" color="#FF0000" size="3"><u>S
</u></font><font face="Arial" color="#FF0000" size="3">pecification...
</font><font face="Arial" color="#000100" size="3"> option and click once with LMB.<br>* Focus the window containing the model code by clicking the LMB once anywhere in the window - the top panel of the window should then become highlighted in blue (usually) to indicate that the window is currently in focus.<br>* Highlight the word
</font><font face="Arial" color="#FF00FF" size="3">model
</font><font face="Arial" color="#000100" size="3"> at the beginning of the code by double clicking on the word with the LMB.<br>* Check the model syntax by clicking once with LMB on the
</font><font face="Arial" color="#FF0000" size="3">check model
</font><font face="Arial" color="#000100" size="3"> button in the
</font><font face="Arial" color="#FF0000" size="3">Specification Tool
</font><font face="Arial" color="#000100" size="3"> window. A message saying "model is syntactically correct" should appear in the bottom left of the OpenBUGS program window.<br>
</font><font face="Arial" color="#000100" size="3"><strong><br>Step 3
</strong></font><font face="Arial" color="#000100" size="3"><br>We next need to load in the data. The data can be represented using
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/ModelSpecification.html#FormattingOfDataSPlusFormat">S-Plus object notation</a>
</font><font face="Arial" color="#000100" size="3"> (file
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Examples/Seedsdata.html">Example/Seedsdata</a>
</font><font face="Arial" color="#000100" size="3">), or as a combination of an S-Plus object and a
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/ModelSpecification.html#FormattingOfDataRectangularFormat">rectangular array</a>
</font><font face="Arial" color="#000100" size="3"> with labels at the head of each column (file
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Examples/SeedsMixData.html">Examples/SeedsMixData</a>
</font><font face="Arial" color="#000100" size="3">).
</font><font face="Arial" color="#000000" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3">*
</font><font face="Arial" color="#0000FF" size="3">
</font><font face="Arial" color="#000000" size="3">Open one o
</font><font face="Arial" color="#000100" size="3">f the data files now.<br><br>* To load the data in file Examples/Seedsdata:<br>- Highlight the word
</font><font face="Arial" color="#FF00FF" size="3">list
</font><font face="Arial" color="#000100" size="3"> at the beginning of the data file.<br>- Click once with the LMB on the
</font><font face="Arial" color="#FF0000" size="3">load data
</font><font face="Arial" color="#000100" size="3"> button in the
</font><font face="Arial" color="#FF0000" size="3">Specification Tool
</font><font face="Arial" color="#000100" size="3"> window. A message saying "data loaded" should appear in the bottom left of the OpenBUGS program window.<br><br>* To load the data in file Examples/SeedsMixData:<br>- Highlight the word
</font><font face="Arial" color="#FF00FF" size="3">list
</font><font face="Arial" color="#000100" size="3"> at the beginning of the data file.<br>- Click once with the LMB on the
</font><font face="Arial" color="#FF0000" size="3">load data
</font><font face="Arial" color="#000100" size="3"> button in the
</font><font face="Arial" color="#FF0000" size="3">Specification Tool
</font><font face="Arial" color="#000100" size="3"> window. A message saying "data loaded" should appear in the bottom left of the OpenBUGS program window.<br>- Next highlight the whole of the header line (i.e. column labels) of the rectangular array data. - Click once with the LMB on the
</font><font face="Arial" color="#FF0000" size="3">load data
</font><font face="Arial" color="#000100" size="3"> button in the
</font><font face="Arial" color="#FF0000" size="3">Specification Tool
</font><font face="Arial" color="#000100" size="3"> window. A message saying "data loaded" should appear in the bottom left of the OpenBUGS program window.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>Step 4<br>
</strong></font><font face="Arial" color="#000100" size="3">Now we need to select the number of chains (i.e. sets of samples to simulate). The default is 1, but we will use 2 chains for this tutorial, since running multiple chains is one way to
</font><font face="Courier New" color="#0000FF" size="3"><a href="#CheckingConvergence">check the convergence</a>
</font><font face="Arial" color="#000100" size="3"> of your MCMC simulations.<br><br>* Type the number 2 in the white box labelled
</font><font face="Arial" color="#FF0000" size="3">num of chains
</font><font face="Arial" color="#000100" size="3"> in the
</font><font face="Arial" color="#FF0000" size="3">Specification Tool
</font><font face="Arial" color="#000100" size="3"> window. In practice, if you have a fairly complex model, you may wish to do a pilot run using a single chain to check that the model compiles and runs and obtain an estimate of the time taken per iteration. Once you are happy with the model, re-run it using multiple chains (say 2-5 chains) to obtain a final set of posterior estimates.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>Step 5<br>
</strong></font><font face="Arial" color="#000100" size="3">Next compile the model by clicking once with the LMB on the
</font><font face="Arial" color="#FF0000" size="3">compile
</font><font face="Arial" color="#000100" size="3"> button in the
</font><font face="Arial" color="#FF0000" size="3">Specification Tool
</font><font face="Arial" color="#000100" size="3"> window. A message saying "model compiled" should appear in the bottom left of the OpenBUGS program window. This sets up the internal data structures and chooses the specific
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/Introduction.html#IntroductionMCMCMethods">MCMC updating algorithms</a>
</font><font face="Arial" color="#000100" size="3"> to be used by OpenBUGS for your particular model.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>Step 6<br>
</strong></font><font face="Arial" color="#000100" size="3">Finally the MCMC sampler must be given some initial values for each stochastic node. These can be arbitrary values, although in practice, convergence can be poor if wildly inappropriate values are chosen. You will need a different set of initial values for each chain, i.e. two sets are needed for this tutorial since we have specified two chains - these are stored in files
</font><font face="Arial" color="#FF0000" size="3">Examples/Seedsinits1
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#FF0000" size="3">Examples/Seedsinits2
</font><font face="Arial" color="#000100" size="3"><br><br>* Open thess files now.<br>* To load the initial values:<br>- Highlight the word
</font><font face="Arial" color="#FF00FF" size="3">list
</font><font face="Arial" color="#000100" size="3"> at the beginning of the set of initial values.<br>- Click once with the LMB on the
</font><font face="Arial" color="#FF0000" size="3">load inits
</font><font face="Arial" color="#000100" size="3"> button in the
</font><font face="Arial" color="#FF0000" size="3">Specification Tool
</font><font face="Arial" color="#000100" size="3"> window. A message saying "initial values loaded: this or another chain contains uninitialized nodes" should appear in the bottom left of the OpenBUGS program window.- Repeat this process for the second initial values file. A message saying "initial values loaded: model initialized" should now appear in the bottom left of the OpenBUGS program window.<br><br>Note that you do not need to provide a list of initial values [...]
</font><font face="Arial" color="#FF0000" size="3">gen inits
</font><font face="Arial" color="#000100" size="3"> button in the
</font><font face="Arial" color="#FF0000" size="3">Specification Tool
</font><font face="Arial" color="#000100" size="3"> window. OpenBUGS generates initial values by forward sampling from the prior distribution for each parameter. Therefore, you are advised to
</font><font face="Arial" color="#000100" size="3"><strong>provide your own initial values for parameters with vague prior distributions
</strong></font><font face="Arial" color="#000100" size="3"> to avoid wildly inappropriate values.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>Step 7
</strong></font><font face="Arial" color="#000100" size="3"><br>Close the
</font><font face="Arial" color="#FF0000" size="3">Specification Tool
</font><font face="Arial" color="#000100" size="3"> window. You are now ready to start running the simulation. However, before doing so, you will probably want to set some monitors to store the sampled values for selected parameters. For the seeds example, set monitors for the parameters
</font><font face="Arial" color="#000000" size="3">alpha0
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000000" size="3">alpha1
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000000" size="3">alpha2
</font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000000" size="3">alpha12
</font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000000" size="3">sigma
</font><font face="Arial" color="#000100" size="3"> - see
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#MonitoringParameterValues">here</a>
</font><font face="Arial" color="#0000FF" size="3"><strong>
</strong></font><font face="Arial" color="#000100" size="3">for details on how to do this.<br><br>To run the simulation:<br><br>* Select the
</font><font face="Arial" color="#FF0000" size="3">Update...
</font><font face="Arial" color="#000100" size="3"> option from the
</font><font face="Arial" color="#FF0000" size="3">Model
</font><font face="Arial" color="#000100" size="3"> menu.<br>* Type the number of updates (iterations of the simulation) you require in the appropriate white box (labelled
</font><font face="Arial" color="#FF0000" size="3">updates
</font><font face="Arial" color="#000100" size="3">) - the default value is 1000.<br>* Click once on the
</font><font face="Arial" color="#FF0000" size="3">update
</font><font face="Arial" color="#000100" size="3"> button: the program will now start simulating values for each parameter in the model. This may take a few seconds - the box marked
</font><font face="Arial" color="#FF0000" size="3">iteration
</font><font face="Arial" color="#000100" size="3"> will tell you how many updates have currently been completed. The number of times this value is revised depends on the value you have set for the
</font><font face="Arial" color="#FF0000" size="3">refresh
</font><font face="Arial" color="#000100" size="3"> option in the white box above the
</font><font face="Arial" color="#FF0000" size="3">iteration
</font><font face="Arial" color="#000100" size="3"> box. The default is every 100 iterations, but you can ask the program to report more frequently by changing
</font><font face="Arial" color="#FF0000" size="3">refresh
</font><font face="Arial" color="#000100" size="3"> to, say, 10 or 1. A sensible choice will depend on how quickly the program runs. For the seeds example, experiment with changing the refresh option from 100 to 10 and then 1.<br>* When the updates are finished, the message "updates took *** s" will appear in the bottom left of the OpenBUGS program window (where *** is the number of seconds taken to complete the simulation).<br>* If you previously set monitors for any parameters [...]
</font><font face="Courier New" color="#0000FF" size="3"><a href="#CheckingConvergence">Checking convergence</a>
</font><font face="Arial" color="#0000FF" size="3"><strong>
</strong></font><font face="Arial" color="#000100" size="3">for tips on how to do this (for the seeds example, you should find that at least 2000 iterations are required for convergence).<br>* Once you're happy tha
</font><font face="Arial" color="#000000" size="3">t your simulation has converged, you will need to run some further updates to obtain a sample from the posterior distribution. The section
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#HowManyIterationsAfterConvergence?">How many iterations after convergence?
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> provides tips on deciding how many more updates you should run. For the seeds example, try running a further 10000 updates.<br>* Once you have run enough updates to obtain an appropriate sample from the posterior distribution, you may summarise these samples numerically and graphically (see section
</font><font face="Courier New" color="#0000FF" size="3"><a href="#ObtainingSummariesOfThePosteriorDistribution">Obtaining summaries of the posterior distribution
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> for details on how to do this). For the seeds example, summary statistics for the monitored parameters are shown below:<br><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> alpha0 -0.5473 0.1935 0.003929 -0.9384 -0.5448 -0.1678 4001 14000<br> alpha1 0.06959 0.3203 0.006121 -0.5839 0.08103 0.667 4001 &nbs [...]
</font><font face="Arial" color="#000100" size="3"><br>* To save any files created during your OpenBUGS run, focus the window containing the information you want to save, and select the
</font><font face="Arial" color="#FF0000" size="3">Save As...
</font><font face="Arial" color="#000100" size="3"> option from the
</font><font face="Arial" color="#FF0000" size="3">File
</font><font face="Arial" color="#000100" size="3"> menu.<br>* To quit OpenBUGS, select the
</font><font face="Arial" color="#FF0000" size="3">Exit
</font><font face="Arial" color="#000100" size="3"> option from the
</font><font face="Arial" color="#FF0000" size="3">File
</font><font face="Arial" color="#000100" size="3"> menu.<br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="MonitoringParameterValues">Monitoring parameter values
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">In order to check convergence and obtain posterior summaries of the model parameters, you first need to set
</font><font face="Arial" color="#000100" size="3"><strong>monitors
</strong></font><font face="Arial" color="#000100" size="3"> for each parameter of interest. This tells OpenBUGS to store the values sampled for those parameters; otherwise, OpenBUGS automatically discards the simulated values.<br><br>There are two types of monitor in OpenBUGS:<br><br><a id="SamplesMonitors">
</font><font face="Arial" color="#000100" size="3"><strong>Samples monitors:
</strong></font><font face="Arial" color="#000100" size="3"></a> Setting a samples monitor tells OpenBUGS to store
</font><font face="Arial" color="#000100" size="3"><em> every
</em></font><font face="Arial" color="#000100" size="3"> value it simulates for that parameter. You will need to set a samples monitor if you want to view trace plots of the samples to check convergence (see
</font><font face="Courier New" color="#0000FF" size="3"><a href="#CheckingConvergence">Checking convergence
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">) or if you want to obtain 'exact' posterior quantiles, for example, the posterior 95% Bayesian credible interval for that parameter. (Note that you can also obtain
</font><font face="Arial" color="#000100" size="3"><em>approximate
</em></font><font face="Arial" color="#000100" size="3"> 2.5%, 50% and 97.5% quantiles of the posterior distribution for each parameter using
</font><font face="Courier New" color="#0000FF" size="3"><a href="#SummaryMonitors">summary monitors</a>
</font><font face="Arial" color="#000000" size="3">.
</font><font face="Arial" color="#000100" size="3">)<br><br>To set a samples monitor:<br><br>* Select
</font><font face="Arial" color="#FF0000" size="3">Samples...
</font><font face="Arial" color="#000100" size="3"> from the
</font><font face="Arial" color="#FF0000" size="3">Inference
</font><font face="Arial" color="#000100" size="3"> menu;<br>* Type the name of the parameter to be monitored in the white box marked
</font><font face="Arial" color="#FF0000" size="3">node
</font><font face="Arial" color="#000100" size="3">;<br>* Click once with the LMB on the button marked
</font><font face="Arial" color="#FF0000" size="3">set
</font><font face="Arial" color="#000100" size="3">;<br>* Repeat for each parameter to be monitored.<br><br><a id="SummaryMonitors">
</font><font face="Arial" color="#000100" size="3"><strong>Summary monitors:
</strong></font><font face="Arial" color="#000100" size="3"></a> Setting a summary monitor tells OpenBUGS to store the running mean and standard deviation for the parameter, plus approximate running quantiles (2.5%, 50% and 97.5%). The values saved contain less information than saving each individual sample in the simulation, but require much less storage. This is an important consideration when running long simulations (e.g. 1000's of iterations) and storing values for many variables.<br [...]
</font><font face="Courier New" color="#0000FF" size="3"> <a href="#SamplesMonitors">samples monitors
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> on a small subset of the random effects, plus other relevant parameters (e.g. means and variances), to check convergence.<br><br>To set a summary monitor:<br><br>* Select
</font><font face="Arial" color="#FF0000" size="3">Summary...
</font><font face="Arial" color="#000100" size="3"> from the
</font><font face="Arial" color="#FF0000" size="3">Inference
</font><font face="Arial" color="#000100" size="3"> menu;<br>* Type the name of the parameter to be monitored in the white box marked
</font><font face="Arial" color="#FF0000" size="3">node
</font><font face="Arial" color="#000100" size="3">;<br>* Click once with the LMB on the button marked
</font><font face="Arial" color="#FF0000" size="3">set
</font><font face="Arial" color="#000100" size="3">;<br>* Repeat for each parameter to be monitored.<br> <br>
</font><font face="Arial" color="#000100" size="3"><strong>Note: you should not set a summary monitor until you are happy that convergence has been reached (see
</strong></font><font face="Courier New" color="#0000FF" size="3"><a href="#CheckingConvergence">Checking convergence</a>
</font><font face="Arial" color="#000000" size="3"><strong>), since it is not possible to discard any of the pre-convergence ('burn-in') values from the summary once it is set, ot
</strong></font><font face="Arial" color="#000100" size="3"><strong>her than to clear the monitor and re-set it.<br><br>
</strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><a id="CheckingConvergence">
</font><font face="Courier New" color="#000100" size="5">Checking convergence
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Checking convergence requires considerable care.
</font><font face="Arial" color="#000100" size="3"><strong>It is very difficult to say conclusively that a chain (simulation) has converged, only to diagnose when it definitely hasn't!
</strong></font><font face="Arial" color="#000100" size="3"><br><br>The following are practical guidelines for assessing convergence:<br><br>* For models with many parameters, it is impractical to check convergence for every parameter, so just choose a selection of relevant parameters to monitor. For example, rather than checking convergence for every element of a vector of random effects, just choose a random subset (say, the first 5 or 10).<br>* Examine trace plots of the sample values [...]
</font><font face="Arial" color="#FF0000" size="3">Samples...
</font><font face="Arial" color="#000100" size="3"> from the
</font><font face="Arial" color="#FF0000" size="3">Inference
</font><font face="Arial" color="#000100" size="3">menu.<br>- Type the name of the parameter in the white box marked
</font><font face="Arial" color="#FF0000" size="3">node
</font><font face="Arial" color="#000100" size="3">.<br>- Click once with the LMB on the button marked
</font><font face="Arial" color="#FF0000" size="3">trace
</font><font face="Arial" color="#000100" size="3">: an empty graphics window will appear on screen.<br>- Repeat for each parameter of interest.<br>- Once you start running the simulations (using the
</font><font face="Arial" color="#FF0000" size="3">Update...
</font><font face="Arial" color="#000100" size="3"> tool from the
</font><font face="Arial" color="#FF0000" size="3">Model
</font><font face="Arial" color="#000100" size="3"> menu), trace plots for these parameters will appear 'live' in the graphics windows.<br><br>To obtain a trace plot showing the full history of the samples
</font><font face="Arial" color="#000100" size="3"><em>for any parameter for which you have previously set a samples monitor and carried out some updates
</em></font><font face="Arial" color="#000100" size="3">:<br><br>- Select
</font><font face="Arial" color="#FF0000" size="3">Samples...
</font><font face="Arial" color="#000100" size="3"> from the
</font><font face="Arial" color="#FF0000" size="3">Inference
</font><font face="Arial" color="#000100" size="3">menu.<br>- Type the name of the parameter in the white box marked
</font><font face="Arial" color="#FF0000" size="3">node
</font><font face="Arial" color="#000100" size="3"> (or select the name from the pull down list of currently monitored nodes - click once with the LMB on the downward-facing arrowhead to the immediate right of the
</font><font face="Arial" color="#FF0000" size="3">node
</font><font face="Arial" color="#000100" size="3"> field).<br>- Click once with the LMB on the button marked
</font><font face="Arial" color="#FF0000" size="3">history
</font><font face="Arial" color="#000100" size="3">: a graphics window showing the sample trace will appear.<br>- Repeat for each parameter of interest.<br><br>The following plots are examples of: (i) chains for which convergence (in the pragmatic sense) looks reasonable (top two plots); and (ii) chains which have clearly not reached convergence (bottom two plots).
</font><font face="Arial" color="#000100" size="2"><br><br><img src="tutorial1.bmp" alt="[tutorial1]"><br><img src="tutorial2.bmp" alt="[tutorial2]">
</font><font face="Arial" color="#000100" size="2"><br><img src="tutorial3.bmp" alt="[tutorial3]"><img src="tutorial4.bmp" alt="[tutorial4]">
</font><font face="Arial" color="#000100" size="2"><br><br>
</font><font face="Arial" color="#000100" size="3">If you are running more than one chain simultaneously, the trace and history plots will show each chain in a different colour. In this case, we can be reasonably confident that convergence has been achieved if all the chains appear to be overlapping one another.<br><br>The following plots are examples of: (i) multiple chains for which convergence looks reasonable (top); and (ii) multiple chains which have clearly not reached convergence ( [...]
</font><font face="Arial" color="#000100" size="2"><br><br><img src="tutorial5.bmp" alt="[tutorial5]">
</font><font face="Arial" color="#FF00FF" size="5"><strong><br>
</strong></font><font face="Arial" color="#000100" size="2"><br><img src="tutorial6.bmp" alt="[tutorial6]"><br><br>
</font><font face="Arial" color="#000100" size="3">For a more formal approach to convergence diagnosis the software also provides an implementation (see
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/InferenceMenu.html#SamplesDialogBGRDiag">here</a>
</font><font face="Arial" color="#000100" size="3">) of the techniques described in
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/References.html#BGRDiagPaper">Brooks & Gelman (1998)
</font><font face="Arial" color="#000100" size="3"></a>, and a facility for outputting monitored samples in a format that is compatible with the
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/References.html#CODARef">CODA software</a>
</font><font face="Arial" color="#000100" size="3"> - see
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/InferenceMenu.html#SamplesDialogCODA">here</a>.
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="HowManyIterationsAfterConvergence?">
</font><font face="Courier New" color="#000100" size="5">How many iterations after convergence?</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Once you are happy that convergence has been achieved, you will need to run the simulation for a further number of iterations to obtain samples that can be used for posterior inference. The more samples you save, the more accurate will be your posterior estimates.<br><br>One way to assess the accuracy of the posterior estimates is by calculating the Monte Carlo error for each parameter. This is an estimate of the difference between the me [...]
</font><font face="Courier New" color="#0000FF" size="3">.
</font><font face="Arial" color="#000100" size="3"><br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="ObtainingSummariesOfThePosteriorDistribution">Obtaining summaries of the posterior distribution
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The posterior samples may be summarised either graphically, e.g. by kernel density plots, or numerically, by calculating summary statistics such as the mean, variance and quantiles of the sample.<br><br>To obtain summaries of the monitored samples, to be used for posterior inference:<br><br>* Select
</font><font face="Arial" color="#FF0000" size="3">Samples...
</font><font face="Arial" color="#000100" size="3"> from the
</font><font face="Arial" color="#FF0000" size="3">Inference
</font><font face="Arial" color="#000100" size="3">menu.<br>* Type the name of the parameter in the white box marked
</font><font face="Arial" color="#FF0000" size="3">node
</font><font face="Arial" color="#000100" size="3"> (or select the name from the pull down list, or ty
</font><font face="Arial" color="#000000" size="3">pe "*" (star) to
</font><font face="Arial" color="#000100" size="3">select all monitored parameters). * Type the iteration number that you want to start your summary from in the white box marked
</font><font face="Arial" color="#FF0000" size="3">beg
</font><font face="Arial" color="#000100" size="3">: this allows the pre-convergence 'burn-in' samples to be discarded.<br>* Click once with the LMB on the button marked
</font><font face="Arial" color="#FF0000" size="3">stats
</font><font face="Arial" color="#000100" size="3">: a table reporting various summary statistics based on the sampled values of the selected parameter will appear.<br>* Click once with the LMB on the button marked
</font><font face="Arial" color="#FF0000" size="3">density
</font><font face="Arial" color="#000100" size="3">: a window showing kernel density plots based on the sampled values of the selected parameter will appear.<br><br>Please see the manual entry
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Manuals/InferenceMenu.html#Samples">Samples...
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3"> for a detailed description of the
</font><font face="Arial" color="#FF0000" size="3">Sample Monitor Tool
</font><font face="Arial" color="#000100" size="3"> dialog box (i.e. that which appears when
</font><font face="Arial" color="#FF0000" size="3">Samples...
</font><font face="Arial" color="#000100" size="3"> is selected from the
</font><font face="Arial" color="#FF0000" size="3">Inference
</font><font face="Arial" color="#000100" size="3"> menu).<br>
</font>
</p>
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<head>
<title>WinBUGSGraphics</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="winbugsgraphics0.bmp" alt="[winbugsgraphics0]">
</font><font face="Arial" color="#000100" size="6"><strong>
</strong></font><font face="Courier New" color="#000100" size="6">OpenBUGS Graphics
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#0000FF" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="Contents">
</font><font face="Courier New" color="#000100" size="5">Contents
</font><font face="Arial" color="#000100" size="2"></a><br>
</font><font face="Courier New" color="#0000FF" size="3"><br> <a href="#GeneralProperties">General properties</a><br> <a href="#Margins">Margins</a><br> <a href="#AxisBounds">Axis Bounds</a><br> <a href="#Titles">Titles</a><br> <a href="#AllPlots">All Plots</a><br> <a href="#Fonts">Fonts</a><br> <a href="#SpecificPropertiesViaSpecial">Specific properti [...]
</font><font face="Arial" color="#0000FF" size="2"><u><br>
</u></font><font face="Courier New" color="#0000FF" size="3"> <a href="#DensityStrips">Density strips</a><br> <a href="#ModelFitPlot">Model fit plot</a><br> <a href="#Scatterplot">Scatterplot</a><br>
</font><font face="Arial" color="#0000FF" size="5"><u>
</u></font><font face="Arial" color="#0000FF" size="2"><u><br><br>
</u></font><font face="Courier New" color="#000100" size="5"><a id="GeneralProperties">General properties
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">All OpenBUGS graphics have a set of basic properties that can be modified using the
</font><font face="Arial" color="#000100" size="3"><em>Plot Properties
</em></font><font face="Arial" color="#000100" size="3"> dialog box. This is opened as follows: first, focus the relevant plot by left-clicking on it; then select
</font><font face="Arial" color="#000100" size="3"><em>Object Properties...
</em></font><font face="Arial" color="#000100" size="3"> from the
</font><font face="Arial" color="#000100" size="3"><em>Edit
</em></font><font face="Arial" color="#000100" size="3"> menu. Alternatively, right-clicking on a focused plot will reveal a pop-up menu from which
</font><font face="Arial" color="#000100" size="3"><em>Properties...
</em></font><font face="Arial" color="#000100" size="3"> may equivalently be selected. The
</font><font face="Arial" color="#000100" size="3"><em>Plot Properties
</em></font><font face="Arial" color="#000100" size="3"> dialogue box comprises a "tab-view" and two command buttons, namely
</font><font face="Arial" color="#000100" size="3"><em>Apply
</em></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><em>Data...
</em></font><font face="Arial" color="#000100" size="3">. The tab-view contains five tabs that allow the user to make different types of modification - these are discussed below. The
</font><font face="Arial" color="#000100" size="3"><em>Apply
</em></font><font face="Arial" color="#000100" size="3"> command button applies the properties displayed in the currently selected tab to the focused plot. And
</font><font face="Arial" color="#000100" size="3"><em>Data...
</em></font><font face="Arial" color="#000100" size="3"> opens a separate window with the raw data values used to plot the figure in the chosen plot. The other properties of the plot that user can edit are discussed
</font><font face="Courier New" color="#0000FF" size="3"><a href="#SpecificPropertiesViaSpecial">below</a>.
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Margins">Margins
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The
</font><font face="Arial" color="#000100" size="3"><em>Margins
</em></font><font face="Arial" color="#000100" size="3"> tab displays the plot's left, right, top and bottom margins in millimetres (mm). The left and bottom margins are used for drawing the y- and x-axes respectively. The top margin provides room for the plot's title and the right margin is typically used for plots that require a legend. (Note that top margins (and hence titles) are always inside the plotting rectangle, i.e. there is no gap between the plotting rectangle and the top edge [...]
</font><font face="Arial" color="#000100" size="2"><br><br> <img src="winbugsgraphics1.bmp" alt="[winbugsgraphics1]"><br><br>
</font><font face="Arial" color="#000100" size="3"><br>In cases where it is appropriate to alter a plot's margins the user may enter his/her preferred values and click on
</font><font face="Arial" color="#000100" size="3"><em>Apply
</em></font><font face="Arial" color="#000100" size="3"> to effect the desired change. If the specified values are not appropriate, e.g. if left + right is greater than the width of the graphic (which would result in a plotting rectangle of negative width) or if any margin is negative, etc., then either nothing will happen and the
</font><font face="Arial" color="#000100" size="3"><em>Margins
</em></font><font face="Arial" color="#000100" size="3"> tab will reset itself or some form of compromise will be made.<br><br><br>
</font><font face="Arial" color="#000100" size="2"><a id="AxisBounds">
</font><font face="Courier New" color="#000100" size="5">Axis Bounds
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The user may specify new minimum and maximum values for either or both axes using the
</font><font face="Arial" color="#000100" size="3"><em>Axis Bounds
</em></font><font face="Arial" color="#000100" size="3"> tab (followed by the
</font><font face="Arial" color="#000100" size="3"><em>Apply
</em></font><font face="Arial" color="#000100" size="3"> button).<br>
</font><font face="Arial" color="#000100" size="2"><br> <img src="winbugsgraphics2.bmp" alt="[winbugsgraphics2]"><br><br><br>
</font><font face="Arial" color="#000100" size="3">Note that the resulting minima and maxima may not be exactly the same as the values specified because OpenBUGS always tries to ensure that axes range between 'nice' numbers and also have a sufficient number of tick marks. Note also that if max < min is specified then OpenBUGS will ignore it and the
</font><font face="Arial" color="#000100" size="3"><em>Axis Bounds
</em></font><font face="Arial" color="#000100" size="3"> tab will reset itself, but there is no guard against specifying a range that does not coincide with the data being plotted, and so the contents of the plot may disappear!<br><br>(Some types of plot, such as trace plots, do not allow the user to change their axis bounds, because it would be inappropriate to do so.)<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Titles">Titles</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The
</font><font face="Arial" color="#000100" size="3"><em>Titles
</em></font><font face="Arial" color="#000100" size="3"> tab should be self-explanatory.<br>
</font><font face="Arial" color="#000100" size="2"><br> <img src="winbugsgraphics3.bmp" alt="[winbugsgraphics3]"><br><br><br>
</font><font face="Arial" color="#000100" size="3">Note, however, that because OpenBUGS does not (yet) support vertical text, a substantial amount of space may be required in the left margin in order to write the y-axis title horizontally - if sufficient space is not available then the y-axis title may not appear at all (clearly, this can be rectified by increasing the left margin).<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="AllPlots">All Plots
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The idea behind the
</font><font face="Arial" color="#000100" size="3"><em>All Plots
</em></font><font face="Arial" color="#000100" size="3"> tab is to allow the user to apply some or all of the properties of the focused plot to all plots of the same type (as the focused plot) in the same window (as the focused plot).<br>
</font><font face="Arial" color="#000100" size="2"><br> <img src="winbugsgraphics4.bmp" alt="[winbugsgraphics4]"><br><br><br>
</font><font face="Arial" color="#000100" size="3">The user should first configure the focused plot in the desired way and then decide which of the plot's various properties are to be applied to all plots (of the same type, in the same window). The user should then check all relevant check-boxes and click on
</font><font face="Arial" color="#000100" size="3"><em>Apply all
</em></font><font face="Arial" color="#000100" size="3">. Be careful! It is easy to make mistakes here and there is no undo option - the best advice for users who go wrong is to reproduce the relevant graphics window via the
</font><font face="Arial" color="#000100" size="3"><em>Sample Monitor Tool
</em></font><font face="Arial" color="#000100" size="3">or the
</font><font face="Arial" color="#000100" size="3"><em>Comparison Tool.
</em></font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="Fonts">Fonts
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The
</font><font face="Arial" color="#000100" size="3"><em>Fonts
</em></font><font face="Arial" color="#000100" size="3"> tab allows the user to change the font of the plot's title, its axes, and any other text that may be present.<br><br> <img src="winbugsgraphics5.bmp" alt="[winbugsgraphics5]">
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#000100" size="3">First select the font to be modified and click on
</font><font face="Arial" color="#000100" size="3"><em>Modify...
</em></font><font face="Arial" color="#000100" size="3">. (Note that it will only be possible to select
</font><font face="Arial" color="#000100" size="3"><em>other
</em></font><font face="Arial" color="#000100" size="3"> if the focused plot has a third font, i.e. if text other than the title and axes is present on the plot, e.g. the labels on a box plot - see
</font><font face="Courier New" color="#0000FF" size="3"> <a href="../Manuals/The Inference Menu.html#Compare">Compare...
</font><font face="Arial" color="#0000FF" size="3"></a>
</font><font face="Arial" color="#000100" size="3">) The self-explanatory
</font><font face="Arial" color="#000100" size="3"><em>Font
</em></font><font face="Arial" color="#000100" size="3"> dialogue box should appear - select the required font and click on
</font><font face="Arial" color="#000100" size="3"><em>OK
</em></font><font face="Arial" color="#000100" size="3"> (or
</font><font face="Arial" color="#000100" size="3"><em>Cancel
</em></font><font face="Arial" color="#000100" size="3">).<br><br>In order to apply the same font to an arbitrarily large group of plots (not necessarily of the same type), rather than using the
</font><font face="Arial" color="#000100" size="3"><em>All Plots
</em></font><font face="Arial" color="#000100" size="3"> tab, OpenBUGS uses a "drag-and-pick" facility. First focus a single plot and select which font is to be modified for the whole group:
</font><font face="Arial" color="#000100" size="3"><em>title
</em></font><font face="Arial" color="#000100" size="3">,
</font><font face="Arial" color="#000100" size="3"><em>axes
</em></font><font face="Arial" color="#000100" size="3">, or
</font><font face="Arial" color="#000100" size="3"><em>other
</em></font><font face="Arial" color="#000100" size="3"> (if available). Now highlight the group of plots using the mouse. Hold down the ALT key and then the left-hand mouse button and drag the mouse over an area of text with the desired font; then release the mouse button and the ALT key in turn, and the required changes should be made. As an alternative to dragging the mouse over a piece of text with the desired font, the user may instead drag over another plot (even one in the group to [...]
</font><font face="Arial" color="#000100" size="3"><em>Fonts
</em></font><font face="Arial" color="#000100" size="3"> tab.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="SpecificPropertiesViaSpecial">
</font><font face="Courier New" color="#000100" size="5">Specific properties (via Special)</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">Below we describe the special property editors that are available for certain types of plot. These allow user-interaction beyond that afforded by the standard tabs of the
</font><font face="Arial" color="#000100" size="3"><em>Plot Properties
</em></font><font face="Arial" color="#000100" size="3"> dialogue box and are accessed via its
</font><font face="Arial" color="#000100" size="3"><em>Special
</em></font><font face="Arial" color="#000100" size="3"> tab.<br><br>
</font><font face="Arial" color="#000100" size="2"><br><a id="DensityPlot">
</font><font face="Courier New" color="#000100" size="5">Density plot
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">When the
</font><font face="Arial" color="#000100" size="3"><em>density
</em></font><font face="Arial" color="#000100" size="3"> button on the
</font><font face="Arial" color="#000100" size="3"><em>Sample Monitor Tool
</em></font><font face="Arial" color="#000100" size="3"> is pressed, the output depends on whether the specified variable is discrete or continuous - if the variable is discrete then a histogram is produced whereas if it is continuous a kernel density estimate is produced instead. The specialized property editor that appears when
</font><font face="Arial" color="#000100" size="3"><em>Special
</em></font><font face="Arial" color="#000100" size="3"> tab on the
</font><font face="Arial" color="#000100" size="3"><em>Plot Properties
</em></font><font face="Arial" color="#000100" size="3"> dialogue box is selected also differs slightly depending on the nature of the specified variable. In both cases the editor comprises a numeric field and two command buttons (
</font><font face="Arial" color="#000100" size="3"><em>apply
</em></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><em>apply all
</em></font><font face="Arial" color="#000100" size="3">) but in the case of a histogram the numeric field corresponds to the "bin-size" whereas for kernel density estimates it is the smoothing parameter* (see below):<br>
</font><font face="Arial" color="#000100" size="2"><br> <br> <img src="winbugsgraphics6.bmp" alt="[winbugsgraphics6]"><br><br>
</font><font face="Arial" color="#000100" size="3">Property editor for histogram <br>
</font><font face="Arial" color="#000100" size="2"><br> <img src="winbugsgraphics7.bmp" alt="[winbugsgraphics7]"><br> <br>
</font><font face="Arial" color="#000100" size="3">Property editor for kernel density estimate
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">In either case, the
</font><font face="Arial" color="#000100" size="3"><em>apply
</em></font><font face="Arial" color="#000100" size="3"> button sets the bin-size or smoothing parameter of the focused plot to the value currently displayed in the numeric field. The
</font><font face="Arial" color="#000100" size="3"><em>apply all
</em></font><font face="Arial" color="#000100" size="3"> button, on the other hand, applies the value currently displayed in the numeric field to
</font><font face="Arial" color="#000100" size="3"><em>all
</em></font><font face="Arial" color="#000100" size="3"> plots of the same type (as the focused plot) in the same window (as the focused plot).<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>Note
</strong></font><font face="Arial" color="#000000" size="3">*:
</font><font face="Arial" color="#000100" size="3"> We define the smoothing parameter for kernel density estimates, s, via the definition of band-width. Suppose our posterior sample comprises m realisations of variable z - denote these by z
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">, i = 1,..., m:<br><br>band-width = V
</font><font face="Arial" color="#000100" size="3"><sup>1/2
</sup></font><font face="Arial" color="#000100" size="3"> / m
</font><font face="Arial" color="#000100" size="3"><sup>s
</sup></font><font face="Arial" color="#000100" size="3">; V = m
</font><font face="Arial" color="#000100" size="3"><sup>-1
</sup></font><font face="Arial" color="#000100" size="3"><sub>S
</sub></font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">z
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> - (m
</font><font face="Arial" color="#000100" size="3"><sup>-1
</sup></font><font face="Arial" color="#000100" size="3"><sub>S
</sub></font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">z
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3">)
</font><font face="Arial" color="#000100" size="3"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"><br><br>where the summations are from i = 1 to i = m. The default setting for s is 0.2.<br><br><br>
</font><font face="Arial" color="#000100" size="2"><a id="BoxPlot">
</font><font face="Courier New" color="#000100" size="5">Box plot
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The
</font><font face="Arial" color="#000100" size="3"><em>Special
</em></font><font face="Arial" color="#000100" size="3"> tab of the box plot property editor, is described below:<br>
</font><font face="Arial" color="#000100" size="2"><br> <img src="winbugsgraphics8.bmp" alt="[winbugsgraphics8]"><br><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>show baseline:
</em></strong></font><font face="Arial" color="#000100" size="3"> this check-box should be used to specify whether or not a baseline should be shown on the plot. <br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>show labels:
</em></strong></font><font face="Arial" color="#000100" size="3"> check-box that determines whether or not each distribution/box should be labeled with its index in
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> (that is
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> on the
</font><font face="Arial" color="#000100" size="3"><em>Comparison Tool
</em></font><font face="Arial" color="#000100" size="3">). The default setting is that labels should be shown.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>show means
</em></strong></font><font face="Arial" color="#000100" size="3"> or
</font><font face="Arial" color="#000100" size="3"><strong><em>show medians:
</em></strong></font><font face="Arial" color="#000100" size="3"> these radio buttons specify whether the solid black line at the approximate centre of each box is to represent the posterior mean or the posterior median - mean is the default.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>rank:
</em></strong></font><font face="Arial" color="#000100" size="3"> use this check-box to specify whether the distributions should be ranked and plotted in order. The basis for ranking is either the posterior mean or the posterior median, depending on which is chosen to be displayed in the plot (via
</font><font face="Arial" color="#000100" size="3"><em>show means
</em></font><font face="Arial" color="#000100" size="3"> or
</font><font face="Arial" color="#000100" size="3"><em>show medians
</em></font><font face="Arial" color="#000100" size="3">).<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>vert. box
</em></strong></font><font face="Arial" color="#000100" size="3"> or
</font><font face="Arial" color="#000100" size="3"><strong><em>horiz. box:
</em></strong></font><font face="Arial" color="#000100" size="3"> these radio buttons determine the orientation of the plot. The default is "vertical boxes", which means that the scale axis (i.e. that which measures the 'width' of the distributions) is the y-axis.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>log-scale:
</em></strong></font><font face="Arial" color="#000100" size="3"> the scale axis can be given a logarithmic scale by checking this check-box.<br><br>Finally, at the bottom there is a colour field for selecting the fill-colour of the displayed boxes.<br><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#000100" size="5"><a id="CaterpillarPlot">Caterpillar plot</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The
</font><font face="Arial" color="#000100" size="3"><em>Special
</em></font><font face="Arial" color="#000100" size="3">tab of the caterpillar plot property editor is virtually identical to that of the box plot property editor except that there is no fill-colour field on the former:<br>
</font><font face="Arial" color="#000100" size="2"><br> <img src="winbugsgraphics9.bmp" alt="[winbugsgraphics9]"><br><br><br>
</font><font face="Courier New" color="#000100" size="5"><a id="DensityStrips">Density strips</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">The
</font><font face="Arial" color="#000100" size="3"><em>Special tab
</em></font><font face="Arial" color="#000100" size="3">for density strips reveals several ways to customise these plots. <br><br> <img src="winbugsgraphics10.bmp" alt="[winbugsgraphics10]"><br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>show baseline:
</em></strong></font><font face="Arial" color="#000100" size="3"> specify whether or not a baseline should be shown on the plot. The numeric field to the immediate right of the check-box gives the value of that baseline. By default, a baseline equal to the global mean of the posterior means is shown. <br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>show labels:
</em></strong></font><font face="Arial" color="#000100" size="3"> check-box that determines whether or not each strip should be labelled with its index in
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> (that is
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> on the
</font><font face="Arial" color="#000100" size="3"><em>Comparison Tool
</em></font><font face="Arial" color="#000100" size="3">). The default setting is that labels should be shown.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>vert. strip
</em></strong></font><font face="Arial" color="#000100" size="3">or
</font><font face="Arial" color="#000100" size="3"><strong><em>horiz. strip:
</em></strong></font><font face="Arial" color="#000100" size="3"> plot vertically or horizontally-aligned strips.
</font><font face="Arial" color="#000100" size="3"><strong><em><br>
</em></strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>show point estimates:
</em></strong></font><font face="Arial" color="#000100" size="3">determines whether a point estimate is shown by tick marks on each strip. If this is selected, the definition of the point estimate is defined by the choice of
</font><font face="Arial" color="#000100" size="3"><strong><em>mean
</em></strong></font><font face="Arial" color="#000100" size="3">or
</font><font face="Arial" color="#000100" size="3"><strong><em>median
</em></strong></font><font face="Arial" color="#000100" size="3">. The estimates are shown as white lines by default, since the density is usually high, thus the strip is dark, at the posterior mean or median. But if the density is less than 0.2 of the maximum density, then the estimates are shown as black lines on a light strip background.
</font><font face="Arial" color="#000100" size="3"><strong><em><br><br>log scale:
</em></strong></font><font face="Arial" color="#000100" size="3">display the scale axis on a logarithmic scale. <br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>rank:
</em></strong></font><font face="Arial" color="#000100" size="3"> plot the distributions in the order of their posterior means or medians, depending on the selection in the
</font><font face="Arial" color="#000100" size="3"><strong><em>mean
</em></strong></font><font face="Arial" color="#000100" size="3">or
</font><font face="Arial" color="#000100" size="3"><strong><em>median
</em></strong></font><font face="Arial" color="#000100" size="3">radio button. <br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>show 50% interval:
</em></strong></font><font face="Arial" color="#000100" size="3">select to display the 25% and 75% sample quantiles as tick marks on each strip.
</font><font face="Arial" color="#000100" size="3"><strong><em><br><br>show 95% interval:
</em></strong></font><font face="Arial" color="#000100" size="3">select to display the 2.5% and 97.5% sample quantiles as tick marks on each strip.
</font><font face="Arial" color="#000100" size="3"><strong><em><br>
</em></strong></font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>gamma:
</em></strong></font><font face="Arial" color="#000100" size="3">"gamma correction"
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3">for the variation in shading.
</font><font face="Symbol" color="#000100" size="3">g
</font><font face="Arial" color="#000100" size="3">is a real number greater than 0. The shading at a point
</font><font face="Arial" color="#000100" size="3"><em>x
</em></font><font face="Arial" color="#000100" size="3"><em><sub>i
</sub></em></font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">with density
</font><font face="Arial" color="#000100" size="3"><em>d
</em></font><font face="Arial" color="#000100" size="3"><em><sub>i
</sub></em></font><font face="Arial" color="#000100" size="3"><em>
</em></font><font face="Arial" color="#000100" size="3">is defined as a mixture of the colour at the maximum density (black by default) and white, in proportions
</font><font face="Arial" color="#000100" size="3"><em>p = (d
</em></font><font face="Arial" color="#000100" size="3"><em><sub>i
</sub></em></font><font face="Arial" color="#000100" size="3"><em>/ max
</em></font><font face="Arial" color="#000100" size="3"><em><sub>i
</sub></em></font><font face="Arial" color="#000100" size="3"><em>( d
</em></font><font face="Arial" color="#000100" size="3"><em><sub>i
</sub></em></font><font face="Arial" color="#000100" size="3"><em>))
</em></font><font face="Symbol" color="#000100" size="3"><sup>g
</sup></font><font face="Symbol" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="3">and
</font><font face="Arial" color="#000100" size="3"><em>1 - p
</em></font><font face="Arial" color="#000100" size="3"> respectively. By default,
</font><font face="Symbol" color="#000100" size="3">g =
</font><font face="Arial" color="#000100" size="3">1, so that the perceived darkness is proportional to the density.
</font><font face="Arial" color="#000100" size="3"><br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>smooth:
</em></strong></font><font face="Arial" color="#000100" size="3">the smoothing parameter
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="3">for the density estimate, as described under
</font><font face="Arial" color="#0000FF" size="3"><u><a href="../Manuals/WinBUGSGraphics.html#DensityPlot">Density plot
</u></font><font face="Arial" color="#0000FF" size="3"><strong><u></a>
</u></strong></font><font face="Arial" color="#000100" size="3"><strong>.
</strong></font><font face="Arial" color="#000100" size="3">This is a value between 0 and 1, with smaller values producing smoother estimates. <br><br>If the data are discrete, then the bin size for the histogram is defined by the closest integer to the band-width implied by the supplied value of
</font><font face="Symbol" color="#000100" size="3">s,
</font><font face="Arial" color="#000100" size="3">or 1 if this is greater. Smaller
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="3">give greater bin sizes, up to a maximum bin size equal to the closest integer to the standard deviation of the sample. Values of
</font><font face="Symbol" color="#000100" size="3">s
</font><font face="Arial" color="#000100" size="3">closer to 1 give smaller bin sizes, up to a minimum bin size of 1, or of the closest integer to the standard deviation divided by the sample size if this is greater. <br><br>To update the plot after typing in a new smoothing parameter, click
</font><font face="Arial" color="#000100" size="3"><em>Apply
</em></font><font face="Arial" color="#000100" size="3">. The plot does not update automatically, since recalculating the density may be slow for large samples. <br>
</font><font face="Arial" color="#000100" size="3"><strong><em><br>Colour:
</em></strong></font><font face="Arial" color="#000100" size="3">In the right-hand side of the dialog there is a colour field for selecting the colour at the point of maximum density. The colours for the rest of the strip are defined by interpolating between this colour and white, which represents zero density, so that the darkness of the strip increases with the density.<br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="2"><a id="ModelFitPlot">
</font><font face="Courier New" color="#000100" size="5">Model fit plot</a>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">In cases where an axis is defined on a strictly positive range, it may be given a logarithmic scale by checking the appropriate check-box:<br>
</font><font face="Arial" color="#000100" size="2"><br> <img src="winbugsgraphics11.bmp" alt="[winbugsgraphics11]"><br><br><br><br><a id="Scatterplot">
</font><font face="Courier New" color="#000100" size="5">Scatterplot
</font><font face="Arial" color="#000100" size="2"></a>
</font><font face="Courier New" color="#0000FF" size="3">[<a href="#Contents">top</a>]
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">With a scatterplot focused, select the
</font><font face="Arial" color="#000100" size="3"><em>Special
</em></font><font face="Arial" color="#000100" size="3">tab on the
</font><font face="Arial" color="#000100" size="3"><em>Plot Properties
</em></font><font face="Arial" color="#000100" size="3"> dialogue box to obtain the following property editor:<br>
</font><font face="Arial" color="#000100" size="2"><br> <img src="winbugsgraphics12.bmp" alt="[winbugsgraphics12]"><br><br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>show means
</em></strong></font><font face="Arial" color="#000100" size="3"> or
</font><font face="Arial" color="#000100" size="3"><strong><em>show medians:
</em></strong></font><font face="Arial" color="#000100" size="3"> these radio buttons determine whether it is the posterior means or medians of
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> that are plotted/scattered against
</font><font face="Arial" color="#000100" size="3"><em>axis
</em></font><font face="Arial" color="#000100" size="3"> to form the plot (that is
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> and
</font><font face="Arial" color="#000100" size="3"><em>axis
</em></font><font face="Arial" color="#000100" size="3"> on the
</font><font face="Arial" color="#000100" size="3"><em>Comparison Tool
</em></font><font face="Arial" color="#000100" size="3">) - the default is means.<br><br>Immediately beneath the
</font><font face="Arial" color="#000100" size="3"><strong><em>show means
</em></strong></font><font face="Arial" color="#000100" size="3"> or
</font><font face="Arial" color="#000100" size="3"><strong><em>show medians
</em></strong></font><font face="Arial" color="#000100" size="3"> radio buttons is a colour field for selecting the colour of the scattered points.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>log-x-/log-y-scale:
</em></strong></font><font face="Arial" color="#000100" size="3"> either or both axes may be given a logarithmic scale (assuming they are defined on strictly positive ranges) by checking the appropriate check-box(es).<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>show bars:
</em></strong></font><font face="Arial" color="#000100" size="3"> 95 per cent posterior intervals (2.5% - 97.5%) for
</font><font face="Arial" color="#000100" size="3"><em>node
</em></font><font face="Arial" color="#000100" size="3"> will be shown on the plot (as vertical bars) if this box is checked.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>show line:
</em></strong></font><font face="Arial" color="#000100" size="3"> use this check-box to specify whether or not a reference line (either a straight line specified via its intercept and gradient or an exponentially weighted smoother - see below) is to be displayed.<br><br>To the immediate right of the
</font><font face="Arial" color="#000100" size="3"><strong><em>show line
</em></strong></font><font face="Arial" color="#000100" size="3"> check-box is a colour field that determines the reference line's colour (if displayed).<br><br>
</font><font face="Arial" color="#000100" size="3"><strong><em>linear
</em></strong></font><font face="Arial" color="#000100" size="3"> or
</font><font face="Arial" color="#000100" size="3"><strong><em>smooth:
</em></strong></font><font face="Arial" color="#000100" size="3"> these radio buttons are used to specify whether the reference line (if it is to be displayed) should be linear or whether an exponentially weighted smoother should be fitted instead. In the case where a linear line is required, its intercept and gradient should be entered in the two numeric fields to the right of the
</font><font face="Arial" color="#000100" size="3"><em>linear
</em></font><font face="Arial" color="#000100" size="3"> radio button (in that order). If a smoother is required instead, then the desired degree of smoothing* (see below) should be entered in the numeric field to the right of the
</font><font face="Arial" color="#000100" size="3"><em>smooth
</em></font><font face="Arial" color="#000100" size="3"> radio button. To save unnecessary redrawing of the plot as the various numeric parameters are changed, the
</font><font face="Arial" color="#000100" size="3"><em>Redraw line
</em></font><font face="Arial" color="#000100" size="3"> command button is used to inform OpenBUGS when all alterations to the parameters have been completed.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>Note
</strong></font><font face="Arial" color="#000100" size="3">*: The exponentially weighted smoother that OpenBUGS uses on scatterplots is defined as:<br><br> s
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> =
</font><font face="Arial" color="#000100" size="3"><sub>S
</sub></font><font face="Arial" color="#000100" size="3"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">w
</font><font face="Arial" color="#000100" size="3"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3">y
</font><font face="Arial" color="#000100" size="3"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> /
</font><font face="Arial" color="#000100" size="3"><sub>S
</sub></font><font face="Arial" color="#000100" size="3"><sub>j
</sub></font><font face="Arial" color="#000100" size="3">w
</font><font face="Arial" color="#000100" size="3"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> i = 1,..., n<br><br>where n is the number of scattered points and the summations are from j = 1 to j = n. The weights w
</font><font face="Arial" color="#000100" size="3"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> are given by<br><br> w
</font><font face="Arial" color="#000100" size="3"><sub>ij
</sub></font><font face="Arial" color="#000100" size="3"> = exp(-|x
</font><font face="Arial" color="#000100" size="3"><sub>i
</sub></font><font face="Arial" color="#000100" size="3"> - x
</font><font face="Arial" color="#000100" size="3"><sub>j
</sub></font><font face="Arial" color="#000100" size="3"> | / s )<br><br>where s is the smoothing parameter defined in the
</font><font face="Arial" color="#000100" size="3"><em>Scatterplot properties
</em></font><font face="Arial" color="#000100" size="3"> dialogue box (next to the
</font><font face="Arial" color="#000100" size="3"><em>smooth
</em></font><font face="Arial" color="#000100" size="3"> radio button). The default setting for s is (somewhat arbitrarily) {max(x) - min(x)} / 20.<br><br>
</font>
</p>
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diff --git a/doc/OpenBUGS.1 b/doc/OpenBUGS.1
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--- /dev/null
+++ b/doc/OpenBUGS.1
@@ -0,0 +1,65 @@
+.TH OpenBUGS 1 "March 2014" "Version 3.2.3" ""
+.SH SYNOPSIS
+
+.B OpenBUGS
+[options] [args]
+
+.SH EXAMPLES
+
+.B
+OpenBUGS
+
+.B
+OpenBUGS
+script.txt
+
+.B
+OpenBUGS
+script.txt > res.lst
+
+.B
+OpenBUGS
+< script.txt >res.lst
+
+.B
+OpenBUGS
+-t script.txt
+
+env
+BUGSIN="/dif/dir" BUGSOUT="/other/dir" OpenBUGS script.txt > /path/to/res.lst
+
+.SH DESCRIPTION
+
+Invoke OpenBUGS, usually specifying a script and performing template
+expansion inside the script file to specifiy directory paths.
+
+Names inside of curly brackets in a script file are interpreted as
+environmental variables and the values of the environmental variables
+are substituted. The environmental variables can be set temporarily
+on the same command line as OpenBUGS execution using the env function,
+or on a separate line or in a default startup file.
+
+Note: the OpenBUGS script command 'modelSetWD('path')' can now be used
+as an easier way to set the path where OpenBUGS looks for model, data
+and initial value files. The environment variable mechanism is still
+available however, for backward compatibility.
+
+.SH OPTIONS
+.TP
+\-d
+Dry run. Script will be printed on stdout.
+.TP
+\-b
+Specify the number of curly brackets used to delimit template names.
+.TP
+\-h
+help
+.TP
+\-t
+do not perform template expansion
+
+.SH SEE ALSO
+The main documentation for OpenBUGS is provided as HTML pages. By default,
+these are installed in /usr/local, and the top-level page is
+
+/usr/local/lib/OpenBUGS/doc/Manuals/Contents.html
diff --git a/doc/Reliability/Examples/BSInits.html b/doc/Reliability/Examples/BSInits.html
new file mode 100755
index 0000000..191d203
--- /dev/null
+++ b/doc/Reliability/Examples/BSInits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BSInits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=1.0, beta=50.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BSInits1.html b/doc/Reliability/Examples/BSInits1.html
new file mode 100755
index 0000000..5228c30
--- /dev/null
+++ b/doc/Reliability/Examples/BSInits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BSInits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=2.0, beta=200.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BS_Ex.html b/doc/Reliability/Examples/BS_Ex.html
new file mode 100755
index 0000000..c456868
--- /dev/null
+++ b/doc/Reliability/Examples/BS_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BS_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="bs_ex0.bmp" alt="[bs_ex0]">
</font><font face="Courier New" color="#000100" size="6"> Birnbaum-Saunders Model
</font><font face="Arial" color="#000000" size="2"><br><br> <img src="bs_ex1.bmp" alt="[bs_ex1]"><br> <br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> { <br> x[i] ~ dbs(alpha, beta)<br> }<br> <br> # Prior distributions of the model parameters &nbs [...]
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">The following data 'psi31' are taken from Birnbaum and Saunders(1969).<br><br>
</font><font face="Arial" color="#000000" size="2">Birnbaum, Z. W. and Saunders, S. C. (1969). Estimation for a family of life distributions with applications to fatigue.
</font><font face="Arial" color="#000000" size="2"><em> J. Appl. Probab.
</em></font><font face="Arial" color="#000000" size="2">6(2), 328-347.<br><br>Leiva, V., Hernández, H., and Riquelme, M. (2006). A New Package for the Birnbaum-Saunders Distribution.
</font><font face="Arial" color="#000000" size="2"><em>Rnews
</em></font><font face="Arial" color="#000000" size="2">, 6/4, 35-40.
</font><font face="Arial" color="#000000" size="3"><br><br>The MLE's are obtained using 'bs' package in R alpha.mle = 0.1703847 beta.mle = 131.8188<br>.<br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/BSdata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/BSinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/BSinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center><img src="bs_ex2.bmp" alt="[bs_ex2]"><br><br>
</font><font face="Arial" color="#000000" size="3"><img src="bs_ex3.bmp" alt="[bs_ex3]"><br>
</font><font face="Arial" color="#0000FF" size="5"><br><img src="bs_ex4.bmp" alt="[bs_ex4]"><br><br><img src="bs_ex5.bmp" alt="[bs_ex5]"><br><img src="bs_ex6.bmp" alt="[bs_ex6]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BSdata.html b/doc/Reliability/Examples/BSdata.html
new file mode 100755
index 0000000..1daed7b
--- /dev/null
+++ b/doc/Reliability/Examples/BSdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BSdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">list(N=101, x=c( 70, 90, 96, 97, 99, 100, 103, 104, 104, 105, 107, 108, 108, 108, 109, 109,<br>112, 112, 113, 114, 114, 114, 116, 119, 120, 120, 120, 121, 121, 123, 124, 124, 124, 124, 124, <br>128, 128, 129, 129, 130, 130, 130, 131, 131, 131, 131, 131, 132, 132, 132, 133, 134, 134, 134,<br>134, 134, 136, 136, 137, 138, 138, 138, 139, 139, 141, 141, 142, 142, 142, 142, 142, 142, 144,<br>144, 145, 146, 148, 148, 149, 151, 151, 152, 155, 156, 157, [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BSdata.txt b/doc/Reliability/Examples/BSdata.txt
new file mode 100755
index 0000000..334b2cf
--- /dev/null
+++ b/doc/Reliability/Examples/BSdata.txt
@@ -0,0 +1,6 @@
+list(N=101, x=c( 70, 90, 96, 97, 99, 100, 103, 104, 104, 105, 107, 108, 108, 108, 109, 109,
+ 112, 112, 113, 114, 114, 114, 116, 119, 120, 120, 120, 121, 121, 123, 124, 124, 124, 124, 124,
+ 128, 128, 129, 129, 130, 130, 130, 131, 131, 131, 131, 131, 132, 132, 132, 133, 134, 134, 134,
+ 134, 134, 136, 136, 137, 138, 138, 138, 139, 139, 141, 141, 142, 142, 142, 142, 142, 142, 144,
+ 144, 145, 146, 148, 148, 149, 151, 151, 152, 155, 156, 157, 157, 157, 157, 158, 159, 162, 163,
+ 163, 164, 166, 166, 168, 170, 174, 196, 212))
diff --git a/doc/Reliability/Examples/BSmodel.html b/doc/Reliability/Examples/BSmodel.html
new file mode 100755
index 0000000..4683dce
--- /dev/null
+++ b/doc/Reliability/Examples/BSmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BSmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> { <br> x[i] ~ dbs(alpha, beta)<br> }<br> <br> # Prior distributions of the model parameters &n [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BSmodel.txt b/doc/Reliability/Examples/BSmodel.txt
new file mode 100755
index 0000000..5664760
--- /dev/null
+++ b/doc/Reliability/Examples/BSmodel.txt
@@ -0,0 +1,11 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dbs(alpha, beta)
+ }
+
+ # Prior distributions of the model parameters
+ alpha ~ dunif(0.01, 5.0)
+ beta~ dunif(0.01, 300.0)
+ }
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BurrXII_Ex.html b/doc/Reliability/Examples/BurrXII_Ex.html
new file mode 100755
index 0000000..c1f717d
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXII_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BurrXII_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="burrxii_ex0.bmp" alt="[burrxii_ex0]">
</font><font face="Courier New" color="#000100" size="6"> Burr XII Model
</font><font face="Arial" color="#000000" size="3"><br> <img src="burrxii_ex1.bmp" alt="[burrxii_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dburrXII(alpha, beta)<br> <br> }<br> <br> alpha ~ dunif( [...]
</font><font face="Arial" color="#000000" size="3"><br><br>Simulated data set with alpha = 2.0 and beta = 5.0 <br>
</font><font face="Arial" color="#000000" size="3">The MLE’s are using 'maxLik' package in R
</font><font face="Arial" color="#000000" size="3">alpha.mle = 2.11996 beta.mle = 4.03369 <br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/BurrXIIdata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/BurrXIIinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/BurrXIIinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center>
</font><font face="Arial" color="#0000FF" size="5"><u><img src="burrxii_ex2.bmp" alt="[burrxii_ex2]"><br><br>
</u></font><font face="Arial" color="#000000" size="3"><img src="burrxii_ex3.bmp" alt="[burrxii_ex3]">
</font><font face="Arial" color="#0000FF" size="5"><u><br><br><img src="burrxii_ex4.bmp" alt="[burrxii_ex4]"><br><img src="burrxii_ex5.bmp" alt="[burrxii_ex5]"><br><br>
</u></font><font face="Arial" color="#000000" size="3"><img src="burrxii_ex6.bmp" alt="[burrxii_ex6]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BurrXIIdata.html b/doc/Reliability/Examples/BurrXIIdata.html
new file mode 100755
index 0000000..a2843e2
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXIIdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BurrXIIdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(N=30, x=c(1.3104183, 1.0720485, 0.3748349, 0.6313278, 1.3653709, 0.7758386, 0.5586983,1.0547609, 0.8484189, 1.1714541, 0.6496190, 0.4721445, 0.6450944, 1.1540506, 0.6946741, 0.7307015, 0.7611312, 0.6225298, 1.0603977, 0.2639594, 0.5878855, 1.2542625, 0.6167935, 0.6843502, 0.6144164, 0.9843655, 0.9506997, 1.0561631, 0.7506981, 0.7833595))<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BurrXIIdata.txt b/doc/Reliability/Examples/BurrXIIdata.txt
new file mode 100755
index 0000000..2213c46
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXIIdata.txt
@@ -0,0 +1 @@
+list(N=30, x=c(1.3104183, 1.0720485, 0.3748349, 0.6313278, 1.3653709, 0.7758386, 0.5586983,1.0547609, 0.8484189, 1.1714541, 0.6496190, 0.4721445, 0.6450944, 1.1540506, 0.6946741, 0.7307015, 0.7611312, 0.6225298, 1.0603977, 0.2639594, 0.5878855, 1.2542625, 0.6167935, 0.6843502, 0.6144164, 0.9843655, 0.9506997, 1.0561631, 0.7506981, 0.7833595))
diff --git a/doc/Reliability/Examples/BurrXIIinits.html b/doc/Reliability/Examples/BurrXIIinits.html
new file mode 100755
index 0000000..524205b
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXIIinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BurrXIIinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=1.0, beta=4.0)
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/BurrXIIinits.txt b/doc/Reliability/Examples/BurrXIIinits.txt
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+list(alpha=1.0, beta=4.0)
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diff --git a/doc/Reliability/Examples/BurrXIIinits1.html b/doc/Reliability/Examples/BurrXIIinits1.html
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@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BurrXIIinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=5.0, beta=8.0)
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/BurrXIIinits1.txt b/doc/Reliability/Examples/BurrXIIinits1.txt
new file mode 100755
index 0000000..ea541ba
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXIIinits1.txt
@@ -0,0 +1 @@
+list(alpha=5.0, beta=8.0)
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diff --git a/doc/Reliability/Examples/BurrXIImodel.html b/doc/Reliability/Examples/BurrXIImodel.html
new file mode 100755
index 0000000..161357b
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXIImodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BurrXIImodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dburrXII(alpha, beta)<br> <br> }<br> <br> alpha ~ dunif( [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/BurrXIImodel.txt b/doc/Reliability/Examples/BurrXIImodel.txt
new file mode 100755
index 0000000..745a9ba
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXIImodel.txt
@@ -0,0 +1,14 @@
+
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dburrXII(alpha, beta)
+
+ }
+
+ alpha ~ dunif(0.01, 10.0)
+ beta~ dunif(0.01, 10.0)
+
+
+ }
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BurrX_Ex.html b/doc/Reliability/Examples/BurrX_Ex.html
new file mode 100755
index 0000000..6908d53
--- /dev/null
+++ b/doc/Reliability/Examples/BurrX_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BurrX_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="burrx_ex0.bmp" alt="[burrx_ex0]">
</font><font face="Courier New" color="#000100" size="6">BurrX Model
</font><font face="Arial" color="#000000" size="3"><br><br> <img src="burrx_ex1.bmp" alt="[burrx_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dburrX(alpha, lambda)<br> }<br> <br> # Prior distributions of the model parameters <br> # Uniform priors <br> &nbs [...]
</font><font face="Times New Roman" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"> <br>The data given here arose in tests on endurance of deep groove ball bearings.The data are the number of million revolutions before failure for each of the 23 ball bearings in the life test. The data are taken from Lawless(2003, pp. 99 ).<br><br>
</font><font face="Arial" color="#000000" size="2">Lawless, J.F. (2003).
</font><font face="Arial" color="#000000" size="2"><em> Statistical Models and Methods for Lifetime data
</em></font><font face="Arial" color="#000000" size="2">, Second edition, John Wiley & Sons, New York.
</font><font face="Arial" color="#000000" size="3"><br><br>The MLE’s are using 'maxLik' package in R alpha=1.1989515 lambda= 0.0130847
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/BurrXdata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )<br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/BurrXinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/BurrXinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center><img src="burrx_ex2.bmp" alt="[burrx_ex2]"><br><br>
</font><font face="Arial" color="#000000" size="3"><img src="burrx_ex3.bmp" alt="[burrx_ex3]">
</font><font face="Arial" color="#0000FF" size="5"><br><br><img src="burrx_ex4.bmp" alt="[burrx_ex4]"><br><img src="burrx_ex5.bmp" alt="[burrx_ex5]"><br><br><img src="burrx_ex6.bmp" alt="[burrx_ex6]"><br>
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/BurrXdata.html b/doc/Reliability/Examples/BurrXdata.html
new file mode 100755
index 0000000..201fe62
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BurrXdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list( N=23, x = c(17.88, 28.92, 33.00, 41.52, 42.12, 45.60, 48.80, 51.84, 51.96, 54.12, 55.56, 67.80, 68.64, 68.64, 68.88, 84.12, 93.12, 98.64, 105.12, 105.84, 127.92, 128.04, 173.40))
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/BurrXdata.txt b/doc/Reliability/Examples/BurrXdata.txt
new file mode 100755
index 0000000..932b29c
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXdata.txt
@@ -0,0 +1 @@
+list( N=23, x = c(17.88, 28.92, 33.00, 41.52, 42.12, 45.60, 48.80, 51.84, 51.96, 54.12, 55.56, 67.80, 68.64, 68.64, 68.88, 84.12, 93.12, 98.64, 105.12, 105.84, 127.92, 128.04, 173.40))
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diff --git a/doc/Reliability/Examples/BurrXinits.html b/doc/Reliability/Examples/BurrXinits.html
new file mode 100755
index 0000000..49c14c4
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BurrXinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=0.5, lambda=0.05)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BurrXinits.txt b/doc/Reliability/Examples/BurrXinits.txt
new file mode 100755
index 0000000..1fdedd6
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXinits.txt
@@ -0,0 +1 @@
+list(alpha=0.5, lambda=0.05)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BurrXinits1.html b/doc/Reliability/Examples/BurrXinits1.html
new file mode 100755
index 0000000..3f18658
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BurrXinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=1.5, lambda=0.10)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BurrXinits1.txt b/doc/Reliability/Examples/BurrXinits1.txt
new file mode 100755
index 0000000..b4044d1
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXinits1.txt
@@ -0,0 +1 @@
+list(alpha=1.5, lambda=0.10)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/BurrXmodel.html b/doc/Reliability/Examples/BurrXmodel.html
new file mode 100755
index 0000000..a716a87
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>BurrXmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dburrX(alpha, lambda)<br> }<br> <br> # Prior distributions of the model parameters <br> # Uniform priors <br> &n [...]
</font><font face="Times New Roman" color="#000000" size="3"><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/BurrXmodel.txt b/doc/Reliability/Examples/BurrXmodel.txt
new file mode 100755
index 0000000..f7b2eab
--- /dev/null
+++ b/doc/Reliability/Examples/BurrXmodel.txt
@@ -0,0 +1,12 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dburrX(alpha, lambda)
+ }
+
+ # Prior distributions of the model parameters
+ # Uniform priors
+ alpha ~ dunif(0.1, 5.0)
+ lambda~ dunif(0.001, 1.0)
+ }
diff --git a/doc/Reliability/Examples/Examples.html b/doc/Reliability/Examples/Examples.html
new file mode 100755
index 0000000..05b1edb
--- /dev/null
+++ b/doc/Reliability/Examples/Examples.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Examples</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="2"><img src="examples0.bmp" alt="[examples0]">
</font><font face="Courier New" color="#000100" size="6">ReliaBUGS Examples
</font><font face="Arial" color="#000100" size="6"><strong><sup><br><br>
</sup></strong></font><font face="Arial" color="#0000FF" size="3"><u><br>
</u></font><font face="Courier New" color="#0000FF" size="3"> <a href="../Reliability/Examples/BS_Ex.html">Birnbuam-Saunders Model: <br> 'psi31' data from B&S(1969)</a><br><br> <br> <a href="../Reliability/Examples/BurrX_Ex.html">BurrX Model: <br> 'Ball bearing' data from Lawless(2003) [...]
</font><font face="Arial" color="#0000FF" size="3"><u><br>
</u></font><font face="Courier New" color="#0000FF" size="3"> <a href="../Reliability/Examples/BurrXII_Ex.html">BurrXII Model: <br> Simulated example </a><br> <br> <a href="../Reliability/Examples/ExpoWeibull_Ex.html">Two Parameter Exponentiated Weibull Example Model: <br> &nbs [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ExpPower_Ex.html b/doc/Reliability/Examples/ExpPower_Ex.html
new file mode 100755
index 0000000..1334008
--- /dev/null
+++ b/doc/Reliability/Examples/ExpPower_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ExpPower_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="exppower_ex0.bmp" alt="[exppower_ex0]">
</font><font face="Courier New" color="#000100" size="6"> Exponential Power Model
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"><br> <img src="exppower_ex1.bmp" alt="[exppower_ex1]"><br> <br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dexp.power(alpha, lambda)<br> }<br> <br> # Prior distributions of [...]
</font><font face="Arial" color="#000000" size="3">Simulated data set with alpha = 2.5 and lambda = 0.25
</font><font face="Arial" color="#000000" size="3"><br>The MLEs are alpha = 2.5920853 and lambda = 0.2042697<br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/ExpPowerdata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/ExpPowerinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/ExpPowerinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><center>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"></center>
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> alpha 2.581 0.3843 0.001915 1.875 2.564 3.38 1001 50000<br> lambda 0.2034 0.008843 4.204E-5 0.1857 0.2035 0.2207 1001 50000<br [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> Dbar Dhat DIC pD <br>
</strong></font><font face="Arial" color="#000100" size="2">x 107.9 105.9 109.9 1.993<br>total 107.9 105.9 109.9 1.993<br><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"><img src="exppower_ex2.bmp" alt="[exppower_ex2]"><img src="exppower_ex3.bmp" alt="[exppower_ex3]">
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="exppower_ex4.bmp" alt="[exppower_ex4]"><img src="exppower_ex5.bmp" alt="[exppower_ex5]">
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="exppower_ex6.bmp" alt="[exppower_ex6]"><img src="exppower_ex7.bmp" alt="[exppower_ex7]">
</font><font face="Arial" color="#000100" size="1"><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ExpPowerdata.html b/doc/Reliability/Examples/ExpPowerdata.html
new file mode 100755
index 0000000..0808d76
--- /dev/null
+++ b/doc/Reliability/Examples/ExpPowerdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ExpPowerdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(N=33, x=c(0.7924519, 1.3798784, 1.7264492, 1.9919010, 2.2133770, 2.4065532, 2.5797627, 2.7380554, 2.8847681, 3.0222479, 3.1522276, 3.2760370, 3.3947323, 3.5091779, 3.6201017, 3.7281341, 3.8338369, 3.9377261, 4.0402905, 4.1420092, 4.2433687, 4.3448821, 4.4471122, 4.5507015, 4.6564147, 4.7652034, 4.8783082, 4.9974344, 5.1250778, 5.2651932, 5.4247750, 5.6185011, 5.8890629))
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ExpPowerdata.txt b/doc/Reliability/Examples/ExpPowerdata.txt
new file mode 100755
index 0000000..16a7e9d
--- /dev/null
+++ b/doc/Reliability/Examples/ExpPowerdata.txt
@@ -0,0 +1 @@
+list(N=33, x=c(0.7924519, 1.3798784, 1.7264492, 1.9919010, 2.2133770, 2.4065532, 2.5797627, 2.7380554, 2.8847681, 3.0222479, 3.1522276, 3.2760370, 3.3947323, 3.5091779, 3.6201017, 3.7281341, 3.8338369, 3.9377261, 4.0402905, 4.1420092, 4.2433687, 4.3448821, 4.4471122, 4.5507015, 4.6564147, 4.7652034, 4.8783082, 4.9974344, 5.1250778, 5.2651932, 5.4247750, 5.6185011, 5.8890629))
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diff --git a/doc/Reliability/Examples/ExpPowerinits.html b/doc/Reliability/Examples/ExpPowerinits.html
new file mode 100755
index 0000000..c4aa522
--- /dev/null
+++ b/doc/Reliability/Examples/ExpPowerinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ExpPowerinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=2.0, lambda=0.1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/ExpPowerinits.txt b/doc/Reliability/Examples/ExpPowerinits.txt
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index 0000000..eee509a
--- /dev/null
+++ b/doc/Reliability/Examples/ExpPowerinits.txt
@@ -0,0 +1 @@
+list(alpha=2.0, lambda=0.1)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/ExpPowerinits1.html b/doc/Reliability/Examples/ExpPowerinits1.html
new file mode 100755
index 0000000..6a5d37c
--- /dev/null
+++ b/doc/Reliability/Examples/ExpPowerinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ExpPowerinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=1.0, lambda=0.2)
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ExpPowerinits1.txt b/doc/Reliability/Examples/ExpPowerinits1.txt
new file mode 100755
index 0000000..b5f96ea
--- /dev/null
+++ b/doc/Reliability/Examples/ExpPowerinits1.txt
@@ -0,0 +1 @@
+list(alpha=1.0, lambda=0.2)
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diff --git a/doc/Reliability/Examples/ExpPowermodel.html b/doc/Reliability/Examples/ExpPowermodel.html
new file mode 100755
index 0000000..f9bb05d
--- /dev/null
+++ b/doc/Reliability/Examples/ExpPowermodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ExpPowermodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dexp.power(alpha, lambda)<br> }<br> <br> # Prior distributions of the model parameters <br> <br> &nb [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ExpPowermodel.txt b/doc/Reliability/Examples/ExpPowermodel.txt
new file mode 100755
index 0000000..a73370d
--- /dev/null
+++ b/doc/Reliability/Examples/ExpPowermodel.txt
@@ -0,0 +1,12 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dexp.power(alpha, lambda)
+ }
+
+ # Prior distributions of the model parameters
+
+ alpha ~ dunif(0, 20.0)
+ lambda~ dunif(0, 1.0)
+ }
diff --git a/doc/Reliability/Examples/ExpoWeibull_Ex.html b/doc/Reliability/Examples/ExpoWeibull_Ex.html
new file mode 100755
index 0000000..4171fbe
--- /dev/null
+++ b/doc/Reliability/Examples/ExpoWeibull_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ExpoWeibull_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="expoweibull_ex0.bmp" alt="[expoweibull_ex0]">
</font><font face="Courier New" color="#000100" size="6"> Exponentiated Weibull Model
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"><br> <br> <img src="expoweibull_ex1.bmp" alt="[expoweibull_ex1]"><br> <br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dexp.weib(alpha, theta)<br> <br> &nbs [...]
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Times New Roman" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3">The data set gives 100 observations on breaking stress of carbon fibres,Nichols and Padgett(2006).<br><br>
</font><font face="Arial" color="#000000" size="2">Nichols, M.D. and W.J. Padgett, W.J. (2006). A bootstrap control chart for Weibull percentiles,
</font><font face="Arial" color="#000000" size="2"><em>Quality and Reliability Engineering International
</em></font><font face="Arial" color="#000000" size="2">, 22, 141-151.
</font><font face="Arial" color="#000000" size="3"><br><br>The MLE's are alpha.mle = 1.026465 theta.mle = 7.824943
</font><font face="Times New Roman" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/ExpoWeibulldata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Times New Roman" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/ExpoWeibullinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/ExpoWeibullinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center><img src="expoweibull_ex2.bmp" alt="[expoweibull_ex2]"><br><br>
</font><font face="Arial" color="#000000" size="3"><img src="expoweibull_ex3.bmp" alt="[expoweibull_ex3]">
</font><font face="Arial" color="#0000FF" size="5"><br><br><img src="expoweibull_ex4.bmp" alt="[expoweibull_ex4]"><br><img src="expoweibull_ex5.bmp" alt="[expoweibull_ex5]"><br><img src="expoweibull_ex6.bmp" alt="[expoweibull_ex6]"><br>
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ExpoWeibulldata.html b/doc/Reliability/Examples/ExpoWeibulldata.html
new file mode 100755
index 0000000..06b8274
--- /dev/null
+++ b/doc/Reliability/Examples/ExpoWeibulldata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ExpoWeibulldata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list( N=100, x=c(3.70, 2.74, 2.73, 2.50, 3.60, 3.11, 3.27, 2.87, 1.47, 3.11,<br>4.42, 2.41, 3.19, 3.22, 1.69, 3.28, 3.09, 1.87, 3.15, 4.90,<br>3.75, 2.43, 2.95, 2.97, 3.39, 2.96, 2.53, 2.67, 2.93, 3.22,<br>3.39, 2.81, 4.20, 3.33, 2.55, 3.31, 3.31, 2.85, 2.56, 3.56,<br>3.15, 2.35, 2.55, 2.59, 2.38, 2.81, 2.77, 2.17, 2.83, 1.92,<br>1.41, 3.68, 2.97, 1.36, 0.98, 2.76, 4.91, 3.68, 1.84, 1.59,<br>3.19, 1.57, 0.81, 5.56, 1.73, 1.59, 2.00, 1.22, 1.12, [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ExpoWeibulldata.txt b/doc/Reliability/Examples/ExpoWeibulldata.txt
new file mode 100755
index 0000000..9380be2
--- /dev/null
+++ b/doc/Reliability/Examples/ExpoWeibulldata.txt
@@ -0,0 +1,10 @@
+list( N=100, x=c(3.70, 2.74, 2.73, 2.50, 3.60, 3.11, 3.27, 2.87, 1.47, 3.11,
+4.42, 2.41, 3.19, 3.22, 1.69, 3.28, 3.09, 1.87, 3.15, 4.90,
+3.75, 2.43, 2.95, 2.97, 3.39, 2.96, 2.53, 2.67, 2.93, 3.22,
+3.39, 2.81, 4.20, 3.33, 2.55, 3.31, 3.31, 2.85, 2.56, 3.56,
+3.15, 2.35, 2.55, 2.59, 2.38, 2.81, 2.77, 2.17, 2.83, 1.92,
+1.41, 3.68, 2.97, 1.36, 0.98, 2.76, 4.91, 3.68, 1.84, 1.59,
+3.19, 1.57, 0.81, 5.56, 1.73, 1.59, 2.00, 1.22, 1.12, 1.71,
+2.17, 1.17, 5.08, 2.48, 1.18, 3.51, 2.17, 1.69, 1.25, 4.38,
+1.84, 0.39, 3.68, 2.48, 0.85, 1.61, 2.79, 4.70, 2.03, 1.80,
+1.57, 1.08, 2.03, 1.61, 2.12, 1.89, 2.88, 2.82, 2.05, 3.65))
diff --git a/doc/Reliability/Examples/ExpoWeibullinits.html b/doc/Reliability/Examples/ExpoWeibullinits.html
new file mode 100755
index 0000000..d404edf
--- /dev/null
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+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ExpoWeibullinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=0.5, theta=2.0)
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ExpoWeibullinits.txt b/doc/Reliability/Examples/ExpoWeibullinits.txt
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index 0000000..3d37643
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+++ b/doc/Reliability/Examples/ExpoWeibullinits.txt
@@ -0,0 +1 @@
+list(alpha=0.5, theta=2.0)
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diff --git a/doc/Reliability/Examples/ExpoWeibullinits1.html b/doc/Reliability/Examples/ExpoWeibullinits1.html
new file mode 100755
index 0000000..8e39bb3
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+++ b/doc/Reliability/Examples/ExpoWeibullinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ExpoWeibullinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=2.5, theta=11.0)<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ExpoWeibullinits1.txt b/doc/Reliability/Examples/ExpoWeibullinits1.txt
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index 0000000..e715794
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+++ b/doc/Reliability/Examples/ExpoWeibullinits1.txt
@@ -0,0 +1 @@
+list(alpha=2.5, theta=11.0)
diff --git a/doc/Reliability/Examples/ExpoWeibullmodel.html b/doc/Reliability/Examples/ExpoWeibullmodel.html
new file mode 100755
index 0000000..5489599
--- /dev/null
+++ b/doc/Reliability/Examples/ExpoWeibullmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ExpoWeibullmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dexp.weib(alpha, theta)<br> <br> }<br> <br> # Prior distributions of the model parameters&nb [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ExpoWeibullmodel.txt b/doc/Reliability/Examples/ExpoWeibullmodel.txt
new file mode 100755
index 0000000..f69a980
--- /dev/null
+++ b/doc/Reliability/Examples/ExpoWeibullmodel.txt
@@ -0,0 +1,16 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dexp.weib(alpha, theta)
+
+ }
+
+ # Prior distributions of the model parameters
+
+ #alpha ~ dunif(0.001, 5.0)
+ #theta~ dunif(0.01, 20.0)
+
+ alpha ~ dgamma(0.001, 0.001)
+ theta~ dgamma(0.001, 0.001)
+ }
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diff --git a/doc/Reliability/Examples/Ext_Weibull_Ex.html b/doc/Reliability/Examples/Ext_Weibull_Ex.html
new file mode 100755
index 0000000..4c2f086
--- /dev/null
+++ b/doc/Reliability/Examples/Ext_Weibull_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ext_Weibull_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="ext_weibull_ex0.bmp" alt="[ext_weibull_ex0]">
</font><font face="Courier New" color="#000100" size="6"> Extended Weibull Model <br> (Marshall-Olkin)
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"><br> <br> <img src="ext_weibull_ex1.bmp" alt="[ext_weibull_ex1]"><br> <br> model<br> {<br> for(i in 1 : N) <br> {<br> x[i] ~ dext.weib(alpha, lambda)<br> }<br> <br> [...]
</font><font face="Arial" color="#000100" size="2">Marshall, A. W. and Olkin, I. (1997). A new method for adding a parameter to a family of distributions with application to the exponential and Weibull families.
</font><font face="Arial" color="#000100" size="2"><em>Biometrika
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>84(3)
</strong></font><font face="Arial" color="#000100" size="2">, 641-652.<br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="2">Nichols, M.D. and W.J. Padgett, W.J. (2006). A bootstrap control chart for Weibull percentiles,
</font><font face="Arial" color="#000000" size="2"><em>Quality and Reliability Engineering International
</em></font><font face="Arial" color="#000000" size="2">, 22, 141-151.
</font><font face="Arial" color="#000000" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/Ext_Weibulldata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/Ext_Weibullinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <br><br><a href="../Reliability/Examples/Ext_Weibullinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#0000FF" size="5"><br>Results <br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> alpha 0.2934 0.02427 3.197E-4 0.2433 0.2942 0.3384 1001 50000<br> lambda 141.5 111.7 1.387 31.88 110.7 430.3 1001 50000<br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> Dbar Dhat DIC pD <br>
</strong></font><font face="Arial" color="#000100" size="2">x 260.0 262.1 257.9 -2.096<br>x.cen 19.55 16.15 22.94 3.394<br>total 279.5 278.2 280.8 1.298<br>
</font><font face="Arial" color="#000000" size="3"><br><img src="ext_weibull_ex2.bmp" alt="[ext_weibull_ex2]"><br><img src="ext_weibull_ex3.bmp" alt="[ext_weibull_ex3]"><br><br><img src="ext_weibull_ex4.bmp" alt="[ext_weibull_ex4]"><br>
</font>
</p>
</body>
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diff --git a/doc/Reliability/Examples/Ext_Weibulldata.html b/doc/Reliability/Examples/Ext_Weibulldata.html
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index 0000000..0c6ed08
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+++ b/doc/Reliability/Examples/Ext_Weibulldata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ext_Weibulldata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(N=21, x=c(275, 106, 88, 13, 247,147, 28, 23, 212, 243, 181, 23, 65, 10, 2, 80, 261, 245, 173, 293, 266), t.cen = 300, Ncen = 9)
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/Ext_Weibulldata.txt b/doc/Reliability/Examples/Ext_Weibulldata.txt
new file mode 100755
index 0000000..ccef513
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+++ b/doc/Reliability/Examples/Ext_Weibulldata.txt
@@ -0,0 +1 @@
+list(N=21, x=c(275, 106, 88, 13, 247,147, 28, 23, 212, 243, 181, 23, 65, 10, 2, 80, 261, 245, 173, 293, 266), t.cen = 300, Ncen = 9)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Ext_Weibullinits.html b/doc/Reliability/Examples/Ext_Weibullinits.html
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index 0000000..c3d475e
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+++ b/doc/Reliability/Examples/Ext_Weibullinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ext_Weibullinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=0.2, lambda=200.0, x.cen = c(400, 400, 400, 400, 400, 400, 400, 400, 400))
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/Ext_Weibullinits.txt b/doc/Reliability/Examples/Ext_Weibullinits.txt
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index 0000000..84843ef
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+++ b/doc/Reliability/Examples/Ext_Weibullinits.txt
@@ -0,0 +1 @@
+list(alpha=0.2, lambda=200.0, x.cen = c(400, 400, 400, 400, 400, 400, 400, 400, 400))
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diff --git a/doc/Reliability/Examples/Ext_Weibullinits1.html b/doc/Reliability/Examples/Ext_Weibullinits1.html
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index 0000000..0b080b9
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+++ b/doc/Reliability/Examples/Ext_Weibullinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ext_Weibullinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=0.4, lambda=300.0, x.cen = c(310, 310, 310, 310, 310, 310, 310, 310, 310))
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/Ext_Weibullinits1.txt b/doc/Reliability/Examples/Ext_Weibullinits1.txt
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index 0000000..9819f0f
--- /dev/null
+++ b/doc/Reliability/Examples/Ext_Weibullinits1.txt
@@ -0,0 +1 @@
+list(alpha=0.4, lambda=300.0, x.cen = c(310, 310, 310, 310, 310, 310, 310, 310, 310))
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Ext_Weibullmodel.html b/doc/Reliability/Examples/Ext_Weibullmodel.html
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index 0000000..a6fac91
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+++ b/doc/Reliability/Examples/Ext_Weibullmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ext_Weibullmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dext.weib(alpha, lambda)<br> }<br> <br> # Prior distributions of the model parameters <br> <br> &nbs [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/Ext_Weibullmodel.txt b/doc/Reliability/Examples/Ext_Weibullmodel.txt
new file mode 100755
index 0000000..ee18025
--- /dev/null
+++ b/doc/Reliability/Examples/Ext_Weibullmodel.txt
@@ -0,0 +1,13 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dext.weib(alpha, lambda)
+ }
+
+ # Prior distributions of the model parameters
+
+ alpha ~ dunif(0, 5.0)
+ lambda~ dgamma(0.001, 0.001)
+
+ }
diff --git a/doc/Reliability/Examples/Ext_exponential_Ex.html b/doc/Reliability/Examples/Ext_exponential_Ex.html
new file mode 100755
index 0000000..18595a1
--- /dev/null
+++ b/doc/Reliability/Examples/Ext_exponential_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ext_exponential_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="ext_exponential_ex0.bmp" alt="[ext_exponential_ex0]">
</font><font face="Courier New" color="#000100" size="6"> Extended Exponential Model
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="2">
</font><font face="Courier New" color="#000100" size="6">(Marshall-Olkin)
</font><font face="Arial" color="#000000" size="3"><br> <br> <img src="ext_exponential_ex1.bmp" alt="[ext_exponential_ex1]"><br> <br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dext.exp(alpha, lambda)<br> }<br> & [...]
</font><font face="Arial" color="#000100" size="2">Marshall, A. W. and Olkin, I. (1997). A new method for adding a parameter to a family of distributions with application to the exponential and Weibull families.
</font><font face="Arial" color="#000100" size="2"><em>Biometrika
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>84(3)
</strong></font><font face="Arial" color="#000100" size="2">, 641-652.<br>
</font><font face="Arial" color="#000000" size="2"><br>Nichols, M.D. and W.J. Padgett, W.J. (2006). A bootstrap control chart for Weibull percentiles,
</font><font face="Arial" color="#000000" size="2"><em>Quality and Reliability Engineering International
</em></font><font face="Arial" color="#000000" size="2">, 22, 141-151.
</font><font face="Arial" color="#000000" size="3"><br><br>The MLE’s are alpha =75.67982, ; lambda= 1.67576,<br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/Ext_exponentialdata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/Ext_exponentialinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/Ext_exponentialinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br> <br><center><img src="ext_exponential_ex2.bmp" alt="[ext_exponential_ex2]"><br><br><img src="ext_exponential_ex3.bmp" alt="[ext_exponential_ex3]"><br><br><img src="ext_exponential_ex4.bmp" alt="[ext_exponential_ex4]"><br><img src="ext_exponential_ex5.bmp" alt="[ext_exponential_ex5]"><br><img src="ext_exponential_ex6.bmp" alt="[ext_exponential_ex6]"><br><br><br><br><br>
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/Ext_exponentialdata.html b/doc/Reliability/Examples/Ext_exponentialdata.html
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index 0000000..6d3ecd9
--- /dev/null
+++ b/doc/Reliability/Examples/Ext_exponentialdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ext_exponentialdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list( N=100, x=c(3.70, 2.74, 2.73, 2.50, 3.60, 3.11, 3.27, 2.87, 1.47, 3.11,<br>4.42, 2.41, 3.19, 3.22, 1.69, 3.28, 3.09, 1.87, 3.15, 4.90,<br>3.75, 2.43, 2.95, 2.97, 3.39, 2.96, 2.53, 2.67, 2.93, 3.22,<br>3.39, 2.81, 4.20, 3.33, 2.55, 3.31, 3.31, 2.85, 2.56, 3.56,<br>3.15, 2.35, 2.55, 2.59, 2.38, 2.81, 2.77, 2.17, 2.83, 1.92,<br>1.41, 3.68, 2.97, 1.36, 0.98, 2.76, 4.91, 3.68, 1.84, 1.59,<br>3.19, 1.57, 0.81, 5.56, 1.73, 1.59, 2.00, 1.22, 1.12, [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Ext_exponentialdata.txt b/doc/Reliability/Examples/Ext_exponentialdata.txt
new file mode 100755
index 0000000..9380be2
--- /dev/null
+++ b/doc/Reliability/Examples/Ext_exponentialdata.txt
@@ -0,0 +1,10 @@
+list( N=100, x=c(3.70, 2.74, 2.73, 2.50, 3.60, 3.11, 3.27, 2.87, 1.47, 3.11,
+4.42, 2.41, 3.19, 3.22, 1.69, 3.28, 3.09, 1.87, 3.15, 4.90,
+3.75, 2.43, 2.95, 2.97, 3.39, 2.96, 2.53, 2.67, 2.93, 3.22,
+3.39, 2.81, 4.20, 3.33, 2.55, 3.31, 3.31, 2.85, 2.56, 3.56,
+3.15, 2.35, 2.55, 2.59, 2.38, 2.81, 2.77, 2.17, 2.83, 1.92,
+1.41, 3.68, 2.97, 1.36, 0.98, 2.76, 4.91, 3.68, 1.84, 1.59,
+3.19, 1.57, 0.81, 5.56, 1.73, 1.59, 2.00, 1.22, 1.12, 1.71,
+2.17, 1.17, 5.08, 2.48, 1.18, 3.51, 2.17, 1.69, 1.25, 4.38,
+1.84, 0.39, 3.68, 2.48, 0.85, 1.61, 2.79, 4.70, 2.03, 1.80,
+1.57, 1.08, 2.03, 1.61, 2.12, 1.89, 2.88, 2.82, 2.05, 3.65))
diff --git a/doc/Reliability/Examples/Ext_exponentialinits.html b/doc/Reliability/Examples/Ext_exponentialinits.html
new file mode 100755
index 0000000..c5f724e
--- /dev/null
+++ b/doc/Reliability/Examples/Ext_exponentialinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ext_exponentialinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=10.0, lambda=2.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Ext_exponentialinits.txt b/doc/Reliability/Examples/Ext_exponentialinits.txt
new file mode 100755
index 0000000..6e712f2
--- /dev/null
+++ b/doc/Reliability/Examples/Ext_exponentialinits.txt
@@ -0,0 +1 @@
+list(alpha=10.0, lambda=2.0)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Ext_exponentialinits1.html b/doc/Reliability/Examples/Ext_exponentialinits1.html
new file mode 100755
index 0000000..95a945d
--- /dev/null
+++ b/doc/Reliability/Examples/Ext_exponentialinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ext_exponentialinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=5.0, lambda=1.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Ext_exponentialinits1.txt b/doc/Reliability/Examples/Ext_exponentialinits1.txt
new file mode 100755
index 0000000..7dcf999
--- /dev/null
+++ b/doc/Reliability/Examples/Ext_exponentialinits1.txt
@@ -0,0 +1 @@
+list(alpha=5.0, lambda=1.0)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Ext_exponentialmodel.html b/doc/Reliability/Examples/Ext_exponentialmodel.html
new file mode 100755
index 0000000..8f28425
--- /dev/null
+++ b/doc/Reliability/Examples/Ext_exponentialmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Ext_exponentialmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dext.exp(alpha, lambda)<br> }<br> <br> # Prior distributions of the model parameters <br> <br>   [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Ext_exponentialmodel.txt b/doc/Reliability/Examples/Ext_exponentialmodel.txt
new file mode 100755
index 0000000..7e00ea8
--- /dev/null
+++ b/doc/Reliability/Examples/Ext_exponentialmodel.txt
@@ -0,0 +1,13 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dext.exp(alpha, lambda)
+ }
+
+ # Prior distributions of the model parameters
+
+ alpha ~ dgamma(0.001, 0.001)
+ lambda ~ dnorm(0.001, 0.001)
+
+ }
diff --git a/doc/Reliability/Examples/FlexibleWeibull_Ex.html b/doc/Reliability/Examples/FlexibleWeibull_Ex.html
new file mode 100755
index 0000000..34a5c3d
--- /dev/null
+++ b/doc/Reliability/Examples/FlexibleWeibull_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>FlexibleWeibull_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2"><img src="flexibleweibull_ex0.bmp" alt="[flexibleweibull_ex0]">
</font><font face="Courier New" color="#000100" size="6">Flexible Weibull Model
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="2"><br> <img src="flexibleweibull_ex1.bmp" alt="[flexibleweibull_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dflex.weib(alpha, beta)<br> } <br> # Prior distributions of the model parameters <br> &nb [...]
</font><font face="Arial" color="#000000" size="2"><br>Bebbington, M., Lai, C.D. and Zitikis, R. (2007) A flexible Weibull extension.
</font><font face="Arial" color="#000000" size="2"><em>Reliability Engineering and System Safety
</em></font><font face="Arial" color="#000000" size="2">, 92, 719-726.
</font><font face="Arial" color="#000000" size="3"><br><br>The MLE's are alpha = 0.0207 beta = 0.25875 <br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/FlexibleWeibulldata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/FlexibleWeibullinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/FlexibleWeibullinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><center>
</font><font face="Arial" color="#000000" size="3"><br><img src="flexibleweibull_ex2.bmp" alt="[flexibleweibull_ex2]"><br><br><img src="flexibleweibull_ex3.bmp" alt="[flexibleweibull_ex3]"><br><br><img src="flexibleweibull_ex4.bmp" alt="[flexibleweibull_ex4]"><br><br><img src="flexibleweibull_ex5.bmp" alt="[flexibleweibull_ex5]"><br><br><img src="flexibleweibull_ex6.bmp" alt="[flexibleweibull_ex6]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/FlexibleWeibulldata.html b/doc/Reliability/Examples/FlexibleWeibulldata.html
new file mode 100755
index 0000000..fa76857
--- /dev/null
+++ b/doc/Reliability/Examples/FlexibleWeibulldata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>FlexibleWeibulldata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(N=23, x=c(2.160, 0.746, 0.402, 0.954, 0.491, 6.560, 4.992, 0.347, 0.150, 0.358, 0.101, 1.359, 3.465, 1.060, 0.614, 1.921, 4.082, 0.199, 0.605, 0.273, 0.070, 0.062, 5.320))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/FlexibleWeibulldata.txt b/doc/Reliability/Examples/FlexibleWeibulldata.txt
new file mode 100755
index 0000000..053e21c
--- /dev/null
+++ b/doc/Reliability/Examples/FlexibleWeibulldata.txt
@@ -0,0 +1 @@
+list(N=23, x=c(2.160, 0.746, 0.402, 0.954, 0.491, 6.560, 4.992, 0.347, 0.150, 0.358, 0.101, 1.359, 3.465, 1.060, 0.614, 1.921, 4.082, 0.199, 0.605, 0.273, 0.070, 0.062, 5.320))
\ No newline at end of file
diff --git a/doc/Reliability/Examples/FlexibleWeibullinits.html b/doc/Reliability/Examples/FlexibleWeibullinits.html
new file mode 100755
index 0000000..f4eabe7
--- /dev/null
+++ b/doc/Reliability/Examples/FlexibleWeibullinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>FlexibleWeibullinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=0.1, beta= 0.2)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/FlexibleWeibullinits.txt b/doc/Reliability/Examples/FlexibleWeibullinits.txt
new file mode 100755
index 0000000..5c3c9bd
--- /dev/null
+++ b/doc/Reliability/Examples/FlexibleWeibullinits.txt
@@ -0,0 +1 @@
+list(alpha=0.1, beta= 0.2)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/FlexibleWeibullinits1.html b/doc/Reliability/Examples/FlexibleWeibullinits1.html
new file mode 100755
index 0000000..7cd7174
--- /dev/null
+++ b/doc/Reliability/Examples/FlexibleWeibullinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>FlexibleWeibullinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=0.2, beta= 5.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/FlexibleWeibullinits1.txt b/doc/Reliability/Examples/FlexibleWeibullinits1.txt
new file mode 100755
index 0000000..47234ab
--- /dev/null
+++ b/doc/Reliability/Examples/FlexibleWeibullinits1.txt
@@ -0,0 +1 @@
+list(alpha=0.2, beta= 5.0)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/FlexibleWeibullmodel.html b/doc/Reliability/Examples/FlexibleWeibullmodel.html
new file mode 100755
index 0000000..f83863a
--- /dev/null
+++ b/doc/Reliability/Examples/FlexibleWeibullmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>FlexibleWeibullmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dflex.weib(alpha, beta)<br> } <br> # Prior distributions of the model parameters <br> & [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/FlexibleWeibullmodel.txt b/doc/Reliability/Examples/FlexibleWeibullmodel.txt
new file mode 100755
index 0000000..5e02b91
--- /dev/null
+++ b/doc/Reliability/Examples/FlexibleWeibullmodel.txt
@@ -0,0 +1,11 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dflex.weib(alpha, beta)
+ }
+ # Prior distributions of the model parameters
+
+ alpha ~ dgamma(0.001, 0.001)
+ beta ~ dgamma(0.001, 0.001)
+ }
diff --git a/doc/Reliability/Examples/GPWeibull_Ex.html b/doc/Reliability/Examples/GPWeibull_Ex.html
new file mode 100755
index 0000000..1c0d83c
--- /dev/null
+++ b/doc/Reliability/Examples/GPWeibull_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GPWeibull_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="gpweibull_ex0.bmp" alt="[gpweibull_ex0]">
</font><font face="Courier New" color="#000100" size="6">Generalized Power Weibull Model
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="2"> <img src="gpweibull_ex1.bmp" alt="[gpweibull_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dgp.weib(alpha, theta) <br> }<br> <br> # Prior distributions of the model parameters <br> [...]
</font><font face="Arial" color="#000000" size="2">Nichols, M.D. and W.J. Padgett, W.J. (2006). A bootstrap control chart for Weibull percentiles,
</font><font face="Arial" color="#000000" size="2"><em>Quality and Reliability Engineering International
</em></font><font face="Arial" color="#000000" size="2">, 22, 141-151.
</font><font face="Arial" color="#000000" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/GPWeibulldata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/GPWeibullinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/GPWeibullinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><center>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><img src="gpweibull_ex2.bmp" alt="[gpweibull_ex2]"><br><br>
</font><font face="Arial" color="#000000" size="3"><img src="gpweibull_ex3.bmp" alt="[gpweibull_ex3]">
</font><font face="Arial" color="#0000FF" size="5"><br><br><img src="gpweibull_ex4.bmp" alt="[gpweibull_ex4]"><br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><img src="gpweibull_ex5.bmp" alt="[gpweibull_ex5]"><br><img src="gpweibull_ex6.bmp" alt="[gpweibull_ex6]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GPWeibulldata.html b/doc/Reliability/Examples/GPWeibulldata.html
new file mode 100755
index 0000000..00205d3
--- /dev/null
+++ b/doc/Reliability/Examples/GPWeibulldata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GPWeibulldata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list( N=100, x=c(3.70, 2.74, 2.73, 2.50, 3.60, 3.11, 3.27, 2.87, 1.47, 3.11,<br>4.42, 2.41, 3.19, 3.22, 1.69, 3.28, 3.09, 1.87, 3.15, 4.90,<br>3.75, 2.43, 2.95, 2.97, 3.39, 2.96, 2.53, 2.67, 2.93, 3.22,<br>3.39, 2.81, 4.20, 3.33, 2.55, 3.31, 3.31, 2.85, 2.56, 3.56,<br>3.15, 2.35, 2.55, 2.59, 2.38, 2.81, 2.77, 2.17, 2.83, 1.92,<br>1.41, 3.68, 2.97, 1.36, 0.98, 2.76, 4.91, 3.68, 1.84, 1.59,<br>3.19, 1.57, 0.81, 5.56, 1.73, 1.59, 2.00, 1.22, 1.12, [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GPWeibulldata.txt b/doc/Reliability/Examples/GPWeibulldata.txt
new file mode 100755
index 0000000..9380be2
--- /dev/null
+++ b/doc/Reliability/Examples/GPWeibulldata.txt
@@ -0,0 +1,10 @@
+list( N=100, x=c(3.70, 2.74, 2.73, 2.50, 3.60, 3.11, 3.27, 2.87, 1.47, 3.11,
+4.42, 2.41, 3.19, 3.22, 1.69, 3.28, 3.09, 1.87, 3.15, 4.90,
+3.75, 2.43, 2.95, 2.97, 3.39, 2.96, 2.53, 2.67, 2.93, 3.22,
+3.39, 2.81, 4.20, 3.33, 2.55, 3.31, 3.31, 2.85, 2.56, 3.56,
+3.15, 2.35, 2.55, 2.59, 2.38, 2.81, 2.77, 2.17, 2.83, 1.92,
+1.41, 3.68, 2.97, 1.36, 0.98, 2.76, 4.91, 3.68, 1.84, 1.59,
+3.19, 1.57, 0.81, 5.56, 1.73, 1.59, 2.00, 1.22, 1.12, 1.71,
+2.17, 1.17, 5.08, 2.48, 1.18, 3.51, 2.17, 1.69, 1.25, 4.38,
+1.84, 0.39, 3.68, 2.48, 0.85, 1.61, 2.79, 4.70, 2.03, 1.80,
+1.57, 1.08, 2.03, 1.61, 2.12, 1.89, 2.88, 2.82, 2.05, 3.65))
diff --git a/doc/Reliability/Examples/GPWeibullinits.html b/doc/Reliability/Examples/GPWeibullinits.html
new file mode 100755
index 0000000..0bd6a72
--- /dev/null
+++ b/doc/Reliability/Examples/GPWeibullinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GPWeibullinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=0.5, theta=2.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GPWeibullinits.txt b/doc/Reliability/Examples/GPWeibullinits.txt
new file mode 100755
index 0000000..3d37643
--- /dev/null
+++ b/doc/Reliability/Examples/GPWeibullinits.txt
@@ -0,0 +1 @@
+list(alpha=0.5, theta=2.0)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GPWeibullinits1.html b/doc/Reliability/Examples/GPWeibullinits1.html
new file mode 100755
index 0000000..b3c310f
--- /dev/null
+++ b/doc/Reliability/Examples/GPWeibullinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GPWeibullinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=2.5, theta=11.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GPWeibullinits1.txt b/doc/Reliability/Examples/GPWeibullinits1.txt
new file mode 100755
index 0000000..b811406
--- /dev/null
+++ b/doc/Reliability/Examples/GPWeibullinits1.txt
@@ -0,0 +1 @@
+list(alpha=2.5, theta=11.0)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GPWeibullmodel.html b/doc/Reliability/Examples/GPWeibullmodel.html
new file mode 100755
index 0000000..63f043b
--- /dev/null
+++ b/doc/Reliability/Examples/GPWeibullmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GPWeibullmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dgp.weib(alpha, theta) <br> }<br> <br> # Prior distributions of the model parameters <br>&nbs [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GPWeibullmodel.txt b/doc/Reliability/Examples/GPWeibullmodel.txt
new file mode 100755
index 0000000..125c030
--- /dev/null
+++ b/doc/Reliability/Examples/GPWeibullmodel.txt
@@ -0,0 +1,12 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dgp.weib(alpha, theta)
+ }
+
+ # Prior distributions of the model parameters
+
+ alpha ~ dgamma(0.001, 0.001)
+ theta~ dgamma(0.001, 0.001)
+ }
diff --git a/doc/Reliability/Examples/GenExponential_Cen_Ex.html b/doc/Reliability/Examples/GenExponential_Cen_Ex.html
new file mode 100755
index 0000000..c4f164b
--- /dev/null
+++ b/doc/Reliability/Examples/GenExponential_Cen_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GenExponential_Cen_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="genexponential_cen_ex0.bmp" alt="[genexponential_cen_ex0]">
</font><font face="Courier New" color="#000100" size="6"> Censored Generalized Exponential<br> Model
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="2"> <img src="genexponential_cen_ex1.bmp" alt="[genexponential_cen_ex1]">
</font><font face="Arial" color="#000000" size="3"><br><br>In this example the experiment is stoped after all but three of the N test items have failed. The last three items are therefore left censored at the failure time of the N - 3 item. The software<br>predicts the unobserved failure times of the last three items. Sorting these failure time then gives<br>predictions on when the N - 2, N - 1 and N th failure will occur.<br> <br> model< [...]
</font><font face="Arial" color="#000000" size="2">Lawless, J.F. (2003).
</font><font face="Arial" color="#000000" size="2"><em>Statistical Models and Methods for Lifetime data
</em></font><font face="Arial" color="#000000" size="2">, Second edition, John Wiley & Sons, New York.
</font><font face="Arial" color="#000000" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/GenExponential_Cendata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/GenExponentialinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/GenExponentialinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center><img src="genexponential_cen_ex2.bmp" alt="[genexponential_cen_ex2]"><br><br><img src="genexponential_cen_ex3.bmp" alt="[genexponential_cen_ex3]">
</font><font face="Arial" color="#000000" size="3"><br><br><br><br>
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GenExponential_Cendata.html b/doc/Reliability/Examples/GenExponential_Cendata.html
new file mode 100755
index 0000000..39fcb37
--- /dev/null
+++ b/doc/Reliability/Examples/GenExponential_Cendata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GenExponential_Cendata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list( N=23, x = c(17.88, 28.92, 33.00, 41.52, 42.12, 45.60, 48.80, 51.84, 51.96, 54.12, 55.56, 67.80, 68.64, 68.64, 68.88, 84.12, 93.12, 98.64, 105.12, 105.84, NA, NA, NA))<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GenExponential_Cendata.txt b/doc/Reliability/Examples/GenExponential_Cendata.txt
new file mode 100755
index 0000000..729ea80
--- /dev/null
+++ b/doc/Reliability/Examples/GenExponential_Cendata.txt
@@ -0,0 +1 @@
+list( N=23, x = c(17.88, 28.92, 33.00, 41.52, 42.12, 45.60, 48.80, 51.84, 51.96, 54.12, 55.56, 67.80, 68.64, 68.64, 68.88, 84.12, 93.12, 98.64, 105.12, 105.84, NA, NA, NA))
diff --git a/doc/Reliability/Examples/GenExponential_Ex.html b/doc/Reliability/Examples/GenExponential_Ex.html
new file mode 100755
index 0000000..7bb1456
--- /dev/null
+++ b/doc/Reliability/Examples/GenExponential_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GenExponential_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="genexponential_ex0.bmp" alt="[genexponential_ex0]">
</font><font face="Courier New" color="#000100" size="6">Generalized Exponential Model
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="2"> <img src="genexponential_ex1.bmp" alt="[genexponential_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dgen.exp(alpha, lambda)<br> }<br> <br> # Prior distributions of the model parameters <br>   [...]
</font><font face="Arial" color="#000000" size="2">Lawless, J.F. (2003).
</font><font face="Arial" color="#000000" size="2"><em>Statistical Models and Methods for Lifetime data
</em></font><font face="Arial" color="#000000" size="2">, Second edition, John Wiley & Sons, New York.
</font><font face="Arial" color="#000000" size="3"><br><br>The MLE’s are alpha = 5.2589; lambda = 0 .0314 <br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/GenExponentialdata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/GenExponentialinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/GenExponentialinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center>
</font><font face="Arial" color="#000000" size="3"><br><img src="genexponential_ex2.bmp" alt="[genexponential_ex2]"><br><br><img src="genexponential_ex3.bmp" alt="[genexponential_ex3]"><br><br><img src="genexponential_ex4.bmp" alt="[genexponential_ex4]"><br><img src="genexponential_ex5.bmp" alt="[genexponential_ex5]"><br><img src="genexponential_ex6.bmp" alt="[genexponential_ex6]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GenExponentialdata.html b/doc/Reliability/Examples/GenExponentialdata.html
new file mode 100755
index 0000000..81eabe9
--- /dev/null
+++ b/doc/Reliability/Examples/GenExponentialdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GenExponentialdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list( N=23, x = c(17.88, 28.92, 33.00, 41.52, 42.12, 45.60, 48.80, 51.84, 51.96, 54.12, 55.56, 67.80, 68.64, 68.64, 68.88, 84.12, 93.12, 98.64, 105.12, 105.84, 127.92, 128.04, 173.40))<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GenExponentialdata.txt b/doc/Reliability/Examples/GenExponentialdata.txt
new file mode 100755
index 0000000..585bd59
--- /dev/null
+++ b/doc/Reliability/Examples/GenExponentialdata.txt
@@ -0,0 +1 @@
+list( N=23, x = c(17.88, 28.92, 33.00, 41.52, 42.12, 45.60, 48.80, 51.84, 51.96, 54.12, 55.56, 67.80, 68.64, 68.64, 68.88, 84.12, 93.12, 98.64, 105.12, 105.84, 127.92, 128.04, 173.40))
diff --git a/doc/Reliability/Examples/GenExponentialinits.html b/doc/Reliability/Examples/GenExponentialinits.html
new file mode 100755
index 0000000..7d2ffcd
--- /dev/null
+++ b/doc/Reliability/Examples/GenExponentialinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GenExponentialinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=4.0, lambda=0.01)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GenExponentialinits.txt b/doc/Reliability/Examples/GenExponentialinits.txt
new file mode 100755
index 0000000..936e06c
--- /dev/null
+++ b/doc/Reliability/Examples/GenExponentialinits.txt
@@ -0,0 +1 @@
+list(alpha=4.0, lambda=0.01)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GenExponentialinits1.html b/doc/Reliability/Examples/GenExponentialinits1.html
new file mode 100755
index 0000000..17b723f
--- /dev/null
+++ b/doc/Reliability/Examples/GenExponentialinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GenExponentialinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=8.0, lambda=0.1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GenExponentialinits1.txt b/doc/Reliability/Examples/GenExponentialinits1.txt
new file mode 100755
index 0000000..10d4488
--- /dev/null
+++ b/doc/Reliability/Examples/GenExponentialinits1.txt
@@ -0,0 +1 @@
+list(alpha=8.0, lambda=0.1)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GenExponentialmodel.html b/doc/Reliability/Examples/GenExponentialmodel.html
new file mode 100755
index 0000000..d02ecd5
--- /dev/null
+++ b/doc/Reliability/Examples/GenExponentialmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>GenExponentialmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dgen.exp(alpha, lambda)<br> }<br> <br> # Prior distributions of the model parameters <br> alp [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/GenExponentialmodel.txt b/doc/Reliability/Examples/GenExponentialmodel.txt
new file mode 100755
index 0000000..7a027ab
--- /dev/null
+++ b/doc/Reliability/Examples/GenExponentialmodel.txt
@@ -0,0 +1,11 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dgen.exp(alpha, lambda)
+ }
+
+ # Prior distributions of the model parameters
+ alpha~ dgamma(0.001, 0.001)
+ lambda~ dgamma(0.001, 0.001)
+ }
diff --git a/doc/Reliability/Examples/Gompertz_Ex.html b/doc/Reliability/Examples/Gompertz_Ex.html
new file mode 100755
index 0000000..642b8b2
--- /dev/null
+++ b/doc/Reliability/Examples/Gompertz_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gompertz_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="gompertz_ex0.bmp" alt="[gompertz_ex0]">
</font><font face="Courier New" color="#000100" size="6">Gompertz Model
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000000" size="2"><br> <img src="gompertz_ex1.bmp" alt="[gompertz_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dgpz(alpha, theta) <br> } <br> # Prior distributions of the model parameters [...]
</font><font face="Arial" color="#000000" size="2">Murthy, D. N. P., Xie, M., Jiang, R. (2004).
</font><font face="Arial" color="#000000" size="2"><em>Weibull Models
</em></font><font face="Arial" color="#000000" size="2">, Wiley-Interscience.
</font><font face="Arial" color="#000000" size="3"><br><br>MLE's are alpha = 1.968482 theta = 0.019104 <br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/Gompertzdata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/Gompertzinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/Gompertzinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center>
</font><font face="Arial" color="#0000FF" size="5"><u><img src="gompertz_ex2.bmp" alt="[gompertz_ex2]"><br><br>
</u></font><font face="Arial" color="#000000" size="3"><img src="gompertz_ex3.bmp" alt="[gompertz_ex3]">
</font><font face="Arial" color="#0000FF" size="5"><u><br><br><img src="gompertz_ex4.bmp" alt="[gompertz_ex4]"><br><img src="gompertz_ex5.bmp" alt="[gompertz_ex5]"><br><img src="gompertz_ex6.bmp" alt="[gompertz_ex6]">
</u></font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gompertzdata.html b/doc/Reliability/Examples/Gompertzdata.html
new file mode 100755
index 0000000..4a53b0f
--- /dev/null
+++ b/doc/Reliability/Examples/Gompertzdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gompertzdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(N=20, x=c(0.481, 1.196, 1.438, 1.797, 1.811, 1.831, 1.885, 2.104, 2.133, 2.144,<br>2.282, 2.322, 2.334, 2.341, 2.428, 2.447, 2.511, 2.593, 2.715, 3.218))<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gompertzdata.txt b/doc/Reliability/Examples/Gompertzdata.txt
new file mode 100755
index 0000000..92f6c75
--- /dev/null
+++ b/doc/Reliability/Examples/Gompertzdata.txt
@@ -0,0 +1,2 @@
+list(N=20, x=c(0.481, 1.196, 1.438, 1.797, 1.811, 1.831, 1.885, 2.104, 2.133, 2.144,
+2.282, 2.322, 2.334, 2.341, 2.428, 2.447, 2.511, 2.593, 2.715, 3.218))
diff --git a/doc/Reliability/Examples/Gompertzinits.html b/doc/Reliability/Examples/Gompertzinits.html
new file mode 100755
index 0000000..4b0b4cd
--- /dev/null
+++ b/doc/Reliability/Examples/Gompertzinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gompertzinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=1.0, theta=0.1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gompertzinits.txt b/doc/Reliability/Examples/Gompertzinits.txt
new file mode 100755
index 0000000..e679220
--- /dev/null
+++ b/doc/Reliability/Examples/Gompertzinits.txt
@@ -0,0 +1 @@
+list(alpha=1.0, theta=0.1)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gompertzinits1.html b/doc/Reliability/Examples/Gompertzinits1.html
new file mode 100755
index 0000000..044c7d4
--- /dev/null
+++ b/doc/Reliability/Examples/Gompertzinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gompertzinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=5.0, theta=1.2)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gompertzinits1.txt b/doc/Reliability/Examples/Gompertzinits1.txt
new file mode 100755
index 0000000..a617230
--- /dev/null
+++ b/doc/Reliability/Examples/Gompertzinits1.txt
@@ -0,0 +1 @@
+list(alpha=5.0, theta=1.2)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gompertzmodel.html b/doc/Reliability/Examples/Gompertzmodel.html
new file mode 100755
index 0000000..88b35e7
--- /dev/null
+++ b/doc/Reliability/Examples/Gompertzmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gompertzmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dgpz(alpha, theta) <br> } <br> # Prior distributions of the model parameters &nbs [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gompertzmodel.txt b/doc/Reliability/Examples/Gompertzmodel.txt
new file mode 100755
index 0000000..b5ae320
--- /dev/null
+++ b/doc/Reliability/Examples/Gompertzmodel.txt
@@ -0,0 +1,11 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dgpz(alpha, theta)
+ }
+ # Prior distributions of the model parameters
+ # Gamma Prior
+ alpha ~ dgamma(0.001, 0.001)
+ theta~ dgamma(0.001, 0.001)
+ }
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gumbel_Ex.html b/doc/Reliability/Examples/Gumbel_Ex.html
new file mode 100755
index 0000000..76a840d
--- /dev/null
+++ b/doc/Reliability/Examples/Gumbel_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gumbel_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2"><img src="gumbel_ex0.bmp" alt="[gumbel_ex0]">
</font><font face="Courier New" color="#000100" size="6">Gumbel distribution
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="2"> <img src="gumbel_ex1.bmp" alt="[gumbel_ex1]"><img src="gumbel_ex2.bmp" alt="[gumbel_ex2]"><br> <br>
</font><font face="Arial" color="#000000" size="3">model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dgumbel(alpha, tau) <br> }<br> <br> # Prior distributions of the model parameters <br> & [...]
</font><font face="Arial" color="#000000" size="2">Murthy, D. N. P., Xie, M., Jiang, R. (2004).
</font><font face="Arial" color="#000000" size="2"><em>Weibull Models
</em></font><font face="Arial" color="#000000" size="2">, Wiley-Interscience.
</font><font face="Arial" color="#000000" size="3"><br><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/Gumbeldata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/Gumbelinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/Gumbelinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#0000FF" size="5"><u><img src="gumbel_ex3.bmp" alt="[gumbel_ex3]"><br><br>
</u></font><font face="Arial" color="#000000" size="3"><img src="gumbel_ex4.bmp" alt="[gumbel_ex4]">
</font><font face="Arial" color="#0000FF" size="5"><u><br><br><img src="gumbel_ex5.bmp" alt="[gumbel_ex5]"><br><img src="gumbel_ex6.bmp" alt="[gumbel_ex6]"><br><img src="gumbel_ex7.bmp" alt="[gumbel_ex7]">
</u></font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gumbeldata.html b/doc/Reliability/Examples/Gumbeldata.html
new file mode 100755
index 0000000..4280e45
--- /dev/null
+++ b/doc/Reliability/Examples/Gumbeldata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gumbeldata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(N=20, x=c(0.481, 1.196, 1.438, 1.797, 1.811, 1.831, 1.885, 2.104, 2.133, 2.144,<br>2.282, 2.322, 2.334, 2.341, 2.428, 2.447, 2.511, 2.593, 2.715, 3.218))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gumbeldata.txt b/doc/Reliability/Examples/Gumbeldata.txt
new file mode 100755
index 0000000..b8f0bba
--- /dev/null
+++ b/doc/Reliability/Examples/Gumbeldata.txt
@@ -0,0 +1,2 @@
+list(N=20, x=c(0.481, 1.196, 1.438, 1.797, 1.811, 1.831, 1.885, 2.104, 2.133, 2.144,
+2.282, 2.322, 2.334, 2.341, 2.428, 2.447, 2.511, 2.593, 2.715, 3.218))
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gumbelinits.html b/doc/Reliability/Examples/Gumbelinits.html
new file mode 100755
index 0000000..be7d4cc
--- /dev/null
+++ b/doc/Reliability/Examples/Gumbelinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gumbelinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=1.0, tau=0.1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gumbelinits.txt b/doc/Reliability/Examples/Gumbelinits.txt
new file mode 100755
index 0000000..6dea25e
--- /dev/null
+++ b/doc/Reliability/Examples/Gumbelinits.txt
@@ -0,0 +1 @@
+list(alpha=1.0, tau=0.1)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gumbelinits1.html b/doc/Reliability/Examples/Gumbelinits1.html
new file mode 100755
index 0000000..7c9c363
--- /dev/null
+++ b/doc/Reliability/Examples/Gumbelinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gumbelinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=5.0, tau=1.2)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gumbelinits1.txt b/doc/Reliability/Examples/Gumbelinits1.txt
new file mode 100755
index 0000000..a37c50e
--- /dev/null
+++ b/doc/Reliability/Examples/Gumbelinits1.txt
@@ -0,0 +1 @@
+list(alpha=5.0, tau=1.2)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gumbelmodel.html b/doc/Reliability/Examples/Gumbelmodel.html
new file mode 100755
index 0000000..a6ffec1
--- /dev/null
+++ b/doc/Reliability/Examples/Gumbelmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Gumbelmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dgumbel(alpha, tau) <br> }<br> <br> # Prior distributions of the model parameters   [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Gumbelmodel.txt b/doc/Reliability/Examples/Gumbelmodel.txt
new file mode 100755
index 0000000..d0d62e4
--- /dev/null
+++ b/doc/Reliability/Examples/Gumbelmodel.txt
@@ -0,0 +1,13 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dgumbel(alpha, tau)
+ }
+
+ # Prior distributions of the model parameters
+ # Gamma Prior
+ alpha ~ dgamma(0.001, 0.001)
+ tau~ dgamma(0.001, 0.001)
+
+ }
\ No newline at end of file
diff --git a/doc/Reliability/Examples/InvGaussian_Ex.html b/doc/Reliability/Examples/InvGaussian_Ex.html
new file mode 100755
index 0000000..a0939f2
--- /dev/null
+++ b/doc/Reliability/Examples/InvGaussian_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>InvGaussian_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="invgaussian_ex0.bmp" alt="[invgaussian_ex0]">
</font><font face="Courier New" color="#000100" size="6">Inverse Gaussian
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="2"> <img src="invgaussian_ex1.bmp" alt="[invgaussian_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dinv.gauss(mu, lambda)<br> <br> }<br> <br> # Prior distributions of the model parameters [...]
</font><font face="Arial" color="#000000" size="2"><br>Chhikara R.S, Folks J.L.(1977). The inverse Gaussian distribution as a lifetime model.
</font><font face="Arial" color="#000000" size="2"><em>Technometrics,
</em></font><font face="Arial" color="#000000" size="2"><strong>19
</strong></font><font face="Arial" color="#000000" size="2">, 461-468.
</font><font face="Arial" color="#000000" size="3"><br><br>The MLE's are obtained using 'maxLik' package in R mu = 3.606522 lambda = 1.658853<br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/InvGaussiandata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/InvGaussianinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/InvGaussianinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center>
</font><font face="Arial" color="#000000" size="3"><img src="invgaussian_ex2.bmp" alt="[invgaussian_ex2]"><br></center><br>The distribution of mu is quite skewed with its mode occuring at 3.70 for chain one and 3.58 for chain two in good agreement with the MLE.<br><br><center><img src="invgaussian_ex3.bmp" alt="[invgaussian_ex3]"><br><br><img src="invgaussian_ex4.bmp" alt="[invgaussian_ex4]"><br><img src="invgaussian_ex5.bmp" alt="[invgaussian_ex5]"><br><img src="invgaussian_ex6.bmp" alt= [...]
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/InvGaussiandata.html b/doc/Reliability/Examples/InvGaussiandata.html
new file mode 100755
index 0000000..fdd993c
--- /dev/null
+++ b/doc/Reliability/Examples/InvGaussiandata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>InvGaussiandata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list( N=46, x = c(0.2, 0.3, 0.5, 0.5, 0.5, 0.5, 0.6, 0.6, 0.7, 0.7, 0.7, 0.8, 0.8, 1.0, 1.0, 1.0, 1.0,<br>1.1, 1.3, 1.5, 1.5, 1.5, 1.5, 2.0, 2.0, 2.2, 2.5, 2.7, 3.0, 3.0, 3.3, 3.3, 4.0, 4.0, 4.5, 4.7, 5.0, 5.4, 5.4, 7.0, 7.5, 8.8, 9.0, 10.3, 22.0, 24.5))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/InvGaussiandata.txt b/doc/Reliability/Examples/InvGaussiandata.txt
new file mode 100755
index 0000000..41171b6
--- /dev/null
+++ b/doc/Reliability/Examples/InvGaussiandata.txt
@@ -0,0 +1,2 @@
+list( N=46, x = c(0.2, 0.3, 0.5, 0.5, 0.5, 0.5, 0.6, 0.6, 0.7, 0.7, 0.7, 0.8, 0.8, 1.0, 1.0, 1.0, 1.0,
+1.1, 1.3, 1.5, 1.5, 1.5, 1.5, 2.0, 2.0, 2.2, 2.5, 2.7, 3.0, 3.0, 3.3, 3.3, 4.0, 4.0, 4.5, 4.7, 5.0, 5.4, 5.4, 7.0, 7.5, 8.8, 9.0, 10.3, 22.0, 24.5))
\ No newline at end of file
diff --git a/doc/Reliability/Examples/InvGaussianinits.html b/doc/Reliability/Examples/InvGaussianinits.html
new file mode 100755
index 0000000..4186b57
--- /dev/null
+++ b/doc/Reliability/Examples/InvGaussianinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>InvGaussianinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(mu=2.0, lambda=1.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/InvGaussianinits.txt b/doc/Reliability/Examples/InvGaussianinits.txt
new file mode 100755
index 0000000..f8693b5
--- /dev/null
+++ b/doc/Reliability/Examples/InvGaussianinits.txt
@@ -0,0 +1 @@
+list(mu=2.0, lambda=1.0)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/InvGaussianinits1.html b/doc/Reliability/Examples/InvGaussianinits1.html
new file mode 100755
index 0000000..9a37086
--- /dev/null
+++ b/doc/Reliability/Examples/InvGaussianinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>InvGaussianinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(mu=5.0, lambda=3.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/InvGaussianinits1.txt b/doc/Reliability/Examples/InvGaussianinits1.txt
new file mode 100755
index 0000000..b825fbd
--- /dev/null
+++ b/doc/Reliability/Examples/InvGaussianinits1.txt
@@ -0,0 +1 @@
+list(mu=5.0, lambda=3.0)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/InvGaussianmodel.html b/doc/Reliability/Examples/InvGaussianmodel.html
new file mode 100755
index 0000000..6f6ce2d
--- /dev/null
+++ b/doc/Reliability/Examples/InvGaussianmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>InvGaussianmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dinv.gauss(mu, lambda)<br> <br> }<br> <br> # Prior distributions of the model parameters&nbs [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/InvGaussianmodel.txt b/doc/Reliability/Examples/InvGaussianmodel.txt
new file mode 100755
index 0000000..31fb30c
--- /dev/null
+++ b/doc/Reliability/Examples/InvGaussianmodel.txt
@@ -0,0 +1,13 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dinv.gauss(mu, lambda)
+
+ }
+
+ # Prior distributions of the model parameters
+
+ mu ~ dunif(0.001, 10.0)
+ lambda~ dunif(0.01, 5.0)
+ }
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Inv_Weibull_Ex.html b/doc/Reliability/Examples/Inv_Weibull_Ex.html
new file mode 100755
index 0000000..221d3b1
--- /dev/null
+++ b/doc/Reliability/Examples/Inv_Weibull_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Inv_Weibull_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="inv_weibull_ex0.bmp" alt="[inv_weibull_ex0]">
</font><font face="Courier New" color="#000100" size="6">Inverse Weibull Model
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="2"> <img src="inv_weibull_ex1.bmp" alt="[inv_weibull_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dinv.weib(beta, lambda)<br> }<br> <br> #Prior distributions of the model parameters <br> # Gamma Prior   [...]
</font><font face="Arial" color="#000000" size="2">Murthy, D. N. P., Xie, M., Jiang, R. (2004).
</font><font face="Arial" color="#000000" size="2"><em>Weibull Models
</em></font><font face="Arial" color="#000000" size="2">, Wiley-Interscience.
</font><font face="Arial" color="#000000" size="3"><br><br>MLE's are beta = 3.888075, lambda = 0.803668 <br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/Inv_Weibulldata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/Inv_Weibullinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/Inv_Weibullinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center>
</font><font face="Arial" color="#000000" size="3"><img src="inv_weibull_ex2.bmp" alt="[inv_weibull_ex2]"><br><br><img src="inv_weibull_ex3.bmp" alt="[inv_weibull_ex3]"><br><br><img src="inv_weibull_ex4.bmp" alt="[inv_weibull_ex4]"><br><img src="inv_weibull_ex5.bmp" alt="[inv_weibull_ex5]"><br><img src="inv_weibull_ex6.bmp" alt="[inv_weibull_ex6]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Inv_Weibulldata.html b/doc/Reliability/Examples/Inv_Weibulldata.html
new file mode 100755
index 0000000..b887e4a
--- /dev/null
+++ b/doc/Reliability/Examples/Inv_Weibulldata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Inv_Weibulldata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(N=30,x=c(0.602, 0.603, 0.603, 0.615, 0.652, 0.663, 0.688, 0.705, 0.761, 0.770, <br>0.868, 0.884, 0.898, 0.901, 0.911, 0.918, 0.935, 0.953, 0.983, 1.009, 1.040, <br>1.097, 1.097, 1.148, 1.296, 1.343, 1.422, 1.540, 1.555, 1.653))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Inv_Weibulldata.txt b/doc/Reliability/Examples/Inv_Weibulldata.txt
new file mode 100755
index 0000000..207fc52
--- /dev/null
+++ b/doc/Reliability/Examples/Inv_Weibulldata.txt
@@ -0,0 +1,3 @@
+list(N=30,x=c(0.602, 0.603, 0.603, 0.615, 0.652, 0.663, 0.688, 0.705, 0.761, 0.770,
+0.868, 0.884, 0.898, 0.901, 0.911, 0.918, 0.935, 0.953, 0.983, 1.009, 1.040,
+1.097, 1.097, 1.148, 1.296, 1.343, 1.422, 1.540, 1.555, 1.653))
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Inv_Weibullinits.html b/doc/Reliability/Examples/Inv_Weibullinits.html
new file mode 100755
index 0000000..20c8bab
--- /dev/null
+++ b/doc/Reliability/Examples/Inv_Weibullinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Inv_Weibullinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(beta=1.0, lambda=0.1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Inv_Weibullinits.txt b/doc/Reliability/Examples/Inv_Weibullinits.txt
new file mode 100755
index 0000000..747a3ae
--- /dev/null
+++ b/doc/Reliability/Examples/Inv_Weibullinits.txt
@@ -0,0 +1 @@
+list(beta=1.0, lambda=0.1)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Inv_Weibullinits1.html b/doc/Reliability/Examples/Inv_Weibullinits1.html
new file mode 100755
index 0000000..a1506ce
--- /dev/null
+++ b/doc/Reliability/Examples/Inv_Weibullinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Inv_Weibullinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(beta=7.0, lambda=1.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Inv_Weibullinits1.txt b/doc/Reliability/Examples/Inv_Weibullinits1.txt
new file mode 100755
index 0000000..e4affbf
--- /dev/null
+++ b/doc/Reliability/Examples/Inv_Weibullinits1.txt
@@ -0,0 +1 @@
+list(beta=7.0, lambda=1.0)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Inv_Weibullmodel.html b/doc/Reliability/Examples/Inv_Weibullmodel.html
new file mode 100755
index 0000000..c877409
--- /dev/null
+++ b/doc/Reliability/Examples/Inv_Weibullmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Inv_Weibullmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dinv.weib(beta, lambda)<br> }<br> <br> #Prior distributions of the model parameters <br> # Gamma Prior &nb [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Inv_Weibullmodel.txt b/doc/Reliability/Examples/Inv_Weibullmodel.txt
new file mode 100755
index 0000000..05690d4
--- /dev/null
+++ b/doc/Reliability/Examples/Inv_Weibullmodel.txt
@@ -0,0 +1,12 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dinv.weib(beta, lambda)
+ }
+
+ #Prior distributions of the model parameters
+ # Gamma Prior
+ beta ~ dgamma(0.001, 0.001)
+ lambda~ dgamma(0.001, 0.001)
+ }
diff --git a/doc/Reliability/Examples/LinearFailure_Ex.html b/doc/Reliability/Examples/LinearFailure_Ex.html
new file mode 100755
index 0000000..998f5e0
--- /dev/null
+++ b/doc/Reliability/Examples/LinearFailure_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LinearFailure_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="linearfailure_ex0.bmp" alt="[linearfailure_ex0]">
</font><font face="Courier New" color="#000100" size="6">Linear Failure Rate Model
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="2"> <img src="linearfailure_ex1.bmp" alt="[linearfailure_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dlin.fr(alpha, beta)<br> }<br> <br> # Prior distributions of the model parameters <br> <br> &nbs [...]
</font><font face="NimbusRomNo9L-Regu" color="#000000" size="2">The data set is taken from DACS Software Reliability Dataset, Lyu (1996). The data represents the time-between-failures (time unit in miliseconds) of a software. The data given here is transformed from time-between-failures to failure times.<br>
</font><font face="NimbusRomNo9L-Medi" color="#000000" size="2"><br>
</font><font face="NimbusRomNo9L-Regu" color="#000000" size="2">Lyu, M. R. (1996).
</font><font face="NimbusRomNo9L-ReguItal" color="#000000" size="2"><em>Handbook of Software Reliability Engineering
</em></font><font face="NimbusRomNo9L-Regu" color="#000000" size="2">, IEEE Computer Society Press,<br>
</font><font face="NimbusMonL-Regu" color="#000000" size="2">http://www.cse.cuhk.edu.hk/~lyu/book/reliability/
</font><font face="NimbusRomNo9L-Regu" color="#000000" size="2"><br>
</font><font face="Arial" color="#000000" size="3"><br>The MLE's are alpha =
</font><font face="Arial" color="#000000" size="3">1.7777e-03, beta=2.7776e-06
</font><font face="Arial" color="#000000" size="3"> <br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/LinearFailuredata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/LinearFailureinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/LinearFailureinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br>
</font><font face="Arial" color="#000100" size="1">Node statistics<br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> mean sd MC_error val2.5pc median val97.5pc start sample<br>
</strong></font><font face="Arial" color="#000100" size="2"> alpha 0.001736 3.851E-4 2.984E-6 0.001028 0.00172 0.00253 1001 50000<br> beta 3.013E-6 1.146E-6 8.734E-9 8.449E-7 2.985E-6 5.361E-6 1001 & [...]
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="2"><strong> Dbar Dhat DIC pD <br>
</strong></font><font face="Arial" color="#000100" size="2">x 1190.0 1188.0 1192.0 1.968<br>total 1190.0 1188.0 1192.0 1.968<br>
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="linearfailure_ex2.bmp" alt="[linearfailure_ex2]"><img src="linearfailure_ex3.bmp" alt="[linearfailure_ex3]">
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="linearfailure_ex4.bmp" alt="[linearfailure_ex4]"><img src="linearfailure_ex5.bmp" alt="[linearfailure_ex5]"><br>
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="linearfailure_ex6.bmp" alt="[linearfailure_ex6]"><img src="linearfailure_ex7.bmp" alt="[linearfailure_ex7]">
</font><font face="Arial" color="#000100" size="1"><br><br><br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/LinearFailuredata.html b/doc/Reliability/Examples/LinearFailuredata.html
new file mode 100755
index 0000000..aafb454
--- /dev/null
+++ b/doc/Reliability/Examples/LinearFailuredata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LinearFailuredata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(N=86,
</font><font face="Arial" color="#000100" size="3">x =c(4.79, 7.45, 10.22, 15.76, 26.10, 28.59, 35.52, 41.49, 42.66,<br>44.36, 45.53, 58.27, 62.96, 74.70, 81.63, 100.71, 102.06, 104.83,110.79, 118.36, 122.73, 145.03, 149.40, 152.80, 156.85, 162.20, 164.97,168.60, 173.82, 179.95, 182.72, 195.72, 203.93, 206.06, 222.26, 238.27, 241.25, 249.99, 256.17, 282.57, 282.62, 284.11, 294.45, 318.86, 323.46, 329.11, 340.30, 344.67, 353.94, 398.56, 405.70, 407.51, 422.36, 429.93,<br>461.47, 482.62, 49 [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LinearFailuredata.txt b/doc/Reliability/Examples/LinearFailuredata.txt
new file mode 100755
index 0000000..63b9c21
--- /dev/null
+++ b/doc/Reliability/Examples/LinearFailuredata.txt
@@ -0,0 +1,3 @@
+list(N=86, x =c(4.79, 7.45, 10.22, 15.76, 26.10, 28.59, 35.52, 41.49, 42.66,
+44.36, 45.53, 58.27, 62.96, 74.70, 81.63, 100.71, 102.06, 104.83,110.79, 118.36, 122.73, 145.03, 149.40, 152.80, 156.85, 162.20, 164.97,168.60, 173.82, 179.95, 182.72, 195.72, 203.93, 206.06, 222.26, 238.27, 241.25, 249.99, 256.17, 282.57, 282.62, 284.11, 294.45, 318.86, 323.46, 329.11, 340.30, 344.67, 353.94, 398.56, 405.70, 407.51, 422.36, 429.93,
+461.47, 482.62, 491.46, 511.83, 526.64, 532.23, 537.13, 543.06, 560.75, 561.60, 589.96, 592.09, 610.75, 615.65, 630.52, 673.74, 687.92, 698.15, 753.05, 768.25, 801.06, 828.22, 849.97, 885.02, 892.27, 911.90, 951.69, 962.59, 965.04, 976.98, 986.92, 1025.94))
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LinearFailureinits.html b/doc/Reliability/Examples/LinearFailureinits.html
new file mode 100755
index 0000000..7e3ef7e
--- /dev/null
+++ b/doc/Reliability/Examples/LinearFailureinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LinearFailureinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=0.001, beta= 0.001)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LinearFailureinits.txt b/doc/Reliability/Examples/LinearFailureinits.txt
new file mode 100755
index 0000000..6e31e60
--- /dev/null
+++ b/doc/Reliability/Examples/LinearFailureinits.txt
@@ -0,0 +1 @@
+list(alpha=0.001, beta= 0.001)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LinearFailureinits1.html b/doc/Reliability/Examples/LinearFailureinits1.html
new file mode 100755
index 0000000..5b8eea3
--- /dev/null
+++ b/doc/Reliability/Examples/LinearFailureinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LinearFailureinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=0.02, beta= 0.05)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LinearFailureinits1.txt b/doc/Reliability/Examples/LinearFailureinits1.txt
new file mode 100755
index 0000000..a1e517f
--- /dev/null
+++ b/doc/Reliability/Examples/LinearFailureinits1.txt
@@ -0,0 +1 @@
+list(alpha=0.02, beta= 0.05)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LinearFailuremodel.html b/doc/Reliability/Examples/LinearFailuremodel.html
new file mode 100755
index 0000000..5b0c662
--- /dev/null
+++ b/doc/Reliability/Examples/LinearFailuremodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LinearFailuremodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dlin.fr(alpha, beta)<br> }<br> <br> # Prior distributions of the model parameters <br> <br> &n [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LinearFailuremodel.txt b/doc/Reliability/Examples/LinearFailuremodel.txt
new file mode 100755
index 0000000..55c63b8
--- /dev/null
+++ b/doc/Reliability/Examples/LinearFailuremodel.txt
@@ -0,0 +1,12 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dlin.fr(alpha, beta)
+ }
+
+ # Prior distributions of the model parameters
+
+ alpha ~ dgamma(0.001, 0.001)
+ beta ~ dunif(0, 1.0)
+ }
diff --git a/doc/Reliability/Examples/LogWeibull_Ex.html b/doc/Reliability/Examples/LogWeibull_Ex.html
new file mode 100755
index 0000000..12a28c4
--- /dev/null
+++ b/doc/Reliability/Examples/LogWeibull_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LogWeibull_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="logweibull_ex0.bmp" alt="[logweibull_ex0]">
</font><font face="Courier New" color="#000100" size="6"> Log-Weibull Model
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000100" size="1"><img src="logweibull_ex1.bmp" alt="[logweibull_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dlog.weib(mu, sigma)<br> }<br> <br> # Prior distributions of the model parameters <br><br> &nbs [...]
</font><font face="Arial" color="#000000" size="2">Murthy, D. N. P., Xie, M., Jiang, R. (2004),
</font><font face="Arial" color="#000000" size="2"><em>Weibull Models
</em></font><font face="Arial" color="#000000" size="2">, Wiley-Interscience.
</font><font face="Arial" color="#000000" size="3"><br><br>MLE's are mu = 2.36573, sigma.= 0.49440 <br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/LogWeibulldata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/LogWeibullinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/LogWeibullinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center>
</font><font face="Arial" color="#000000" size="3"><img src="logweibull_ex2.bmp" alt="[logweibull_ex2]"><br><br><img src="logweibull_ex3.bmp" alt="[logweibull_ex3]"><br><br><br><br><img src="logweibull_ex4.bmp" alt="[logweibull_ex4]"><br><img src="logweibull_ex5.bmp" alt="[logweibull_ex5]"><br><br><img src="logweibull_ex6.bmp" alt="[logweibull_ex6]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogWeibulldata.html b/doc/Reliability/Examples/LogWeibulldata.html
new file mode 100755
index 0000000..5f74225
--- /dev/null
+++ b/doc/Reliability/Examples/LogWeibulldata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LogWeibulldata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(N=20, x=c(0.481, 1.196, 1.438, 1.797, 1.811, 1.831, 1.885, 2.104, 2.133, 2.144,<br>2.282, 2.322, 2.334, 2.341, 2.428, 2.447, 2.511, 2.593, 2.715, 3.218))<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogWeibulldata.txt b/doc/Reliability/Examples/LogWeibulldata.txt
new file mode 100755
index 0000000..92f6c75
--- /dev/null
+++ b/doc/Reliability/Examples/LogWeibulldata.txt
@@ -0,0 +1,2 @@
+list(N=20, x=c(0.481, 1.196, 1.438, 1.797, 1.811, 1.831, 1.885, 2.104, 2.133, 2.144,
+2.282, 2.322, 2.334, 2.341, 2.428, 2.447, 2.511, 2.593, 2.715, 3.218))
diff --git a/doc/Reliability/Examples/LogWeibullinits.html b/doc/Reliability/Examples/LogWeibullinits.html
new file mode 100755
index 0000000..5a30dce
--- /dev/null
+++ b/doc/Reliability/Examples/LogWeibullinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LogWeibullinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(mu=1.0, sigma=0.1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogWeibullinits.txt b/doc/Reliability/Examples/LogWeibullinits.txt
new file mode 100755
index 0000000..59bbd7d
--- /dev/null
+++ b/doc/Reliability/Examples/LogWeibullinits.txt
@@ -0,0 +1 @@
+list(mu=1.0, sigma=0.1)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogWeibullinits1.html b/doc/Reliability/Examples/LogWeibullinits1.html
new file mode 100755
index 0000000..147e298
--- /dev/null
+++ b/doc/Reliability/Examples/LogWeibullinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LogWeibullinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(mu=5.0, sigma=1.2)<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogWeibullinits1.txt b/doc/Reliability/Examples/LogWeibullinits1.txt
new file mode 100755
index 0000000..59cc122
--- /dev/null
+++ b/doc/Reliability/Examples/LogWeibullinits1.txt
@@ -0,0 +1 @@
+list(mu=5.0, sigma=1.2)
diff --git a/doc/Reliability/Examples/LogWeibullmodel.html b/doc/Reliability/Examples/LogWeibullmodel.html
new file mode 100755
index 0000000..101d5f7
--- /dev/null
+++ b/doc/Reliability/Examples/LogWeibullmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LogWeibullmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dlog.weib(mu, sigma)<br> }<br> <br> # Prior distributions of the model parameters <br><br> # [...]
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogWeibullmodel.txt b/doc/Reliability/Examples/LogWeibullmodel.txt
new file mode 100755
index 0000000..a1b11f8
--- /dev/null
+++ b/doc/Reliability/Examples/LogWeibullmodel.txt
@@ -0,0 +1,14 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dlog.weib(mu, sigma)
+ }
+
+ # Prior distributions of the model parameters
+
+ # Gamma Prior
+ mu ~ dgamma(0.001, 0.001)
+ sigma~ dgamma(0.001, 0.001)
+
+ }
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogisticExponential_Ex.html b/doc/Reliability/Examples/LogisticExponential_Ex.html
new file mode 100755
index 0000000..85eb05a
--- /dev/null
+++ b/doc/Reliability/Examples/LogisticExponential_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LogisticExponential_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="logisticexponential_ex0.bmp" alt="[logisticexponential_ex0]">
</font><font face="Courier New" color="#000100" size="6"> Logistic-Exponential Model
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="2"> <img src="logisticexponential_ex1.bmp" alt="[logisticexponential_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dlogistic.exp(alpha, lambda)<br> }<br> <br> # Prior distributions of the model parameters <br> <br> &n [...]
</font><font face="Arial" color="#000000" size="2">Lan, Y. and Leemis, L. M. (2008). : The Log-Exponential Distribution.
</font><font face="Arial" color="#000000" size="2"><em>Naval Research Logistics
</em></font><font face="Arial" color="#000000" size="2">,
</font><font face="Arial" color="#000000" size="2"><strong>55
</strong></font><font face="Arial" color="#000000" size="2">, 252-264. <br><br>Lawless, J.F. (2003).
</font><font face="Arial" color="#000000" size="2"><em>Statistical Models and Methods for Lifetime data
</em></font><font face="Arial" color="#000000" size="2">, Second edition, John Wiley & Sons, New York.
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/LogisticExponentialdata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/LogisticExponentialinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/LogisticExponentialinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center>
</font><font face="Arial" color="#000000" size="3"><img src="logisticexponential_ex2.bmp" alt="[logisticexponential_ex2]"><br><br><img src="logisticexponential_ex3.bmp" alt="[logisticexponential_ex3]"><br><br><img src="logisticexponential_ex4.bmp" alt="[logisticexponential_ex4]"><br><img src="logisticexponential_ex5.bmp" alt="[logisticexponential_ex5]"><br><img src="logisticexponential_ex6.bmp" alt="[logisticexponential_ex6]">
</font>
</center>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogisticExponentialdata.html b/doc/Reliability/Examples/LogisticExponentialdata.html
new file mode 100755
index 0000000..a89bc4d
--- /dev/null
+++ b/doc/Reliability/Examples/LogisticExponentialdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LogisticExponentialdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list( N=23, x = c(17.88, 28.92, 33.00, 41.52, 42.12, 45.60, 48.80, 51.84, 51.96, 54.12, 55.56, 67.80, 68.64, 68.88, 84.12, 93.12, 98.64, 105.12, 105.84, 127.92, 128.04, 173.40, 68.64))
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogisticExponentialdata.txt b/doc/Reliability/Examples/LogisticExponentialdata.txt
new file mode 100755
index 0000000..1e35a56
--- /dev/null
+++ b/doc/Reliability/Examples/LogisticExponentialdata.txt
@@ -0,0 +1 @@
+list( N=23, x = c(17.88, 28.92, 33.00, 41.52, 42.12, 45.60, 48.80, 51.84, 51.96, 54.12, 55.56, 67.80, 68.64, 68.88, 84.12, 93.12, 98.64, 105.12, 105.84, 127.92, 128.04, 173.40, 68.64))
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogisticExponentialinits.html b/doc/Reliability/Examples/LogisticExponentialinits.html
new file mode 100755
index 0000000..3dc6d04
--- /dev/null
+++ b/doc/Reliability/Examples/LogisticExponentialinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LogisticExponentialinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=5.0, lambda=0.5)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogisticExponentialinits.txt b/doc/Reliability/Examples/LogisticExponentialinits.txt
new file mode 100755
index 0000000..c3add93
--- /dev/null
+++ b/doc/Reliability/Examples/LogisticExponentialinits.txt
@@ -0,0 +1 @@
+list(alpha=5.0, lambda=0.5)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogisticExponentialinits1.html b/doc/Reliability/Examples/LogisticExponentialinits1.html
new file mode 100755
index 0000000..d19df5d
--- /dev/null
+++ b/doc/Reliability/Examples/LogisticExponentialinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LogisticExponentialinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=3.0, lambda=0.1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogisticExponentialinits1.txt b/doc/Reliability/Examples/LogisticExponentialinits1.txt
new file mode 100755
index 0000000..9a327c2
--- /dev/null
+++ b/doc/Reliability/Examples/LogisticExponentialinits1.txt
@@ -0,0 +1 @@
+list(alpha=3.0, lambda=0.1)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/LogisticExponentialmodel.html b/doc/Reliability/Examples/LogisticExponentialmodel.html
new file mode 100755
index 0000000..7a9da63
--- /dev/null
+++ b/doc/Reliability/Examples/LogisticExponentialmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>LogisticExponentialmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dlogistic.exp(alpha, lambda)<br> }<br> <br> # Prior distributions of the model parameters <br> <br> [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/LogisticExponentialmodel.txt b/doc/Reliability/Examples/LogisticExponentialmodel.txt
new file mode 100755
index 0000000..a54a10f
--- /dev/null
+++ b/doc/Reliability/Examples/LogisticExponentialmodel.txt
@@ -0,0 +1,12 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dlogistic.exp(alpha, lambda)
+ }
+
+ # Prior distributions of the model parameters
+
+ alpha ~ dunif(0.0, 10.0)
+ lambda~ dunif(0, 2.0)
+ }
diff --git a/doc/Reliability/Examples/Loglogistic_Ex.html b/doc/Reliability/Examples/Loglogistic_Ex.html
new file mode 100755
index 0000000..906d08d
--- /dev/null
+++ b/doc/Reliability/Examples/Loglogistic_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Loglogistic_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="loglogistic_ex0.bmp" alt="[loglogistic_ex0]">
</font><font face="Courier New" color="#000100" size="6">Log-Logistic Model
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="2"> <img src="loglogistic_ex1.bmp" alt="[loglogistic_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dlog.logis(beta, theta)<br> }<br> <br> # Prior distributions of the model parameters <br> &nbs [...]
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/Loglogisticdata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/Loglogisticinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/Loglogisticinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center>
</font><font face="Arial" color="#000000" size="3"><br><img src="loglogistic_ex2.bmp" alt="[loglogistic_ex2]"><br><br><img src="loglogistic_ex3.bmp" alt="[loglogistic_ex3]"><br><br><img src="loglogistic_ex4.bmp" alt="[loglogistic_ex4]"><br><img src="loglogistic_ex5.bmp" alt="[loglogistic_ex5]"><br><img src="loglogistic_ex6.bmp" alt="[loglogistic_ex6]">
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/Loglogisticdata.html b/doc/Reliability/Examples/Loglogisticdata.html
new file mode 100755
index 0000000..3ddca0b
--- /dev/null
+++ b/doc/Reliability/Examples/Loglogisticdata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Loglogisticdata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(N=40, x=c(0.92, 1.24, 1.64, 2.03, 2.43, 2.44, 3.26, 3.32, 3.41, 3.42, 3.44, 3.54,<br>3.60, 3.71, 3.82, 3.94, 4.05, 4.17, 4.20, 4.69, 4.69, 4.81, 5.11, 5.43, 5.99, 6.23, 6.39, 6.44, 6.80, 7.49, 7.65, 7.96, 8.25, 9.00, 9.08, 9.48, 10.42, 11.79, 11.96, 12.03))<br>
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Loglogisticdata.txt b/doc/Reliability/Examples/Loglogisticdata.txt
new file mode 100755
index 0000000..237fb59
--- /dev/null
+++ b/doc/Reliability/Examples/Loglogisticdata.txt
@@ -0,0 +1,2 @@
+list(N=40, x=c(0.92, 1.24, 1.64, 2.03, 2.43, 2.44, 3.26, 3.32, 3.41, 3.42, 3.44, 3.54,
+3.60, 3.71, 3.82, 3.94, 4.05, 4.17, 4.20, 4.69, 4.69, 4.81, 5.11, 5.43, 5.99, 6.23, 6.39, 6.44, 6.80, 7.49, 7.65, 7.96, 8.25, 9.00, 9.08, 9.48, 10.42, 11.79, 11.96, 12.03))
diff --git a/doc/Reliability/Examples/Loglogisticinits.html b/doc/Reliability/Examples/Loglogisticinits.html
new file mode 100755
index 0000000..5691c64
--- /dev/null
+++ b/doc/Reliability/Examples/Loglogisticinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Loglogisticinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(beta=1.5, theta=4.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Loglogisticinits.txt b/doc/Reliability/Examples/Loglogisticinits.txt
new file mode 100755
index 0000000..007908e
--- /dev/null
+++ b/doc/Reliability/Examples/Loglogisticinits.txt
@@ -0,0 +1 @@
+list(beta=1.5, theta=4.0)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Loglogisticinits1.html b/doc/Reliability/Examples/Loglogisticinits1.html
new file mode 100755
index 0000000..8d50292
--- /dev/null
+++ b/doc/Reliability/Examples/Loglogisticinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Loglogisticinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(beta=6.5, theta=6.0)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/Loglogisticinits1.txt b/doc/Reliability/Examples/Loglogisticinits1.txt
new file mode 100755
index 0000000..d5f2b21
--- /dev/null
+++ b/doc/Reliability/Examples/Loglogisticinits1.txt
@@ -0,0 +1 @@
+list(beta=6.5, theta=6.0)
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diff --git a/doc/Reliability/Examples/Loglogisticmodel.html b/doc/Reliability/Examples/Loglogisticmodel.html
new file mode 100755
index 0000000..843c067
--- /dev/null
+++ b/doc/Reliability/Examples/Loglogisticmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>Loglogisticmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dlog.logis(beta, theta)<br> }<br> <br> # Prior distributions of the model parameters <br> <b [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/Loglogisticmodel.txt b/doc/Reliability/Examples/Loglogisticmodel.txt
new file mode 100755
index 0000000..b8d7b5f
--- /dev/null
+++ b/doc/Reliability/Examples/Loglogisticmodel.txt
@@ -0,0 +1,12 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dlog.logis(beta, theta)
+ }
+
+ # Prior distributions of the model parameters
+
+ beta ~ dunif(0.1, 10.0)
+ theta~ dunif(0.1, 10.0)
+ }
\ No newline at end of file
diff --git a/doc/Reliability/Examples/ModifiedWeibull_Ex.html b/doc/Reliability/Examples/ModifiedWeibull_Ex.html
new file mode 100755
index 0000000..45261bb
--- /dev/null
+++ b/doc/Reliability/Examples/ModifiedWeibull_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ModifiedWeibull_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="modifiedweibull_ex0.bmp" alt="[modifiedweibull_ex0]">
</font><font face="Courier New" color="#000100" size="6">Modified Weibull Model
</font><font face="Arial" color="#000000" size="3"><br><br>
</font><font face="Arial" color="#000000" size="2"> <img src="modifiedweibull_ex1.bmp" alt="[modifiedweibull_ex1]"><br>
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dweib.modified(alpha, beta, lambda)<br> hrf[i] <- hrf(x[i], x[i])<br> reliability[i] <- R(x[i], x[i]) <br>   [...]
</font><font face="Arial" color="#000100" size="3"><br>The data set is taken from Aarset(1987).<br>
</font><font face="Arial" color="#000100" size="2"><br>Lai, C.D. , Xie, M. and Murthy, D.N.P. (2003). A modified Weibull distribution,
</font><font face="Arial" color="#000100" size="2"><em>IEEE Trans. Reliab
</em></font><font face="Arial" color="#000100" size="2">., 52, 33–37.<br><br>Ng, H.K.T.(2005). Parameter estimation for a modified Weibull distribution, for progressively type-II censored samples,
</font><font face="Arial" color="#000100" size="2"><em>IEEE Trans. Reliab
</em></font><font face="Arial" color="#000100" size="2">., 54, 374–380.<br>
</font><font face="Arial" color="#000000" size="2"><br>Aarset, M.V.(1987). How to identify bathtub hazard rate.
</font><font face="Arial" color="#000000" size="2"><em> IEEE Trans Reliab
</em></font><font face="Arial" color="#000000" size="2">., 36(1), 106 –108.
</font><font face="Arial" color="#000000" size="3"><br><br>The MLE’s ( Lai et al., 2003) are <br>alpha = 0.0876 beta = 0.389; lambda = 0 .01512 <br><br>The linear regression estimates (Ng, 2005) are <br>alpha = 0.0624 beta = 0.355; lambda = 0 .02332 <br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/ModifiedWeibulldata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/ModifiedWeibullinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/ModifiedWeibullinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"><center><img src="modifiedweibull_ex2.bmp" alt="[modifiedweibull_ex2]"><br><br><br> <img src="modifiedweibull_ex3.bmp" alt="[modifiedweibull_ex3]"><br> <br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#000100" size="2"><img src="modifiedweibull_ex4.bmp" alt="[modifiedweibull_ex4]"><img src="modifiedweibull_ex5.bmp" alt="[modifiedweibull_ex5]"><img src="modifiedweibull_ex6.bmp" alt="[modifiedweibull_ex6]">
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="modifiedweibull_ex7.bmp" alt="[modifiedweibull_ex7]"><img src="modifiedweibull_ex8.bmp" alt="[modifiedweibull_ex8]"><img src="modifiedweibull_ex9.bmp" alt="[modifiedweibull_ex9]">
</font><font face="Arial" color="#000100" size="1"><br><br>
</font><font face="Arial" color="#000100" size="2"><img src="modifiedweibull_ex10.bmp" alt="[modifiedweibull_ex10]"><img src="modifiedweibull_ex11.bmp" alt="[modifiedweibull_ex11]"><img src="modifiedweibull_ex12.bmp" alt="[modifiedweibull_ex12]"><br><img src="modifiedweibull_ex13.bmp" alt="[modifiedweibull_ex13]"><br>
</font><font face="Arial" color="#000100" size="1"><img src="modifiedweibull_ex14.bmp" alt="[modifiedweibull_ex14]"><br>
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ModifiedWeibulldata.html b/doc/Reliability/Examples/ModifiedWeibulldata.html
new file mode 100755
index 0000000..b6feac8
--- /dev/null
+++ b/doc/Reliability/Examples/ModifiedWeibulldata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ModifiedWeibulldata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list( N=50, x = c(0.1, 0.2, 1.0, 1.0, 1.0, 1.0, 1.0, 2.0, 3.0, 6.0, 7.0, 11.0, 12.0, 18.0, 18.0, 18.0, 18.0, 18.0, 21.0, 32.0, 36.0, 40.0, 45.0, 45.0, 47.0, 50.0, 55.0, 60.0, 63.0, 63.0, 67.0, 67.0, 67.0, 67.0, 72.0, 75.0, 79.0, 82.0, 82.0, 83.0, 84.0, 84.0, 84.0, 85.0, 85.0, 85.0, 85.0, 85.0, 86.0, 86.0))<br>
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ModifiedWeibulldata.txt b/doc/Reliability/Examples/ModifiedWeibulldata.txt
new file mode 100755
index 0000000..85228e8
--- /dev/null
+++ b/doc/Reliability/Examples/ModifiedWeibulldata.txt
@@ -0,0 +1 @@
+list( N=50, x = c(0.1, 0.2, 1.0, 1.0, 1.0, 1.0, 1.0, 2.0, 3.0, 6.0, 7.0, 11.0, 12.0, 18.0, 18.0, 18.0, 18.0, 18.0, 21.0, 32.0, 36.0, 40.0, 45.0, 45.0, 47.0, 50.0, 55.0, 60.0, 63.0, 63.0, 67.0, 67.0, 67.0, 67.0, 72.0, 75.0, 79.0, 82.0, 82.0, 83.0, 84.0, 84.0, 84.0, 85.0, 85.0, 85.0, 85.0, 85.0, 86.0, 86.0))
diff --git a/doc/Reliability/Examples/ModifiedWeibullinits.html b/doc/Reliability/Examples/ModifiedWeibullinits.html
new file mode 100755
index 0000000..cf195c9
--- /dev/null
+++ b/doc/Reliability/Examples/ModifiedWeibullinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ModifiedWeibullinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=0.1, beta= 0.1 , lambda=0.1)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/ModifiedWeibullinits.txt b/doc/Reliability/Examples/ModifiedWeibullinits.txt
new file mode 100755
index 0000000..8303c45
--- /dev/null
+++ b/doc/Reliability/Examples/ModifiedWeibullinits.txt
@@ -0,0 +1 @@
+list(alpha=0.1, beta= 0.1 , lambda=0.1)
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diff --git a/doc/Reliability/Examples/ModifiedWeibullinits1.html b/doc/Reliability/Examples/ModifiedWeibullinits1.html
new file mode 100755
index 0000000..715319f
--- /dev/null
+++ b/doc/Reliability/Examples/ModifiedWeibullinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ModifiedWeibullinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(alpha=0.2, beta= 0.5 , lambda=0.2)
</font>
</p>
</body>
</html>
\ No newline at end of file
diff --git a/doc/Reliability/Examples/ModifiedWeibullinits1.txt b/doc/Reliability/Examples/ModifiedWeibullinits1.txt
new file mode 100755
index 0000000..9de12dd
--- /dev/null
+++ b/doc/Reliability/Examples/ModifiedWeibullinits1.txt
@@ -0,0 +1 @@
+list(alpha=0.2, beta= 0.5 , lambda=0.2)
\ No newline at end of file
diff --git a/doc/Reliability/Examples/ModifiedWeibullmodel.html b/doc/Reliability/Examples/ModifiedWeibullmodel.html
new file mode 100755
index 0000000..cb0040b
--- /dev/null
+++ b/doc/Reliability/Examples/ModifiedWeibullmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>ModifiedWeibullmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dweib.modified(alpha, beta, lambda)<br> }<br> <br> # Prior distributions of the model parameters <br> <br>   [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/ModifiedWeibullmodel.txt b/doc/Reliability/Examples/ModifiedWeibullmodel.txt
new file mode 100755
index 0000000..1552573
--- /dev/null
+++ b/doc/Reliability/Examples/ModifiedWeibullmodel.txt
@@ -0,0 +1,13 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dweib.modified(alpha, beta, lambda)
+ }
+
+ # Prior distributions of the model parameters
+
+ alpha ~ dunif(0.001, 1.0)
+ beta ~ dunif(0.001, 1.0)
+ lambda~ dunif(0.001, 1.0)
+ }
diff --git a/doc/Reliability/Examples/WeibullShifted_Ex.html b/doc/Reliability/Examples/WeibullShifted_Ex.html
new file mode 100755
index 0000000..71f0baf
--- /dev/null
+++ b/doc/Reliability/Examples/WeibullShifted_Ex.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>WeibullShifted_Ex</title>
</head>
<body>
<p>
<font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000000" size="2"><img src="weibullshifted_ex0.bmp" alt="[weibullshifted_ex0]">
</font><font face="Courier New" color="#000100" size="6">Weibull-Shifted Model
</font><font face="Arial" color="#000000" size="3"><br><img src="weibullshifted_ex1.bmp" alt="[weibullshifted_ex1]"><br>
</font><font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"><br> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dweib3(nu, lambda, x0) <br> }<br> <br> # Prior distributions of the model parameters<br>
</font><font face="Arial" color="#000000" size="3"><strong>
</strong></font><font face="Arial" color="#000000" size="3">nu~ dunif(0, 5)<br> lambda~ dunif(0, 5)
</font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3">x0 ~ dgamma(0.001, 0.001) <br> }<br> <br><a href="../Examples/G_gamma Data.html">Data</a> generated from Weibull shifted distribution with shape(nu)=0.75, scale(lambda) = 0.75 and lcocation(x0) = 5.0 <br><br>
</font><font face="Arial" color="#0000FF" size="5"><u><a href="../Reliability/Examples/WeibullShifteddata.html">Data</a>
</u></font><font face="Arial" color="#000100" size="3"> ( click to open )
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><br>
</font><font face="Arial" color="#0000FF" size="5"><a href="../Reliability/Examples/WeibullShiftedinits.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 1
</u></font><font face="Arial" color="#0000FF" size="5"></a> <a href="../Reliability/Examples/WeibullShiftedinits1.html">
</font><font face="Arial" color="#0000FF" size="5"><u>Inits for chain 2
</u></font><font face="Arial" color="#0000FF" size="5"></a>
</font><font face="Arial" color="#000100" size="3">( click to open )<br><br>
</font><font face="Arial" color="#000100" size="1"><br>
</font><font face="Arial" color="#0000FF" size="5">Results <br><br><center><img src="weibullshifted_ex2.bmp" alt="[weibullshifted_ex2]"><br><br><img src="weibullshifted_ex3.bmp" alt="[weibullshifted_ex3]"><img src="weibullshifted_ex4.bmp" alt="[weibullshifted_ex4]"><br><img src="weibullshifted_ex5.bmp" alt="[weibullshifted_ex5]"><br><br><img src="weibullshifted_ex6.bmp" alt="[weibullshifted_ex6]">
</font>
</center>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/WeibullShifteddata.html b/doc/Reliability/Examples/WeibullShifteddata.html
new file mode 100755
index 0000000..be1f7aa
--- /dev/null
+++ b/doc/Reliability/Examples/WeibullShifteddata.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>WeibullShifteddata</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(N=50, x=c(6.137586, 7.074556, 9.894666, 5.013768, 7.428222, 5.833135, <br>5.061419, 8.666846, 5.888522, 8.503873, 6.434743, 5.264158, 5.019024, 5.959139,<br>7.992135, 5.883465, 5.168402, 8.979449, 5.701817, 7.072784, 8.699820, 5.369439, 10.756600, 5.670287, 5.483465, 5.653821, 5.389355, 5.045285, 5.359706, 7.800460, 6.922263, 13.273442, 5.046622, 23.082790, 6.073328, 5.185828, 5.721390, 6.625921, 5.963122, 8.283738, 5.219268, 5.427565, 7.06 [...]
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/WeibullShifteddata.txt b/doc/Reliability/Examples/WeibullShifteddata.txt
new file mode 100755
index 0000000..17bf97a
--- /dev/null
+++ b/doc/Reliability/Examples/WeibullShifteddata.txt
@@ -0,0 +1,3 @@
+list(N=50, x=c(6.137586, 7.074556, 9.894666, 5.013768, 7.428222, 5.833135,
+5.061419, 8.666846, 5.888522, 8.503873, 6.434743, 5.264158, 5.019024, 5.959139,
+7.992135, 5.883465, 5.168402, 8.979449, 5.701817, 7.072784, 8.699820, 5.369439, 10.756600, 5.670287, 5.483465, 5.653821, 5.389355, 5.045285, 5.359706, 7.800460, 6.922263, 13.273442, 5.046622, 23.082790, 6.073328, 5.185828, 5.721390, 6.625921, 5.963122, 8.283738, 5.219268, 5.427565, 7.062516, 8.093987, 5.143574, 8.968071, 7.455459, 5.060323, 5.329954, 5.203936))
diff --git a/doc/Reliability/Examples/WeibullShiftedinits.html b/doc/Reliability/Examples/WeibullShiftedinits.html
new file mode 100755
index 0000000..7ec9d28
--- /dev/null
+++ b/doc/Reliability/Examples/WeibullShiftedinits.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>WeibullShiftedinits</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(nu = 0.1, lambda = 0.1, x0 = 1.0)
</font>
</p>
</body>
</html>
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new file mode 100755
index 0000000..ee08769
--- /dev/null
+++ b/doc/Reliability/Examples/WeibullShiftedinits.txt
@@ -0,0 +1 @@
+list(nu = 0.1, lambda = 0.1, x0 = 1.0)
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diff --git a/doc/Reliability/Examples/WeibullShiftedinits1.html b/doc/Reliability/Examples/WeibullShiftedinits1.html
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index 0000000..4b91cc5
--- /dev/null
+++ b/doc/Reliability/Examples/WeibullShiftedinits1.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>WeibullShiftedinits1</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="3">list(nu=1.0, lambda= 2.0, x0= 3.0)
</font>
</p>
</body>
</html>
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index 0000000..060c282
--- /dev/null
+++ b/doc/Reliability/Examples/WeibullShiftedinits1.txt
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+list(nu=1.0, lambda= 2.0, x0= 3.0)
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diff --git a/doc/Reliability/Examples/WeibullShiftedmodel.html b/doc/Reliability/Examples/WeibullShiftedmodel.html
new file mode 100755
index 0000000..c8ecc1d
--- /dev/null
+++ b/doc/Reliability/Examples/WeibullShiftedmodel.html
@@ -0,0 +1 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD Html 1.0 Strict//EN" "http://www.w3.org/TR/Html1/DTD/strict.dtd">
<html>
<head>
<title>WeibullShiftedmodel</title>
</head>
<body>
<p>
<font face="Arial" color="#000000" size="2">
</font><font face="Arial" color="#000000" size="3"> model<br> {<br> for( i in 1 : N ) <br> {<br> x[i] ~ dweib3(nu, lambda, x0) <br> }<br> <br> # Prior distributions of the model parameters<br>
</font><font face="Arial" color="#000000" size="3"><strong>
</strong></font><font face="Arial" color="#000000" size="3">nu~ dunif(0, 5)<br> lambda~ dunif(0, 5)
</font><font face="Arial" color="#000000" size="3"><strong><br>
</strong></font><font face="Arial" color="#000000" size="3">x0 ~ dgamma(0.001, 0.001)
</font>
</p>
</body>
</html>
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diff --git a/doc/Reliability/Examples/WeibullShiftedmodel.txt b/doc/Reliability/Examples/WeibullShiftedmodel.txt
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index 0000000..7ab7ef7
--- /dev/null
+++ b/doc/Reliability/Examples/WeibullShiftedmodel.txt
@@ -0,0 +1,11 @@
+ model
+ {
+ for( i in 1 : N )
+ {
+ x[i] ~ dweib3(nu, lambda, x0)
+ }
+
+ # Prior distributions of the model parameters
+ nu~ dunif(0, 5)
+ lambda~ dunif(0, 5)
+ x0 ~ dgamma(0.001, 0.001)
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</head>
<body>
<p>
<font face="Courier New" color="#0000FF" size="3"><strong> <br>
</strong></font><font face="Arial" color="#000100" size="5"><strong><a id="Intro">
</strong></font><font face="Arial" color="#0000FF" size="3"><img src="analysis0.bmp" alt="[analysis0]">
</font><font face="Courier New" color="#000100" size="6"> Introduction
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="#Top"> [top]</a><br><br>
</font><font face="Arial" color="#000100" size="3">ReliaBUGS is an add-on to the OpenBUGS software that makes it easy to do reliability analysis in OpenBUGS. ReliaBUGS consists of many probability distribution useful for reliability analysis plus a small number of helpful logical functions.<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Reliability Analysis">
</strong></font><font face="Courier New" color="#000100" size="6">Reliability Analysis
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="#Top"> [top]</a><br>
</font><font face="Times New Roman" color="#000100" size="4"><br>
</font><font face="Arial" color="#000100" size="3">Reliability analysis evaluates the performance of an equipment/system under consideration. In particular, we use the term reliability to mean the probability that a piece of equipment (component, subsystem or system) successfully performs its intended function for a given period of time under specified (design) conditions. The International Organization for Standardization (ISO) defines reliability as “the ability of an item to perf [...]
</font><font face="Times New Roman" color="#000100" size="4"><br><br>
</font><font face="Arial" color="#000100" size="4">Let random variable X denote the failure time (or time to failure) of some device of interest under stated environmental conditions and let f(x) denote the probability density function (pdf) of X. The cdf F(x), a measure of failure, is defined as the probability that the system will fail by time x.<br><br> F(x) = P(X ≤ x), x ≥ [...]
</font><font face="Arial" color="#000100" size="4"><em> <br>
</em></font><font face="Arial" color="#000100" size="4"><br>where X
</font><font face="Arial" color="#000100" size="4"><em>
</em></font><font face="Arial" color="#000100" size="4">is a random variable denoting the time-to failure or failure time. <br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#000100" size="6">Censoring
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/GenExponential_Cen_Ex.html">[example]</a>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Times New Roman" color="#000100" size="2">
</font><font face="Arial" color="#000100" size="3">In reliability context, the following types of censored data are of particular interest. Censoring occurs frequently because of time limits and other restrictions during the process of data collection. In a life test experiment of manufactured items, for example, it may not be feasible to continue experimentation until all items under study have failed. If the study is terminated before all have failed, then for items that have not failed [...]
</font><font face="Times New Roman" color="#000100" size="4"><br>
</font><font face="Arial" color="#000100" size="3"><br>Let X1, X2; . . . , Xn denote a sample of n-independent random variables from a distribution function F
</font><font face="Arial" color="#000100" size="3">(x,
</font><font face="Symbol" color="#000100" size="3"><strong>q
</strong></font><font face="Arial" color="#000100" size="3">), where
</font><font face="Arial" color="#000100" size="3">
</font><font face="Symbol" color="#000100" size="3"><strong>q
</strong></font><font face="Arial" color="#000100" size="3">is a k-dimensional parameter. These correspond to the life times for n different items in the reliability context.. Let x1, x2; . . . , xn denote the actual realized values of the Xi’s.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>Complete Data
</strong></font><font face="Arial" color="#000100" size="3"><br>The data set available for estimation is the set x1, x2; . . . , xn. In other words, the actual realized values are known for each observation in the data set.<br>
</font><font face="Arial" color="#000100" size="3"><strong><br>Censored Data
</strong></font><font face="Arial" color="#000100" size="3"><br>In this case the actual realized values for some or all of the variables are not known, and this depends on the kind of censoring.<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>(a) Right Type I Censoring
</strong></font><font face="Arial" color="#000100" size="3"><br>Type I censoring often 'arises when a study is conducted over a specified time period. This is also known as time censoring. Let C(t) denote the fixed potential censoring time. Under type I right censoring the data available for estimation is as follows: For item i, the actual realized value of Xi is known only if xi < C(t). When xi > C(t) the only information available is that Xi > C(t).<br><br>
</font><font face="Arial" color="#000100" size="3"><strong>(b) Right Type II Censoring
</strong></font><font face="Arial" color="#000100" size="3"><br>This censoring scheme arises when n individuals start on study at the same time, with the study terminating once r failures (or lifetimes) have been observed. This is also known as item censoring. Let 'r' denote a predetermined number such that r < n. Under type II right censoring the data available for estimation is given by xi (the actual realized value of Xi) for 'r' data and that Xi > x(max) for the remaining (n - r [...]
</font><font face="AdvP41153C" color="#000100" size="2"><br>
</font>
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<p>
<font face="Arial" color="#000100" size="2"><img src="contents0.bmp" alt="[contents0]">
</font><font face="Courier New" color="#000100" size="6">ReliaBUGS User Manual
</font><font face="Arial" color="#000100" size="6"><strong><sup><br>
</sup></strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="4">Version 1.0, November 2010
</font><font face="Arial" color="#000100" size="2"><br><br><br>
</font><font face="Arial" color="#000100" size="3"> Vijay Kumar
</font><font face="Arial" color="#000100" size="1"><sup>1
</sup></font><font face="Arial" color="#000100" size="3"> Uwe Ligges
</font><font face="Arial" color="#000100" size="1"><sup>2
</sup></font><font face="Arial" color="#000100" size="3"> Andrew Thomas
</font><font face="Arial" color="#000100" size="1"><sup>3
</sup></font><font face="Arial" color="#000100" size="3"> <br><br>
</font><font face="Arial" color="#000100" size="1"><sup>1
</sup></font><font face="Arial" color="#000100" size="3"> Department of Mathematics & Statistics<br> DDU Gorakhpur University <br> GORAKHPUR- 273009 (INDIA)<br> <br>
</font><font face="Arial" color="#000100" size="1"><sup>2
</sup></font><font face="Arial" color="#000100" size="3">
</font><font face="CMR9" color="#000100" size="3">Department of Statistics, <br> Technische Universit
</font><font face="Arial" color="#000100" size="3">ä
</font><font face="CMR9" color="#000100" size="3">t Dortmund<br> Germany
</font><font face="Arial" color="#000100" size="3"><br><br>
</font><font face="Arial" color="#000100" size="1"><sup>3
</sup></font><font face="Arial" color="#000100" size="3"> OpenBUGS Foundation
</font><font face="Helvetica" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="3"><br> <br> e-mail: bugs at mrc-bsu.cam.ac.uk [general]<br> vkgkp at rediffmail.com [technical]<br> ligges at statistik.tu-dortmund.de<br><br><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Top">Contents</a>
</strong></font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Arial" color="#000100" size="1">
</font><font face="Arial" color="#000100" size="2"><br>
</font><font face="Courier New" color="#0000FF" size="3">
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Analysis.html#Intro">Introduction</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong> <a href="../Reliability/Manuals/Analysis.html#Reliability Analysis">Reliability Analysis</a><br> <br>
</strong></font><font face="Arial" color="#000100" size="5"><strong>Reliability distributions<br>
</strong></font><font face="Courier New" color="#0000FF" size="3"><strong><br> <a href="../Reliability/Manuals/Distributions.html#BirnSaunders">Birnbaum-Saunders</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Burr X">Burr X</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Burr XII">Burr XII</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Exponential Power">Exponential Power</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Exponentiated Weibull">Exponentiated Weibull</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Extended Exponential">Extended Exponential</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Extended Weibull">Extended Weibull</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Flexible Weibull">Flexible Weibull</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Generalized Exponential">Generalized Exponential</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Generalized Power Weibull">Generalized Power Weibull</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Gompertz">Gompertz</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Gumbel">Gumbel</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Inverse Gaussian">Inverse Gaussian</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Inverse Weibull">Inverse Weibull</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Linear Failure Rate">Linear Failure Rate</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Logistic Exponential">Logistic Exponential</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Log-Logistic">Log-Logistic</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Log-Weibull">Log-Weibull</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong><a href="../Reliability/Manuals/Distributions.html#Modified Weibull">Modified Weibull</a>
</strong></font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><strong> <br>
</strong></font><font face="Arial" color="#000100" size="5"><strong>Useful functions<br>
</strong></font><font face="Courier New" color="#0000FF" size="3"><strong> <br> <a href="../Reliability/Manuals/Functions.html#hrf">Hazard rate function</a><br> <a href="../Reliability/Manuals/Functions.html#Reliability">Reliability function</a><br> <br>
</strong></font><font face="Arial" color="#000100" size="5"><strong>References
</strong></font><font face="Courier New" color="#0000FF" size="3"><strong> <br><a href="../Reliability/Manuals/References.html">References</a><br>
</strong></font><font face="Arial" color="#0000FF" size="3"><br>
</font>
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</head>
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<p>
<font face="Arial" color="#0000FF" size="3"><br><img src="distributions0.bmp" alt="[distributions0]">
</font><font face="Courier New" color="#000100" size="6">Reliability Distributions
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Courier New" color="#000100" size="6"><br><a id="BirnSaunders">Birnbaum-Saunders</a>
</font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/BS_Ex.html">[example]</a>
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">The Birnbaum-Saunders distribution is defined by the pdf<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="2"> <img src="distributions1.bmp" alt="[distributions1]"><img src="distributions2.bmp" alt="[distributions2]"><br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">where alpha and beta are shape parameters, Birnabaum and Saunders(1969). In the BUGS language it is used as<br><br> x ~ dbs(alpha, beta)<br>
</font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Burr X">
</strong></font><font face="Courier New" color="#000100" size="6">Burr X
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/BurrX_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Burr X distribution is defined by the pdf<br><br> <img src="distributions3.bmp" alt="[distributions3]"><br>where alpha is a shape parameter and lambda is a scale parameter,
</font><font face="Arial" color="#000100" size="3">Surles and Padgett (2005)
</font><font face="Arial" color="#000000" size="3">. In the Bugs language it is used as<br><br> x ~ dburrX(alpha, lambda)
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Burr XII">
</strong></font><font face="Courier New" color="#000100" size="6">Burr XII
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/BurrXII_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Burr XII distribution is defined by the pdf<br><br> <img src="distributions4.bmp" alt="[distributions4]"><br><br>where alpha and beta are shape parameters,
</font><font face="Arial" color="#000100" size="3">Klugman et al. (2004)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dburrXII(alpha, beta)
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Exponential Power">
</strong></font><font face="Courier New" color="#000100" size="6">Exponential Power
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/ExpPower_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Exponential power distribution is defined by the pdf<br><br> <img src="distributions5.bmp" alt="[distributions5]"><br><br>where alpha is a shape parameter and lambda a scale parameter,
</font><font face="Arial" color="#000100" size="3">Smith and Bain (1975)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dexp.power(alpha, lambda)
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Exponentiated Weibull">
</strong></font><font face="Courier New" color="#000100" size="6">Exponentiated Weibull
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/ExpoWeibull_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Exponentiated Weibul distribution is defined by the pdf<br><br> <img src="distributions6.bmp" alt="[distributions6]"><br>where alpha and theta are shape parameters,
</font><font face="Arial" color="#000100" size="3">Mudholkar and Srivastava (1993)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br> <br> x ~ dexp.weib(alpha, theta)
</font><font face="Arial" color="#000000" size="3"><br> <br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Extended Exponential">
</strong></font><font face="Courier New" color="#000100" size="6">Extended Exponential
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/Ext_exponential_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Extended Exponential distribution is defined by the pdf<br><br> <img src="distributions7.bmp" alt="[distributions7]"><br><br>where alpha is a shape parameter and lambda is a tilt parameter,
</font><font face="Arial" color="#000100" size="3">Marshall and Olkin (1997, 2007)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dext.exp(alpha, lambda)
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Extended Weibull">
</strong></font><font face="Courier New" color="#000100" size="6">Extended Weibull
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/Ext_weibull_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Extended Weibull distribution is dewfined by the pdf<br><br> <img src="distributions8.bmp" alt="[distributions8]"><br><br>where alpha is a shape parameter and lambda is a tilt parameter,
</font><font face="Arial" color="#000100" size="3">Marshall and Olkin (1997, 2007)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dext.weib(alpha, lambda)
</font><font face="Arial" color="#000000" size="3"><br> <br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Flexible Weibull">
</strong></font><font face="Courier New" color="#000100" size="6">Flexible Weibull
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/FlexibleWeibull_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Flexible Weibull distribution is dewfined by the pdf<br><br> <img src="distributions9.bmp" alt="[distributions9]"><br> <br>where alpha and beta are shape parameters,
</font><font face="Arial" color="#000100" size="3">Bebbington et al. (2007)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dflex.weib(alpha, beta)<br> <br>
</font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Generalized Exponential">
</strong></font><font face="Courier New" color="#000100" size="6">Generalized Exponential
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/GenExponential_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Generalized Exponential distribution is defined by the pdf<br><br> <img src="distributions10.bmp" alt="[distributions10]"><br><br>where alpha is a shape parameter and lambda is a scale parameter,
</font><font face="Arial" color="#000100" size="3">Gupta and Kundu (1999, 2001)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dgen.exp(alpha, lambda)
</font><font face="Arial" color="#000000" size="3"><br> <br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Generalized Power Weibull">
</strong></font><font face="Courier New" color="#000100" size="6">Generalized Power Webull
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/GPWeibull_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Generalized Power Weibull distribution is defined by the pdf<br><br> <img src="distributions11.bmp" alt="[distributions11]"><br><br>where alpha and theta are shape parameters,
</font><font face="Arial" color="#000100" size="3">Nikulin and Haghighi (2006)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br> <br> x ~ dgp.weib(alpha, theta)
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><br><a id="Gompertz">
</strong></font><font face="Courier New" color="#000100" size="6">Gompertz
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/Gompertz_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Gompertz distribution is defined by the pdf<br><br> <img src="distributions12.bmp" alt="[distributions12]"><br><br>where alpha and theta are shape parameters,
</font><font face="Arial" color="#000100" size="3">Marshall and Olkin (2007)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dgpz(alpha, theta)
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Gumbel">
</strong></font><font face="Courier New" color="#000100" size="6">Gumbel
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/Gumbel_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Gumbel distribution is defined by the pdf<br><br> <img src="distributions13.bmp" alt="[distributions13]"><br><br>where alpha is a location parameter and tau is a scale parameter,
</font><font face="Arial" color="#000100" size="3">Marshall and Olkin (2007)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dgumbel(alpha, tau)
</font><font face="Arial" color="#000000" size="3"> <br>
</font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Inverse Gaussian">
</strong></font><font face="Courier New" color="#000100" size="6">Inverse Gaussian
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/InvGaussian_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Inverse Gaussian distribution is defined by the pdf<br><br> <img src="distributions14.bmp" alt="[distributions14]"><br><br>where mu is a location parameter and lambda is a scale parameter,
</font><font face="Arial" color="#000100" size="3">Chhikara and Folks (1977)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dinv.gauss(mu, lambda)
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Inverse Weibull">
</strong></font><font face="Courier New" color="#000100" size="6">Inverse Weibull
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/Inv_Weibull_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Inverse Weibull distribution is defined by the pdf<br><br> <img src="distributions15.bmp" alt="[distributions15]"><br><br>where beta is a shape parameter and lambda is a scale parameter,
</font><font face="Arial" color="#000100" size="3">Jiang and Murthy (2001)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dinv.weib(beta, lambda)
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Linear Failure Rate">
</strong></font><font face="Courier New" color="#000100" size="6">Linear Failure Rate
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/LinearFailure_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Linear Failure Rate distribution is defined by the pdf<br><br> <img src="distributions16.bmp" alt="[distributions16]"><br><br>where alpha and beta are shape parameters.
</font><font face="Arial" color="#000100" size="3">Bain (1974)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dlin.fr(alpha, beta)
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><br><a id="Logistic Exponential">
</strong></font><font face="Courier New" color="#000100" size="6">Logistic Exponential
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/LogisticExponential_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Logistic Exponential distribution is defined by the pdf<br><br> <img src="distributions17.bmp" alt="[distributions17]"><br><br>where alpha is a shape parameter and lambda is a scale parameter,
</font><font face="Arial" color="#000100" size="3">Lan and Leemis (2008)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dlogistic.exp(alpha, lambda)<br>
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><br><a id="Log-Logistic">
</strong></font><font face="Courier New" color="#000100" size="6">Log-Logistic
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/Loglogistic_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Log-Logistic distribution is defined by the pdf<br><br> <img src="distributions18.bmp" alt="[distributions18]"><br><br>where beta is a shape parameter and theta is a scale parameter,
</font><font face="Arial" color="#000000" size="3">Lawless (2003)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dlog.logis(beta, theta)
</font><font face="Arial" color="#000000" size="3"> <br>
</font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Log-Weibull">
</strong></font><font face="Courier New" color="#000100" size="6">Log-Weibull
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/LogWeibull_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Log-Weibull distribution is defined by the pdf<br><br> <img src="distributions19.bmp" alt="[distributions19]"><br><br>where mu is a location parameter and sigma is a scale parameter,
</font><font face="Arial" color="#000100" size="3">Murthy et al. (2004).
</font><font face="Arial" color="#000000" size="3"> In the BUGS language it is used as<br><br> x ~ dlog.weib(mu, sigma)
</font><font face="Arial" color="#000000" size="3"><br>
</font><font face="Courier New" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Modified Weibull">
</strong></font><font face="Courier New" color="#000100" size="6">Modified Weibull
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/ModifiedWeibull_Ex.html">[example]</a><br><br>
</font><font face="Arial" color="#000000" size="3">The Modified Weibull distribution is defined by the pdf<br><br> <img src="distributions20.bmp" alt="[distributions20]"><br><br>where alpha and beta are shape parameters and lambda is a scale parameter,
</font><font face="Arial" color="#000100" size="3">Lai et al..(2003)
</font><font face="Arial" color="#000000" size="3">. In the BUGS language it is used as<br><br> x ~ dweib.modified(alpha, beta, lambda)
</font><font face="Arial" color="#000000" size="3"><br>
</font>
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</head>
<body>
<p>
<font face="Arial" color="#0000FF" size="3"><img src="functions0.bmp" alt="[functions0]">
</font><font face="Courier New" color="#000100" size="6"> Reliability functions
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000000" size="3">
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="hrf">
</strong></font><font face="Courier New" color="#000100" size="6">Hazard rate function
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/ModifiedWeibull_Ex.html">[example]</a>
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">The hazard rate function hrf is defined in terms of the distribution's pdf and cdf as<br><br> hrf(x,
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000000" size="3">) = pdf(x,
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000000" size="3">) / (1 - cdf(x,
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000000" size="3">))<br> <br>In the BUGS language the notation is as follows<br><br> h <- hrf(x0, x1)<br> <br>Where the first argument must be a variable in the model defined by a univariate distribution and the second argument is a scalar. The first argument provides two kinds of information: whi [...]
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000000" size="3"> (the values<br>associated with the relation for x0). The second argument is the value of x at which the hazard rate function should be calculated. The two arguments x0 and x1 can be identical.<br>
</font><font face="Arial" color="#0000FF" size="3"><br>
</font><font face="Arial" color="#000100" size="5"><strong><a id="Reliability">
</strong></font><font face="Courier New" color="#000100" size="6">Reliability function
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="../Reliability/Manuals/Contents.html#Top"> [top]</a>
</font><font face="Courier New" color="#0000FF" size="3"><a href="../Reliability/Examples/ModifiedWeibull_Ex.html">[example]</a>
</font><font face="Arial" color="#0000FF" size="3"><br><br>
</font><font face="Arial" color="#000000" size="3">The reliability function R is defined in terms of the distribution's cdf as<br><br> R(x,
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000000" size="3">) = (1 - cdf(x,
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000000" size="3">))<br> <br>In the BUGS language the notation is as follows<br><br> r <- R(x0, x1)<br> <br>Where the first argument must be a variable in the model defined by a univariate distribution and the second argument is a scalar. The first argument provides two kinds of information: which [...]
</font><font face="Symbol" color="#000100" size="3">q
</font><font face="Arial" color="#000000" size="3"> (the values<br>associated with the relation for x0). The second argument is the value of x at which the reliability function should be calculated. The two arguments x0 and x1 can be identical.<br>
</font>
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</head>
<body>
<p>
<font face="Courier New" color="#000100" size="6">References
</font><font face="Arial" color="#000100" size="5"><strong></a>
</strong></font><font face="Arial" color="#0000FF" size="3"><a href="#Top"> [top]</a><br>
</font><font face="Times New Roman" color="#000100" size="3">
</font><font face="Arial" color="#000100" size="2">Bain, L.J. (1974). Analysis for the Linear Failure-Rate Life-Testing Distribution.
</font><font face="Arial" color="#000100" size="2"><em>Technometrics
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>16(4)
</strong></font><font face="Arial" color="#000100" size="2">, 551 - 559.<br><br>Bebbington, M., Lai, C.D. and Zitikis, R. (2007). A flexible Weibull extension.
</font><font face="Arial" color="#000100" size="2"><em>Reliability Engineering and System Safety
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>92
</strong></font><font face="Arial" color="#000100" size="2">, 719-726.<br><br>Birnbaum, Z. W. and Saunders, S. C. (1969). A new family of life distributions.
</font><font face="Arial" color="#000100" size="2"><em>J. Appl. Probab
</em></font><font face="Arial" color="#000100" size="2">.,
</font><font face="Arial" color="#000100" size="2"><strong>6(2)
</strong></font><font face="Arial" color="#000100" size="2">, 637-652.<br><br>Chhikara, R.S. and Folks, J.L.(1977). The inverse Gaussian distribution as a lifetime model.
</font><font face="Arial" color="#000100" size="2"><em>Technometrics
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>19
</strong></font><font face="Arial" color="#000100" size="2">, 461-468.<br><br>Gupta, R. D. and Kundu, D. (1999). Generalized exponential distributions.
</font><font face="Arial" color="#000100" size="2"><em>Australian and New Zealand Journal of Statistics
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>41(2)
</strong></font><font face="Arial" color="#000100" size="2">, 173 - 188.<br><br>Gupta, R. D. and Kundu, D. (2001). Exponentiated exponential family; an alternative to gamma and Weibull distributions.
</font><font face="Arial" color="#000100" size="2"><em>Biometrical Journal
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>43(1)
</strong></font><font face="Arial" color="#000100" size="2">, 117 - 130.<br><br>Hamada, M.S., Wilson, A.G., Reese, C.S. and Martz, H.F.(2008).
</font><font face="Arial" color="#000100" size="2"><em>Bayesian Reliability
</em></font><font face="Arial" color="#000100" size="2">. Springer, New York.<br><br>Jiang, R. and Murthy, D. N. P. (2001). Models involving two inverse Weibull distributions.
</font><font face="Arial" color="#000100" size="2"><em>Reliability Engineering and System Safety
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>73
</strong></font><font face="Arial" color="#000100" size="2">, 73–81.<br><br>Klugman, S. A., Panjer, H. H. and Willmot, G. E. (2004).
</font><font face="Arial" color="#000100" size="2"><em>Loss Models, From Data to Decisions
</em></font><font face="Arial" color="#000100" size="2">. Second Edition, Wiley.<br><br>Kundu, D. and Raqab, M.Z. (2005). Generalized Rayleigh Distribution: Different Methods of Estimation.
</font><font face="Arial" color="#000100" size="2"><em>Computational Statistics and Data Analysis
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>49
</strong></font><font face="Arial" color="#000100" size="2">, 187-200.<br><br>Lai, C.D., Xie, M. and Murthy, D. N. P.(2003). Modified Weibull model.
</font><font face="Arial" color="#000100" size="2"><em>IEEE Trans. Reliability
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>52
</strong></font><font face="Arial" color="#000100" size="2">, 33–37.<br><br>Lan, Y. and Leemis, L. M. (2008). The Logistic-Exponential Survival Distribution.
</font><font face="Arial" color="#000100" size="2"><em>Naval Research Logistics
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>55
</strong></font><font face="Arial" color="#000100" size="2">, 252-264.<br><br>Lawless, J.F.(2003).
</font><font face="Arial" color="#000100" size="2"><em> Statistical Models and Methods for Lifetime Data
</em></font><font face="Arial" color="#000100" size="2">. John Wiley and Sons, New York.<br><br>
</font><font face="NimbusRomNo9L-Regu" color="#000000" size="2">Lyu, M. R. (1996).
</font><font face="NimbusRomNo9L-ReguItal" color="#000000" size="2">Handbook of Software Reliability Engineering
</font><font face="NimbusRomNo9L-Regu" color="#000000" size="2">, IEEE Computer Society Press,
</font><font face="NimbusMonL-Regu" color="#000000" size="2">http://www.cse.cuhk.edu.hk/~lyu/book/reliability/
</font><font face="Arial" color="#000100" size="2"><br><br>Marshall, A. W. and Olkin, I. (1997). A new method for adding a parameter to a family of distributions with application to the exponential and Weibull families.
</font><font face="Arial" color="#000100" size="2"><em>Biometrika
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>84(3)
</strong></font><font face="Arial" color="#000100" size="2">, 641-652.<br><br>Marshall, A. W. and Olkin, I. (2007).
</font><font face="Arial" color="#000100" size="2"><em>Life Distributions: Structure of Nonparametric, Semiparametric, and Parametric Families.
</em></font><font face="Arial" color="#000100" size="2"> Springer, New York.<br><br>Meeker, W.Q. and Escobar, L.A.(1998).
</font><font face="Arial" color="#000100" size="2"><em>Statistical Methods for Reliability Data.
</em></font><font face="Arial" color="#000100" size="2"> John Wiley & Sons.<br><br>Mudholkar, G.S. and Srivastava, D.K. (1993). Exponentiated Weibull family for analyzing bathtub failure-rate data.
</font><font face="Arial" color="#000100" size="2"><em>IEEE Transactions on Reliability
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>42(2)
</strong></font><font face="Arial" color="#000100" size="2">, 299-302.<br><br>Murthy, D.N.P., Xie, M. and Jiang, R. (2004).
</font><font face="Arial" color="#000100" size="2"><em>Weibull Models
</em></font><font face="Arial" color="#000100" size="2">. Wiley, New York.<br><br>Nikulin, M. and Haghighi, F. (2006). A Chi-squared test for the generalized power Weibull family for the head-and-neck cancer censored data.
</font><font face="Arial" color="#000100" size="2"><em>Journal of Mathematical Sciences
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>133(3)
</strong></font><font face="Arial" color="#000100" size="2">, 1333-1341.<br><br>Pham, H. and Lai, C.D.(2007). On Recent Generalizations of the Weibull Distribution.
</font><font face="Arial" color="#000100" size="2"><em>IEEE Trans. on Reliability
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>56(3)
</strong></font><font face="Arial" color="#000100" size="2">, 454-458.<br><br>Smith, R.M. and Bain, L.J.(1975). An exponential power life-test distribution.
</font><font face="Arial" color="#000100" size="2"><em>Communications in Statistics - Simulation and Computation
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>4(5)
</strong></font><font face="Arial" color="#000100" size="2">, 469 - 481.<br><br>Surles, J.G. and Padgett, W.J. (2005). Some properties of a scaled Burr type X distribution.
</font><font face="Arial" color="#000100" size="2"><em> Journal of Statistical Planning and Inference
</em></font><font face="Arial" color="#000100" size="2">,
</font><font face="Arial" color="#000100" size="2"><strong>128
</strong></font><font face="Arial" color="#000100" size="2">, 271-280.<br><br>
</font>
</p>
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diff --git a/doc/testscript.txt b/doc/testscript.txt
new file mode 100644
index 0000000..6753cf8
--- /dev/null
+++ b/doc/testscript.txt
@@ -0,0 +1,13 @@
+## Installation test script
+modelSetWD("../doc/Examples")
+modelCheck("Ratsmodel.txt")
+modelData("Ratsdata.txt")
+modelCompile(1)
+modelInits("Ratsinits.txt")
+modelUpdate(5000)
+samplesSet("alpha0")
+samplesSet("beta")
+samplesSet("sigma")
+modelUpdate(20000)
+samplesStats("*")
+# modelQuit()
diff --git a/install-sh b/install-sh
new file mode 100755
index 0000000..a9244eb
--- /dev/null
+++ b/install-sh
@@ -0,0 +1,527 @@
+#!/bin/sh
+# install - install a program, script, or datafile
+
+scriptversion=2011-01-19.21; # UTC
+
+# This originates from X11R5 (mit/util/scripts/install.sh), which was
+# later released in X11R6 (xc/config/util/install.sh) with the
+# following copyright and license.
+#
+# Copyright (C) 1994 X Consortium
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to
+# deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+# sell copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Except as contained in this notice, the name of the X Consortium shall not
+# be used in advertising or otherwise to promote the sale, use or other deal-
+# ings in this Software without prior written authorization from the X Consor-
+# tium.
+#
+#
+# FSF changes to this file are in the public domain.
+#
+# Calling this script install-sh is preferred over install.sh, to prevent
+# `make' implicit rules from creating a file called install from it
+# when there is no Makefile.
+#
+# This script is compatible with the BSD install script, but was written
+# from scratch.
+
+nl='
+'
+IFS=" "" $nl"
+
+# set DOITPROG to echo to test this script
+
+# Don't use :- since 4.3BSD and earlier shells don't like it.
+doit=${DOITPROG-}
+if test -z "$doit"; then
+ doit_exec=exec
+else
+ doit_exec=$doit
+fi
+
+# Put in absolute file names if you don't have them in your path;
+# or use environment vars.
+
+chgrpprog=${CHGRPPROG-chgrp}
+chmodprog=${CHMODPROG-chmod}
+chownprog=${CHOWNPROG-chown}
+cmpprog=${CMPPROG-cmp}
+cpprog=${CPPROG-cp}
+mkdirprog=${MKDIRPROG-mkdir}
+mvprog=${MVPROG-mv}
+rmprog=${RMPROG-rm}
+stripprog=${STRIPPROG-strip}
+
+posix_glob='?'
+initialize_posix_glob='
+ test "$posix_glob" != "?" || {
+ if (set -f) 2>/dev/null; then
+ posix_glob=
+ else
+ posix_glob=:
+ fi
+ }
+'
+
+posix_mkdir=
+
+# Desired mode of installed file.
+mode=0755
+
+chgrpcmd=
+chmodcmd=$chmodprog
+chowncmd=
+mvcmd=$mvprog
+rmcmd="$rmprog -f"
+stripcmd=
+
+src=
+dst=
+dir_arg=
+dst_arg=
+
+copy_on_change=false
+no_target_directory=
+
+usage="\
+Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
+ or: $0 [OPTION]... SRCFILES... DIRECTORY
+ or: $0 [OPTION]... -t DIRECTORY SRCFILES...
+ or: $0 [OPTION]... -d DIRECTORIES...
+
+In the 1st form, copy SRCFILE to DSTFILE.
+In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
+In the 4th, create DIRECTORIES.
+
+Options:
+ --help display this help and exit.
+ --version display version info and exit.
+
+ -c (ignored)
+ -C install only if different (preserve the last data modification time)
+ -d create directories instead of installing files.
+ -g GROUP $chgrpprog installed files to GROUP.
+ -m MODE $chmodprog installed files to MODE.
+ -o USER $chownprog installed files to USER.
+ -s $stripprog installed files.
+ -t DIRECTORY install into DIRECTORY.
+ -T report an error if DSTFILE is a directory.
+
+Environment variables override the default commands:
+ CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
+ RMPROG STRIPPROG
+"
+
+while test $# -ne 0; do
+ case $1 in
+ -c) ;;
+
+ -C) copy_on_change=true;;
+
+ -d) dir_arg=true;;
+
+ -g) chgrpcmd="$chgrpprog $2"
+ shift;;
+
+ --help) echo "$usage"; exit $?;;
+
+ -m) mode=$2
+ case $mode in
+ *' '* | *' '* | *'
+'* | *'*'* | *'?'* | *'['*)
+ echo "$0: invalid mode: $mode" >&2
+ exit 1;;
+ esac
+ shift;;
+
+ -o) chowncmd="$chownprog $2"
+ shift;;
+
+ -s) stripcmd=$stripprog;;
+
+ -t) dst_arg=$2
+ # Protect names problematic for `test' and other utilities.
+ case $dst_arg in
+ -* | [=\(\)!]) dst_arg=./$dst_arg;;
+ esac
+ shift;;
+
+ -T) no_target_directory=true;;
+
+ --version) echo "$0 $scriptversion"; exit $?;;
+
+ --) shift
+ break;;
+
+ -*) echo "$0: invalid option: $1" >&2
+ exit 1;;
+
+ *) break;;
+ esac
+ shift
+done
+
+if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
+ # When -d is used, all remaining arguments are directories to create.
+ # When -t is used, the destination is already specified.
+ # Otherwise, the last argument is the destination. Remove it from $@.
+ for arg
+ do
+ if test -n "$dst_arg"; then
+ # $@ is not empty: it contains at least $arg.
+ set fnord "$@" "$dst_arg"
+ shift # fnord
+ fi
+ shift # arg
+ dst_arg=$arg
+ # Protect names problematic for `test' and other utilities.
+ case $dst_arg in
+ -* | [=\(\)!]) dst_arg=./$dst_arg;;
+ esac
+ done
+fi
+
+if test $# -eq 0; then
+ if test -z "$dir_arg"; then
+ echo "$0: no input file specified." >&2
+ exit 1
+ fi
+ # It's OK to call `install-sh -d' without argument.
+ # This can happen when creating conditional directories.
+ exit 0
+fi
+
+if test -z "$dir_arg"; then
+ do_exit='(exit $ret); exit $ret'
+ trap "ret=129; $do_exit" 1
+ trap "ret=130; $do_exit" 2
+ trap "ret=141; $do_exit" 13
+ trap "ret=143; $do_exit" 15
+
+ # Set umask so as not to create temps with too-generous modes.
+ # However, 'strip' requires both read and write access to temps.
+ case $mode in
+ # Optimize common cases.
+ *644) cp_umask=133;;
+ *755) cp_umask=22;;
+
+ *[0-7])
+ if test -z "$stripcmd"; then
+ u_plus_rw=
+ else
+ u_plus_rw='% 200'
+ fi
+ cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
+ *)
+ if test -z "$stripcmd"; then
+ u_plus_rw=
+ else
+ u_plus_rw=,u+rw
+ fi
+ cp_umask=$mode$u_plus_rw;;
+ esac
+fi
+
+for src
+do
+ # Protect names problematic for `test' and other utilities.
+ case $src in
+ -* | [=\(\)!]) src=./$src;;
+ esac
+
+ if test -n "$dir_arg"; then
+ dst=$src
+ dstdir=$dst
+ test -d "$dstdir"
+ dstdir_status=$?
+ else
+
+ # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
+ # might cause directories to be created, which would be especially bad
+ # if $src (and thus $dsttmp) contains '*'.
+ if test ! -f "$src" && test ! -d "$src"; then
+ echo "$0: $src does not exist." >&2
+ exit 1
+ fi
+
+ if test -z "$dst_arg"; then
+ echo "$0: no destination specified." >&2
+ exit 1
+ fi
+ dst=$dst_arg
+
+ # If destination is a directory, append the input filename; won't work
+ # if double slashes aren't ignored.
+ if test -d "$dst"; then
+ if test -n "$no_target_directory"; then
+ echo "$0: $dst_arg: Is a directory" >&2
+ exit 1
+ fi
+ dstdir=$dst
+ dst=$dstdir/`basename "$src"`
+ dstdir_status=0
+ else
+ # Prefer dirname, but fall back on a substitute if dirname fails.
+ dstdir=`
+ (dirname "$dst") 2>/dev/null ||
+ expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$dst" : 'X\(//\)[^/]' \| \
+ X"$dst" : 'X\(//\)$' \| \
+ X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
+ echo X"$dst" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'
+ `
+
+ test -d "$dstdir"
+ dstdir_status=$?
+ fi
+ fi
+
+ obsolete_mkdir_used=false
+
+ if test $dstdir_status != 0; then
+ case $posix_mkdir in
+ '')
+ # Create intermediate dirs using mode 755 as modified by the umask.
+ # This is like FreeBSD 'install' as of 1997-10-28.
+ umask=`umask`
+ case $stripcmd.$umask in
+ # Optimize common cases.
+ *[2367][2367]) mkdir_umask=$umask;;
+ .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
+
+ *[0-7])
+ mkdir_umask=`expr $umask + 22 \
+ - $umask % 100 % 40 + $umask % 20 \
+ - $umask % 10 % 4 + $umask % 2
+ `;;
+ *) mkdir_umask=$umask,go-w;;
+ esac
+
+ # With -d, create the new directory with the user-specified mode.
+ # Otherwise, rely on $mkdir_umask.
+ if test -n "$dir_arg"; then
+ mkdir_mode=-m$mode
+ else
+ mkdir_mode=
+ fi
+
+ posix_mkdir=false
+ case $umask in
+ *[123567][0-7][0-7])
+ # POSIX mkdir -p sets u+wx bits regardless of umask, which
+ # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
+ ;;
+ *)
+ tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
+ trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
+
+ if (umask $mkdir_umask &&
+ exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+ then
+ if test -z "$dir_arg" || {
+ # Check for POSIX incompatibilities with -m.
+ # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
+ # other-writeable bit of parent directory when it shouldn't.
+ # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
+ ls_ld_tmpdir=`ls -ld "$tmpdir"`
+ case $ls_ld_tmpdir in
+ d????-?r-*) different_mode=700;;
+ d????-?--*) different_mode=755;;
+ *) false;;
+ esac &&
+ $mkdirprog -m$different_mode -p -- "$tmpdir" && {
+ ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+ test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
+ }
+ }
+ then posix_mkdir=:
+ fi
+ rmdir "$tmpdir/d" "$tmpdir"
+ else
+ # Remove any dirs left behind by ancient mkdir implementations.
+ rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+ fi
+ trap '' 0;;
+ esac;;
+ esac
+
+ if
+ $posix_mkdir && (
+ umask $mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
+ )
+ then :
+ else
+
+ # The umask is ridiculous, or mkdir does not conform to POSIX,
+ # or it failed possibly due to a race condition. Create the
+ # directory the slow way, step by step, checking for races as we go.
+
+ case $dstdir in
+ /*) prefix='/';;
+ [-=\(\)!]*) prefix='./';;
+ *) prefix='';;
+ esac
+
+ eval "$initialize_posix_glob"
+
+ oIFS=$IFS
+ IFS=/
+ $posix_glob set -f
+ set fnord $dstdir
+ shift
+ $posix_glob set +f
+ IFS=$oIFS
+
+ prefixes=
+
+ for d
+ do
+ test X"$d" = X && continue
+
+ prefix=$prefix$d
+ if test -d "$prefix"; then
+ prefixes=
+ else
+ if $posix_mkdir; then
+ (umask=$mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
+ # Don't fail if two instances are running concurrently.
+ test -d "$prefix" || exit 1
+ else
+ case $prefix in
+ *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
+ *) qprefix=$prefix;;
+ esac
+ prefixes="$prefixes '$qprefix'"
+ fi
+ fi
+ prefix=$prefix/
+ done
+
+ if test -n "$prefixes"; then
+ # Don't fail if two instances are running concurrently.
+ (umask $mkdir_umask &&
+ eval "\$doit_exec \$mkdirprog $prefixes") ||
+ test -d "$dstdir" || exit 1
+ obsolete_mkdir_used=true
+ fi
+ fi
+ fi
+
+ if test -n "$dir_arg"; then
+ { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
+ { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
+ { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
+ test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
+ else
+
+ # Make a couple of temp file names in the proper directory.
+ dsttmp=$dstdir/_inst.$$_
+ rmtmp=$dstdir/_rm.$$_
+
+ # Trap to clean up those temp files at exit.
+ trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
+
+ # Copy the file name to the temp name.
+ (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
+
+ # and set any options; do chmod last to preserve setuid bits.
+ #
+ # If any of these fail, we abort the whole thing. If we want to
+ # ignore errors from any of these, just make sure not to ignore
+ # errors from the above "$doit $cpprog $src $dsttmp" command.
+ #
+ { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
+ { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
+ { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
+ { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
+
+ # If -C, don't bother to copy if it wouldn't change the file.
+ if $copy_on_change &&
+ old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
+ new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
+
+ eval "$initialize_posix_glob" &&
+ $posix_glob set -f &&
+ set X $old && old=:$2:$4:$5:$6 &&
+ set X $new && new=:$2:$4:$5:$6 &&
+ $posix_glob set +f &&
+
+ test "$old" = "$new" &&
+ $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
+ then
+ rm -f "$dsttmp"
+ else
+ # Rename the file to the real destination.
+ $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
+
+ # The rename failed, perhaps because mv can't rename something else
+ # to itself, or perhaps because mv is so ancient that it does not
+ # support -f.
+ {
+ # Now remove or move aside any old file at destination location.
+ # We try this two ways since rm can't unlink itself on some
+ # systems and the destination file might be busy for other
+ # reasons. In this case, the final cleanup might fail but the new
+ # file should still install successfully.
+ {
+ test ! -f "$dst" ||
+ $doit $rmcmd -f "$dst" 2>/dev/null ||
+ { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
+ { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
+ } ||
+ { echo "$0: cannot unlink or rename $dst" >&2
+ (exit 1); exit 1
+ }
+ } &&
+
+ # Now rename the file to the real destination.
+ $doit $mvcmd "$dsttmp" "$dst"
+ }
+ fi || exit 1
+
+ trap '' 0
+ fi
+done
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/lib/libOpenBUGS.so b/lib/libOpenBUGS.so
new file mode 100755
index 0000000..af6d105
Binary files /dev/null and b/lib/libOpenBUGS.so differ
diff --git a/missing b/missing
new file mode 100755
index 0000000..86a8fc3
--- /dev/null
+++ b/missing
@@ -0,0 +1,331 @@
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2012-01-06.13; # UTC
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
+# 2008, 2009, 2010, 2011, 2012 Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+if test $# -eq 0; then
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+fi
+
+run=:
+sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
+sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+ configure_ac=configure.ac
+else
+ configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case $1 in
+--run)
+ # Try to run requested program, and just exit if it succeeds.
+ run=
+ shift
+ "$@" && exit 0
+ # Exit code 63 means version mismatch. This often happens
+ # when the user try to use an ancient version of a tool on
+ # a file that requires a minimum version. In this case we
+ # we should proceed has if the program had been absent, or
+ # if --run hadn't been passed.
+ if test $? = 63; then
+ run=:
+ msg="probably too old"
+ fi
+ ;;
+
+ -h|--h|--he|--hel|--help)
+ echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+ -h, --help display this help and exit
+ -v, --version output version information and exit
+ --run try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+ aclocal touch file \`aclocal.m4'
+ autoconf touch file \`configure'
+ autoheader touch file \`config.h.in'
+ autom4te touch the output file, or create a stub one
+ automake touch all \`Makefile.in' files
+ bison create \`y.tab.[ch]', if possible, from existing .[ch]
+ flex create \`lex.yy.c', if possible, from existing .c
+ help2man touch the output file
+ lex create \`lex.yy.c', if possible, from existing .c
+ makeinfo touch the output file
+ yacc create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
+\`g' are ignored when checking the name.
+
+Send bug reports to <bug-automake at gnu.org>."
+ exit $?
+ ;;
+
+ -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+ echo "missing $scriptversion (GNU Automake)"
+ exit $?
+ ;;
+
+ -*)
+ echo 1>&2 "$0: Unknown \`$1' option"
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+ ;;
+
+esac
+
+# normalize program name to check for.
+program=`echo "$1" | sed '
+ s/^gnu-//; t
+ s/^gnu//; t
+ s/^g//; t'`
+
+# Now exit if we have it, but it failed. Also exit now if we
+# don't have it and --version was passed (most likely to detect
+# the program). This is about non-GNU programs, so use $1 not
+# $program.
+case $1 in
+ lex*|yacc*)
+ # Not GNU programs, they don't have --version.
+ ;;
+
+ *)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ # Could not run --version or --help. This is probably someone
+ # running `$TOOL --version' or `$TOOL --help' to check whether
+ # $TOOL exists and not knowing $TOOL uses missing.
+ exit 1
+ fi
+ ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case $program in
+ aclocal*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acinclude.m4' or \`${configure_ac}'. You might want
+ to install the \`Automake' and \`Perl' packages. Grab them from
+ any GNU archive site."
+ touch aclocal.m4
+ ;;
+
+ autoconf*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`${configure_ac}'. You might want to install the
+ \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
+ archive site."
+ touch configure
+ ;;
+
+ autoheader*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acconfig.h' or \`${configure_ac}'. You might want
+ to install the \`Autoconf' and \`GNU m4' packages. Grab them
+ from any GNU archive site."
+ files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+ test -z "$files" && files="config.h"
+ touch_files=
+ for f in $files; do
+ case $f in
+ *:*) touch_files="$touch_files "`echo "$f" |
+ sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+ *) touch_files="$touch_files $f.in";;
+ esac
+ done
+ touch $touch_files
+ ;;
+
+ automake*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+ You might want to install the \`Automake' and \`Perl' packages.
+ Grab them from any GNU archive site."
+ find . -type f -name Makefile.am -print |
+ sed 's/\.am$/.in/' |
+ while read f; do touch "$f"; done
+ ;;
+
+ autom4te*)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them.
+ You can get \`$1' as part of \`Autoconf' from any GNU
+ archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo "#! /bin/sh"
+ echo "# Created by GNU Automake missing as a replacement of"
+ echo "# $ $@"
+ echo "exit 0"
+ chmod +x $file
+ exit 1
+ fi
+ ;;
+
+ bison*|yacc*)
+ echo 1>&2 "\
+WARNING: \`$1' $msg. You should only need it if
+ you modified a \`.y' file. You may need the \`Bison' package
+ in order for those modifications to take effect. You can get
+ \`Bison' from any GNU archive site."
+ rm -f y.tab.c y.tab.h
+ if test $# -ne 1; then
+ eval LASTARG=\${$#}
+ case $LASTARG in
+ *.y)
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.c
+ fi
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.h
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f y.tab.h; then
+ echo >y.tab.h
+ fi
+ if test ! -f y.tab.c; then
+ echo 'main() { return 0; }' >y.tab.c
+ fi
+ ;;
+
+ lex*|flex*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.l' file. You may need the \`Flex' package
+ in order for those modifications to take effect. You can get
+ \`Flex' from any GNU archive site."
+ rm -f lex.yy.c
+ if test $# -ne 1; then
+ eval LASTARG=\${$#}
+ case $LASTARG in
+ *.l)
+ SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" lex.yy.c
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f lex.yy.c; then
+ echo 'main() { return 0; }' >lex.yy.c
+ fi
+ ;;
+
+ help2man*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a dependency of a manual page. You may need the
+ \`Help2man' package in order for those modifications to take
+ effect. You can get \`Help2man' from any GNU archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo ".ab help2man is required to generate this page"
+ exit $?
+ fi
+ ;;
+
+ makeinfo*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.texi' or \`.texinfo' file, or any other file
+ indirectly affecting the aspect of the manual. The spurious
+ call might also be the consequence of using a buggy \`make' (AIX,
+ DU, IRIX). You might want to install the \`Texinfo' package or
+ the \`GNU make' package. Grab either from any GNU archive site."
+ # The file to touch is that specified with -o ...
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -z "$file"; then
+ # ... or it is the one specified with @setfilename ...
+ infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+ file=`sed -n '
+ /^@setfilename/{
+ s/.* \([^ ]*\) *$/\1/
+ p
+ q
+ }' $infile`
+ # ... or it is derived from the source name (dir/f.texi becomes f.info)
+ test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
+ fi
+ # If the file does not exist, the user really needs makeinfo;
+ # let's fail without touching anything.
+ test -f $file || exit 1
+ touch $file
+ ;;
+
+ *)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them. Check the \`README' file,
+ it often tells you about the needed prerequisites for installing
+ this package. You may also peek at any GNU archive site, in case
+ some other package would contain this missing \`$1' program."
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/src/Makefile.am b/src/Makefile.am
new file mode 100644
index 0000000..9cdb547
--- /dev/null
+++ b/src/Makefile.am
@@ -0,0 +1,37 @@
+LDFLAGS = -L ../lib -Wl,-rpath,\$$ORIGIN/../lib -m32
+LIBS = -lOpenBUGS
+
+all: OpenBUGSCli
+
+OpenBUGSCli:
+ $(CC) -o OpenBUGSCli OpenBUGSCli.c $(LDFLAGS) $(LIBS)
+
+version=`echo "modelQuit()" | ./OpenBUGSCli | sed -ne "s/OpenBUGS version \(.*\) rev \(.*\)/\1/p"`
+
+# rm -f commands to remove symlink installed by v3.2.1, since cp -f replaces the target not the link
+
+install:
+ mkdir -p $(DESTDIR)$(bindir) $(DESTDIR)$(libdir) $(DESTDIR)$(datarootdir)/doc/openbugs-$(version) $(DESTDIR)$(mandir)/man1
+ rm -f $(DESTDIR)$(bindir)/OpenBUGSCli
+ cp -f OpenBUGSCli $(DESTDIR)$(bindir)
+ rm -f $(DESTDIR)$(bindir)/OpenBUGS
+ cp -f ../bin/OpenBUGS $(DESTDIR)$(bindir)
+ chmod 755 $(DESTDIR)$(bindir)/OpenBUGS $(DESTDIR)$(bindir)/OpenBUGSCli
+ cp ../lib/libOpenBUGS.so $(DESTDIR)$(libdir)
+ cp -r ../doc/* $(DESTDIR)$(datarootdir)/doc/openbugs-$(version)
+ cp ../doc/OpenBUGS.1 $(DESTDIR)$(mandir)/man1
+
+uninstall:
+ rm -f $(DESTDIR)$(bindir)/OpenBUGS
+ rm -f $(DESTDIR)$(bindir)/OpenBUGSCli
+ rm -f $(DESTDIR)$(libdir)/libOpenBUGS.so
+ rm -rf $(DESTDIR)$(datarootdir)/doc/openbugs-$(version)
+ rm -f $(DESTDIR)$(mandir)/man1/OpenBUGS.1
+
+clean:
+ rm -f OpenBUGSCli
+
+## Simple test using rats example. Run before make install
+
+check:
+ ./OpenBUGSCli < ../doc/testscript.txt
diff --git a/src/Makefile.in b/src/Makefile.in
new file mode 100644
index 0000000..c0e7438
--- /dev/null
+++ b/src/Makefile.in
@@ -0,0 +1,342 @@
+# Makefile.in generated by automake 1.11.3 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
+# Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+subdir = src
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+SOURCES =
+DIST_SOURCES =
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+AMTAR = @AMTAR@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPPFLAGS = @CPPFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EXEEXT = @EXEEXT@
+INSTALL = @INSTALL@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LDFLAGS = -L ../lib -Wl,-rpath,\$$ORIGIN/../lib -m32
+LIBOBJS = @LIBOBJS@
+LIBS = -lOpenBUGS
+LTLIBOBJS = @LTLIBOBJS@
+MAKEINFO = @MAKEINFO@
+MKDIR_P = @MKDIR_P@
+OBJEXT = @OBJEXT@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_URL = @PACKAGE_URL@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+VERSION = @VERSION@
+abs_builddir = @abs_builddir@
+abs_srcdir = @abs_srcdir@
+abs_top_builddir = @abs_top_builddir@
+abs_top_srcdir = @abs_top_srcdir@
+ac_ct_CC = @ac_ct_CC@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+build_alias = @build_alias@
+builddir = @builddir@
+datadir = @datadir@
+datarootdir = @datarootdir@
+docdir = @docdir@
+dvidir = @dvidir@
+exec_prefix = @exec_prefix@
+host_alias = @host_alias@
+htmldir = @htmldir@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localedir = @localedir@
+localstatedir = @localstatedir@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+pdfdir = @pdfdir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+psdir = @psdir@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+srcdir = @srcdir@
+sysconfdir = @sysconfdir@
+target_alias = @target_alias@
+top_build_prefix = @top_build_prefix@
+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+version = `echo "modelQuit()" | ./OpenBUGSCli | sed -ne "s/OpenBUGS version \(.*\) rev \(.*\)/\1/p"`
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
+ @for dep in $?; do \
+ case '$(am__configure_deps)' in \
+ *$$dep*) \
+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+ && { if test -f $@; then exit 0; else break; fi; }; \
+ exit 1;; \
+ esac; \
+ done; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
+ $(am__cd) $(top_srcdir) && \
+ $(AUTOMAKE) --gnu src/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ @case '$?' in \
+ *config.status*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+ *) \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure: $(am__configure_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ list='$(DISTFILES)'; \
+ dist_files=`for file in $$list; do echo $$file; done | \
+ sed -e "s|^$$srcdirstrip/||;t" \
+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+ case $$dist_files in \
+ */*) $(MKDIR_P) `echo "$$dist_files" | \
+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+ sort -u` ;; \
+ esac; \
+ for file in $$dist_files; do \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ if test -d $$d/$$file; then \
+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test -d "$(distdir)/$$file"; then \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+ else \
+ test -f "$(distdir)/$$file" \
+ || cp -p $$d/$$file "$(distdir)/$$file" \
+ || exit 1; \
+ fi; \
+ done
+check-am: all-am
+check: check-am
+all-am: Makefile
+installdirs:
+install-exec: install-exec-am
+install-data: install-data-am
+
+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+ if test -z '$(STRIP)'; then \
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ install; \
+ else \
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+ fi
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+ -rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am:
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am check check-am clean clean-generic distclean \
+ distclean-generic distdir dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am install-dvi \
+ install-dvi-am install-exec install-exec-am install-html \
+ install-html-am install-info install-info-am install-man \
+ install-pdf install-pdf-am install-ps install-ps-am \
+ install-strip installcheck installcheck-am installdirs \
+ maintainer-clean maintainer-clean-generic mostlyclean \
+ mostlyclean-generic pdf pdf-am ps ps-am uninstall uninstall-am
+
+
+all: OpenBUGSCli
+
+OpenBUGSCli:
+ $(CC) -o OpenBUGSCli OpenBUGSCli.c $(LDFLAGS) $(LIBS)
+
+# rm -f commands to remove symlink installed by v3.2.1, since cp -f replaces the target not the link
+
+install:
+ mkdir -p $(DESTDIR)$(bindir) $(DESTDIR)$(libdir) $(DESTDIR)$(datarootdir)/doc/openbugs-$(version) $(DESTDIR)$(mandir)/man1
+ rm -f $(DESTDIR)$(bindir)/OpenBUGSCli
+ cp -f OpenBUGSCli $(DESTDIR)$(bindir)
+ rm -f $(DESTDIR)$(bindir)/OpenBUGS
+ cp -f ../bin/OpenBUGS $(DESTDIR)$(bindir)
+ chmod 755 $(DESTDIR)$(bindir)/OpenBUGS $(DESTDIR)$(bindir)/OpenBUGSCli
+ cp ../lib/libOpenBUGS.so $(DESTDIR)$(libdir)
+ cp -r ../doc/* $(DESTDIR)$(datarootdir)/doc/openbugs-$(version)
+ cp ../doc/OpenBUGS.1 $(DESTDIR)$(mandir)/man1
+
+uninstall:
+ rm -f $(DESTDIR)$(bindir)/OpenBUGS
+ rm -f $(DESTDIR)$(bindir)/OpenBUGSCli
+ rm -f $(DESTDIR)$(libdir)/libOpenBUGS.so
+ rm -rf $(DESTDIR)$(datarootdir)/doc/openbugs-$(version)
+ rm -f $(DESTDIR)$(mandir)/man1/OpenBUGS.1
+
+clean:
+ rm -f OpenBUGSCli
+
+check:
+ ./OpenBUGSCli < ../doc/testscript.txt
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/OpenBUGS.h b/src/OpenBUGS.h
new file mode 100644
index 0000000..196d891
--- /dev/null
+++ b/src/OpenBUGS.h
@@ -0,0 +1,14 @@
+extern void CLI ();
+extern void BugsCmd(char **command, int *len);
+extern void CharArray (char **procedure, int *len, char **x, int *lenX, int *res);
+extern void CmdInterpreter (char **command, int *len, int *res);
+extern void Guard (char **procedure, int *len, int *x, int *res);
+extern void Integer (char **procedure, int *len, int *x, int *res);
+extern void IntegerAray (char **procedure, int *len, int *x, int *lenX, int *res);
+extern void Real (char **procedure, int *len, double *x, double *y, int *res);
+extern void RealArray (char **procedure, int *len, double *x, int *lenX, int *res);
+extern void SetWorkingDir (char **path, int *len);
+extern void SetTempDir(char **path, int *len);
+extern void UseBufferFile ();
+extern void UseConsole ();
+
diff --git a/src/OpenBUGSCli.c b/src/OpenBUGSCli.c
new file mode 100644
index 0000000..96acd5d
--- /dev/null
+++ b/src/OpenBUGSCli.c
@@ -0,0 +1,17 @@
+#include "OpenBUGS.h"
+#include <stdio.h>
+#include <string.h>
+
+int main (int argc, char **argv)
+{
+ int len, res;
+ char *scriptcmd = "BugsEmbed.isScript := TRUE";
+ if (argc > 1) {
+ if (strcmp(argv[1], "-s") == 0) {
+ len = strlen(scriptcmd);
+ CmdInterpreter(&scriptcmd, &len, &res);
+ }
+ }
+ CLI();
+}
+
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/openbugs.git
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