[med-svn] [r-cran-ape] 01/03: Imported Upstream version 3.1-2
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Tue May 27 17:24:29 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 r-cran-ape.
commit 8ab78152968df2d8454fa7fe04b845855bafbf69
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Tue May 27 19:16:14 2014 +0200
Imported Upstream version 3.1-2
---
COPYING | 340 +++++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 8 +-
MD5 | 43 +++---
NEWS | 46 ++++++
R/CDF.birth.death.R | 4 +-
R/DNA.R | 6 +-
R/SlowinskiGuyer.R | 1 -
R/ace.R | 44 ++++--
R/all.equal.phylo.R | 12 +-
R/chronos.R | 11 +-
R/cophyloplot.R | 26 ++--
R/dist.topo.R | 4 +-
R/plot.phylo.R | 194 +++++++++++++++-----------
R/read.GenBank.R | 6 +-
R/read.nexus.R | 42 +++---
build/vignette.rds | Bin 192 -> 192 bytes
data/hivtree.newick.rda | Bin 2189 -> 2189 bytes
data/landplants.newick.rda | Bin 574 -> 575 bytes
data/opsin.newick.rda | Bin 445 -> 445 bytes
inst/doc/MoranI.pdf | Bin 126448 -> 256525 bytes
man/ace.Rd | 39 +++++-
man/plot.phylo.Rd | 17 +--
src/bionjs.c | 21 ++-
23 files changed, 676 insertions(+), 188 deletions(-)
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..3912109
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,340 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
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+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+ 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
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+ 0. This License applies to any program or other work which contains
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+ END OF TERMS AND CONDITIONS
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+ How to Apply These Terms to Your New Programs
+
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+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ 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 of the License, 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, write to the Free Software
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+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
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+ Gnomovision version 69, Copyright (C) year name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General
+Public License instead of this License.
diff --git a/DESCRIPTION b/DESCRIPTION
index c51419d..cfa009d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: ape
-Version: 3.1-1
-Date: 2014-03-06
+Version: 3.1-2
+Date: 2014-05-27
Title: Analyses of Phylogenetics and Evolution
Authors at R: c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email = "Emmanuel.Paradis at ird.fr"),
person("Ben", "Bolker", role = "aut"),
@@ -28,7 +28,7 @@ ZipData: no
Description: ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolu [...]
License: GPL (>= 2)
URL: http://ape-package.ird.fr/
-Packaged: 2014-03-10 19:32:32 UTC; paradis
+Packaged: 2014-05-27 09:44:56 UTC; paradis
Author: Emmanuel Paradis [aut, cre, cph],
Ben Bolker [aut],
Julien Claude [aut],
@@ -51,4 +51,4 @@ Author: Emmanuel Paradis [aut, cre, cph],
Maintainer: Emmanuel Paradis <Emmanuel.Paradis at ird.fr>
NeedsCompilation: yes
Repository: CRAN
-Date/Publication: 2014-03-11 08:49:37
+Date/Publication: 2014-05-27 12:44:48
diff --git a/MD5 b/MD5
index d0e1afe..3fc0633 100644
--- a/MD5
+++ b/MD5
@@ -1,20 +1,21 @@
-6eca4e9713ddea6c8b8f10a0a91ee38e *DESCRIPTION
+eb723b61539feef013de476e68b5c50a *COPYING
+0886cb4ddb9055dd86d406fd8d35c226 *DESCRIPTION
1434ba4e31040404e8b049f75a705af5 *NAMESPACE
-8b12ae076e2ea8e6bf9b97f448e2ca65 *NEWS
+c12ba812ce8e6465319ef3c40499dee8 *NEWS
0c7bc9101516fd26fb3ddbedbe25b6a3 *R/CADM.global.R
e042efca1d8a00d4178204f5f481b64d *R/CADM.post.R
-08df4be0f8ac832938928f93d66437bb *R/CDF.birth.death.R
+5fd68920346c5aca7e7695fd9dbc1c3c *R/CDF.birth.death.R
fdb9cfa0cbda82bda982b290693e44e3 *R/Cheverud.R
-5e7f355752302ea4822b62213ee3e3c0 *R/DNA.R
+f9400c37c74ed7d92838a27e19d8d12d *R/DNA.R
0fbc7715dfdc8d54ded16d78ca3100f8 *R/MPR.R
bb95af56d882b6162aa517a77140175e *R/MoranI.R
dd2d159ad60c382ecc7331ddb10b3e5b *R/PGLS.R
a683ed4e25ad199edc7d30e7b55181a6 *R/SDM.R
-0c8c5b7322f53936595f169f5fe1c65d *R/SlowinskiGuyer.R
-6f2c167948e151e900507bcacc30099e *R/ace.R
+6b54088bf2514e3aa70edf05fe88127d *R/SlowinskiGuyer.R
+a21847e7a8b02d88840e9464bb04fe3b *R/ace.R
4ce79cf3f3ff49bef989454d86d0c891 *R/additive.R
9fca35b1005cce7b2a260b553dd971a3 *R/alex.R
-bac63a18722805eea425aec102e9e71c *R/all.equal.phylo.R
+9fe874382f024a98f62a0ccfcd6d09ac *R/all.equal.phylo.R
73f08934c47e0dfb29c49a9d0885cdb3 *R/as.bitsplits.R
c94018d5e792c72e20ce84085b2df9e7 *R/as.matching.R
7989b47a70f6003ac477370d92e9655e *R/as.phylo.R
@@ -27,7 +28,7 @@ a28930cdae07a271403e988e86a0c324 *R/biplot.pcoa.R
e43b5dec7eae6d4bf9371e50117bf6ed *R/cherry.R
02bdacc928572e8ab2d88380a075d7a8 *R/chronoMPL.R
74e1019810b06458e808a447bb099a91 *R/chronopl.R
-f255979fbf13017c315569fc5e6ea8ca *R/chronos.R
+8ae1af4a30c40d15676d70e180f3d593 *R/chronos.R
f6f25bb8f94f424dd6bbbab64eedb00d *R/clustal.R
4f52fb37d822be586f0c5971295167dc *R/coalescent.intervals.R
054bec70587f0056636b2cc52754c7f9 *R/collapse.singles.R
@@ -37,11 +38,11 @@ af76fbb797185c9738442161a2c923b4 *R/compar.gee.R
207154a3a9b9ebbe5d7c29995565dc82 *R/compar.ou.R
8d7c71929156744fd0e4fac370bf9456 *R/compute.brtime.R
0092074917dc5631dc62fb9a3016145c *R/cophenetic.phylo.R
-d7db8dd1f147be51bcf4696c157d359a *R/cophyloplot.R
+13f2dac84d7b8a1da3df0e0c11b4ab1c *R/cophyloplot.R
d5ae510a60a962ca6420366e3bc9cb1a *R/dbd.R
93480a5b64e0d37f5450891629557615 *R/delta.plot.R
dfd5bb35f1cb1fd9154d023e0e4cfc2b *R/dist.gene.R
-811adaf272b8fd6a96fccf432f203099 *R/dist.topo.R
+94a256e9220f68f0a8c72f029304055e *R/dist.topo.R
b28ced504fedeb7f991f7eba10ad06df *R/diversi.gof.R
8b2ec4004022afdc7e2cb42f2657b628 *R/diversi.time.R
fd662cd4bbd6ce536ef379eca2e516ab *R/drop.tip.R
@@ -76,16 +77,16 @@ fc0260f9e8e17fc1446117580bbc93cc *R/pcoa.R
4999c85e82105ded85a214204321c3d1 *R/phydataplot.R
2730f72b8b261609ae8a57a7f0c0bb8b *R/phymltest.R
61d1360195bf4d5e6e2d8c30de335dc8 *R/pic.R
-8078e89cfb035143409212a78b99d07f *R/plot.phylo.R
+57478ff610b5d0d3010c12ad17d968f8 *R/plot.phylo.R
e579ec65c808c29e1ecaae1501784b37 *R/plot.popsize.R
736506e2f67e90cf9326abead437d298 *R/plotPhyloCoor.R
1e2485437566ca9af99d93b4580cbbc2 *R/print.lmorigin.R
d0e8bd41d5acc217fdee3578adcf635b *R/print.parafit.R
8c401518738b9cda403fa9f0eb382757 *R/rTrait.R
-ed6dc6a0298853c8a8eac2124f4ac288 *R/read.GenBank.R
+77eddff87cbbebdf5dc2c2fd81e74961 *R/read.GenBank.R
b13dfb8f455b1c9e74a364085f72dbce *R/read.caic.R
0b661f16611ef934c60f0a003734d471 *R/read.dna.R
-399d7ecded9a81f64710dc3d705d46bb *R/read.nexus.R
+fca9cd2c52414a936ab10a522136cf8a *R/read.nexus.R
13ce7f5c7d1bcb7101469d12651e99c8 *R/read.nexus.data.R
8aefdf68a66fc5ad148b4d5211a285ed *R/read.tree.R
b1218f7862a66f566e4f3165f28fe47c *R/reorder.phylo.R
@@ -113,7 +114,7 @@ a918c086a449bcca5ccbb04f7e6d50a9 *R/yule.R
c8d3aa3fe64e75e61af07a1b11c74f3f *R/yule.time.R
1eb44ff9e5a036eb845faa1598ce5009 *R/zoom.R
3387c0d0c1f913f8471e1bb34bd2e516 *R/zzz.R
-cd2b040e90078a8a28a00223b7d0d458 *build/vignette.rds
+a98e7f16070ea2c3d9334626fddd2024 *build/vignette.rds
db9083e8750aff839d5ebf3ed982f1f1 *data/HP.links.rda
9d9f9232839665422709ded1e541d038 *data/bird.families.rda
a14a6df0f3a735ebc056065077788c90 *data/bird.orders.rda
@@ -121,21 +122,21 @@ f74f9ed80c04756021cc093d40ca9ff9 *data/carnivora.csv.gz
4eaf8cbaefa2e8f8d395a9b482ee9967 *data/chiroptera.rda
1c74c3b99d08b0e17eea3ec1065c12d2 *data/cynipids.rda
7fe760c2f3b4deba0554aae6138cb602 *data/gopher.D.rda
-7dd0f4cf4d6c445e72ca417e044365a8 *data/hivtree.newick.rda
+c52ec1cde7c3f659aa4cb60a651a5e41 *data/hivtree.newick.rda
8d14f95319d0a5cdc8faa60a1d0085ce *data/hivtree.table.txt.gz
-cb4d7535f04a45685284beeb3c39b18b *data/landplants.newick.rda
+d9d51e474a3483004b33196c436811e4 *data/landplants.newick.rda
31be81fe3faca11f98d3e74c090bc59e *data/lice.D.rda
38edbd84a0a067322c40db8d71fb1289 *data/lmorigin.ex1.rda
e3ce9e3444182fea2e65df2e150ea0db *data/lmorigin.ex2.rda
ce7a56faebdf286fdf5ba6c8c3699a79 *data/mat3.RData
e2d1339025ed901009bfed58dc6505ff *data/mat5M3ID.RData
101d0ab2e981b0987cde704a2dee1d8d *data/mat5Mrand.RData
-ea280638ed23f89ec89afc5464f368a5 *data/opsin.newick.rda
+7128cd7d6a1de5fabaa047ea73b038d2 *data/opsin.newick.rda
39e4fece2bdc527d7a9d4d83d023a947 *data/woodmouse.rda
828290996b613493f96e0fab024beebb *inst/CITATION
3f54f3775bcf382e25df2a12228894f6 *inst/doc/MoranI.R
abf2e3e84707634e32f3e7cc6a5ee7ae *inst/doc/MoranI.Rnw
-5980fdbb0b3f3e1f181f76072effaa88 *inst/doc/MoranI.pdf
+4dfb14a17dec4621f06dd5981acd5925 *inst/doc/MoranI.pdf
e6876b193a0df06697c788a8e48cf4bc *man/CADM.global.Rd
060222d269ef45f0c7df76bb723e7d45 *man/DNAbin.Rd
8b9bc214e32cde4c6e5970e48ff30c5f *man/Initialize.corPhyl.Rd
@@ -143,7 +144,7 @@ e6876b193a0df06697c788a8e48cf4bc *man/CADM.global.Rd
ff05fd6fa0a2750b53abf025cdc021d3 *man/MPR.Rd
e63ecbd9a4cf6de364e595d5999e3a2e *man/MoranI.Rd
17486c0fd29fb6f4a752c53fe37142c4 *man/SDM.Rd
-24cdb97990ec1fde5482e5abb5972569 *man/ace.Rd
+5027a986894645f46bade673bf835a3e *man/ace.Rd
60adac0f324c7b08a756d8f45c02b024 *man/add.scale.bar.Rd
32d8ad6eeea971901aee33f1f654ae7c *man/additive.Rd
0f37535a86413945bf3205b7a7b7c20b *man/alex.Rd
@@ -250,7 +251,7 @@ c2e2f35f4e233265c86b7967ec2d0630 *man/parafit.Rd
447941526b92322c52b5cfe367cb7088 *man/pic.Rd
0363aa3fa3e86160934e2359c8ac5323 *man/pic.ortho.Rd
265527313d479d3625df7680c7479cd1 *man/plot.correlogram.Rd
-e2440c324afa4a04836d72a93165839d *man/plot.phylo.Rd
+61a347b013548152104ed9786b3f499e *man/plot.phylo.Rd
6bb1cf751772b9b6acf560b5f3c6f3c1 *man/plot.varcomp.Rd
b24438c42cea969302ec6ba61002426e *man/print.phylo.Rd
80bf68fd21b5e665329cf30b10a1655f *man/rTraitCont.Rd
@@ -305,7 +306,7 @@ d11fb19958f2953583a9c5876da82df9 *src/TBR.c
d343190ba59ef1feac9c96752f210687 *src/ape.c
7eaffd3d85df9a1e4460905e9ca5eced *src/ape.h
19b564aab62c464c092cdf2f0d5cf447 *src/bNNI.c
-e9b547980b563db2f6b062bdcf7c4abe *src/bionjs.c
+79ca5c473decf13964192524caebf9f1 *src/bionjs.c
f782a97466ed8008d31afd7a3e9d4ea9 *src/bipartition.c
a5d4f692aca36f6b50e123b443792fa1 *src/bitsplits.c
81e4ad60b418966cdd09e608e074bb28 *src/delta_plot.c
diff --git a/NEWS b/NEWS
index beb0b24..8a73e7b 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,44 @@
+ CHANGES IN APE VERSION 3.1-2
+
+
+NEW FEATURES
+
+ o plot.phylo: the option 'open.angle' now works also when type =
+ "radial". The option 'lab4ut' now works also for type = "radial"
+ or "fan"; the default is now NULL since it will behave
+ differently depending on 'type'.
+
+ o ace(, type = "discrete") gains an option 'marginal' (FALSE by
+ default). The default is now to do a joint reconstruction of
+ ancestral states.
+
+
+BUG FIXES
+
+ o chronos: the gradients were not correctly computed when the age
+ of the root was unknown.
+
+ o prop.part() did not work with objects of class composite like
+ c("chronos", "phylo"). (Thanks to Steve Walker for the fix.)
+
+ o bionjs: a bug was fixed in the C code.
+
+ o read.GenBank() failed if a line starts with "ORIGIN" in the
+ description of the sequence (thanks to Sofia Sal Bregua for the
+ fix).
+
+ o cophyloplot() works better with length.line = 0.
+
+ o The internal function clado.build used to return trees with the
+ 'edge' matrix stored as double instead of integer.
+
+
+OTHER CHANGES
+
+ o base.freq() now checks the class of the data.
+
+
+
CHANGES IN APE VERSION 3.1-1
@@ -6,6 +47,11 @@ BUG FIXES
o rTraitCont: a bug was introduced in the previous release.
+OTHER CHANGES
+
+ o ape now requires R 3.0.0 or higher.
+
+
CHANGES IN APE VERSION 3.1
diff --git a/R/CDF.birth.death.R b/R/CDF.birth.death.R
index 35b9028..8dadfdb 100644
--- a/R/CDF.birth.death.R
+++ b/R/CDF.birth.death.R
@@ -243,7 +243,7 @@ rlineage <-
if (Foo(t, Tmax) < P) return(Tmax + 1)
inc <- 10
x <- t + inc
- while (inc > eps) { # la pr�cision influe sur le temps de calcul
+ while (inc > eps) { # la precision influe sur le temps de calcul
if (Foo(t, x) > P) {
x <- x - inc
inc <- inc/10
@@ -331,7 +331,7 @@ rbdtree <-
if (Foo(t, Tmax) < P) return(Tmax + 1)
inc <- 10
x <- t + inc
- while (inc > eps) { # la pr�cision influe sur le temps de calcul
+ while (inc > eps) { # la precision influe sur le temps de calcul
if (Foo(t, x) > P) {
x <- x - inc
inc <- inc/10
diff --git a/R/DNA.R b/R/DNA.R
index de0c300..6a06778 100644
--- a/R/DNA.R
+++ b/R/DNA.R
@@ -1,8 +1,8 @@
-## DNA.R (2013-08-12)
+## DNA.R (2014-03-12)
## Manipulations and Comparisons of DNA Sequences
-## Copyright 2002-2013 Emmanuel Paradis
+## Copyright 2002-2014 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
@@ -284,6 +284,8 @@ as.character.DNAbin <- function(x, ...)
base.freq <- function(x, freq = FALSE, all = FALSE)
{
+ if (!inherits(x, "DNAbin")) stop('base.freq requires an object of class "DNAbin"')
+
f <- function(x)
.C(BaseProportion, x, as.integer(length(x)), double(17),
NAOK = TRUE)[[3]]
diff --git a/R/SlowinskiGuyer.R b/R/SlowinskiGuyer.R
index b0fc956..353c467 100644
--- a/R/SlowinskiGuyer.R
+++ b/R/SlowinskiGuyer.R
@@ -42,7 +42,6 @@ richness.yule.test <- function(x, t)
n <- c(n1, n2)
tb <- c(t, t)
- ## taken from /home/paradis/data/Projets/FISHLOSS/BDfit.R:
.PrNt.Yule <- function(N, age, birth) {
tmp <- exp(-birth * age)
tmp * (1 - tmp)^(N - 1)
diff --git a/R/ace.R b/R/ace.R
index e2b8c8f..7b5cd73 100644
--- a/R/ace.R
+++ b/R/ace.R
@@ -1,8 +1,8 @@
-## ace.R (2013-08-14)
+## ace.R (2014-05-27)
## Ancestral Character Estimation
-## Copyright 2005-2013 Emmanuel Paradis and Ben Bolker
+## Copyright 2005-2014 Emmanuel Paradis and Ben Bolker
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
@@ -24,7 +24,7 @@ ace <-
method = if (type == "continuous") "REML" else "ML",
CI = TRUE, model = if (type == "continuous") "BM" else "ER",
scaled = TRUE, kappa = 1, corStruct = NULL, ip = 0.1,
- use.expm = FALSE, use.eigen = TRUE)
+ use.expm = FALSE, use.eigen = TRUE, marginal = FALSE)
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
@@ -178,9 +178,9 @@ ace <-
})
} else {
if (ncol(model) != nrow(model))
- stop("the matrix given as 'model' is not square")
+ stop("the matrix given as 'model' is not square")
if (ncol(model) != nl)
- stop("the matrix 'model' must have as many rows as the number of categories in 'x'")
+ stop("the matrix 'model' must have as many rows as the number of categories in 'x'")
rate <- model
np <- max(rate)
}
@@ -233,11 +233,10 @@ ace <-
} else matexpo
dev <- function(p, output.liks = FALSE) {
if (any(is.nan(p)) || any(is.infinite(p))) return(1e50)
- ## from Rich FitzJohn:
- comp <- numeric(nb.tip + nb.node) # Storage...
+ comp <- numeric(nb.tip + nb.node) # from Rich FitzJohn
Q[] <- c(p, 0)[rate]
diag(Q) <- -rowSums(Q)
- for (i in seq(from = 1, by = 2, length.out = nb.node)) {
+ for (i in seq(from = 1, by = 2, length.out = nb.node)) {
j <- i + 1L
anc <- e1[i]
des1 <- e2[i]
@@ -263,14 +262,36 @@ ace <-
out.nlm <- try(nlm(function(p) dev(p), p = obj$rates, iterlim = 1,
stepmax = 0, hessian = TRUE), silent = TRUE)
options(oldwarn)
- obj$se <- if (class(out.nlm) == "try-error") {
+ obj$se <- if (class(out.nlm) == "try-error") {
warning("model fit suspicious: gradients apparently non-finite")
rep(NaN, np)
} else .getSEs(out.nlm)
obj$index.matrix <- index.matrix
if (CI) {
- obj$lik.anc <- dev(obj$rates, TRUE)
- colnames(obj$lik.anc) <- lvls
+ lik.anc <- dev(obj$rates, TRUE)
+ if (!marginal) {
+ Q[] <- c(obj$rates, 0)[rate]
+ diag(Q) <- -rowSums(Q)
+ for (i in seq(to = 1, by = -2, length.out = nb.node)) {
+ anc <- e1[i] - nb.tip
+ des1 <- e2[i] - nb.tip
+ if (des1 > 0) {
+ P <- matexpo(Q * EL[i])
+ tmp <- lik.anc[anc, ] / (lik.anc[des1, ] %*% P)
+ lik.anc[des1, ] <- (tmp %*% P) * lik.anc[des1, ]
+ }
+ j <- i + 1L
+ des2 <- e2[j] - nb.tip
+ if (des2 > 0) {
+ P <- matexpo(Q * EL[j])
+ tmp <- lik.anc[anc, ] / (lik.anc[des2, ] %*% P)
+ lik.anc[des2, ] <- (tmp %*% P) * lik.anc[des2, ]
+ }
+ lik.anc <- lik.anc / rowSums(lik.anc)
+ }
+ }
+ colnames(lik.anc) <- lvls
+ obj$lik.anc <- lik.anc
}
}
obj$call <- match.call()
@@ -278,6 +299,7 @@ ace <-
obj
}
+
logLik.ace <- function(object, ...) object$loglik
deviance.ace <- function(object, ...) -2*object$loglik
diff --git a/R/all.equal.phylo.R b/R/all.equal.phylo.R
index 79533d5..3833075 100644
--- a/R/all.equal.phylo.R
+++ b/R/all.equal.phylo.R
@@ -2,23 +2,23 @@
##
## Global Comparison of two Phylogenies
-## Copyright 2006 Beno�t Durand
+## Copyright 2006 Benoit Durand
## modified by EP for the new coding of "phylo" (2006-10-04)
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
## Recherche de la correspondance entre deux arbres
-## Parcours en profondeur et en parall�le des deux arbres (current et target)
-## current, target: les deux arbres � comparer
+## Parcours en profondeur et en parallele des deux arbres (current et target)
+## current, target: les deux arbres a comparer
## use.edge.length: faut-il comparer les longueurs de branches ?
-## use.tip.label: faut-il comparer les �tiquettes de feuilles ou seulement la
+## use.tip.label: faut-il comparer les etiquettes de feuilles ou seulement la
## topologie des deux arbres ?
## index.return: si TRUE, retourner la matrice de correspondance entre noeuds
-## et feuilles, une matrice � deux colonnes (current et target) avec pour
+## et feuilles, une matrice a deux colonnes (current et target) avec pour
## chaque ligne des paires d'identifiants de noeuds/feuilles, tels qu'ils
## apparaissent dans l'attribut 'edge' des objets phylo
-## tolerance, scale: param�tres de comparaison des longueurs de branches
+## tolerance, scale: parametres de comparaison des longueurs de branches
## (voir 'all.equal')
all.equal.phylo <- function(target, current,
use.edge.length = TRUE,
diff --git a/R/chronos.R b/R/chronos.R
index 115cd19..a7f63a9 100644
--- a/R/chronos.R
+++ b/R/chronos.R
@@ -1,8 +1,8 @@
-## chronos.R (2013-01-03)
+## chronos.R (2014-05-15)
## Molecular Dating With Penalized and Maximum Likelihood
-## Copyright 2013 Emmanuel Paradis
+## Copyright 2013-2014 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
@@ -244,14 +244,15 @@ maybe you need to adjust the calibration dates")
gradient.poisson <- function(rate, node.time) {
age[unknown.ages] <- node.time
real.edge.length <- age[e1] - age[e2]
- #if (any(real.edge.length < 0))
- # return(numeric(N + length(unknown.ages)))
+
## gradient for the rates:
gr <- el/rate - real.edge.length
## gradient for the dates:
tmp <- el/real.edge.length - rate
- gr.dates <- sapply(A_ki, function(x) sum(tmp[x])) - tmp[D_ki]
+ tmp2 <- tmp[D_ki]
+ tmp2[is.na(tmp2)] <- 0
+ gr.dates <- sapply(A_ki, function(x) sum(tmp[x])) - tmp2
c(gr, gr.dates)
}
diff --git a/R/cophyloplot.R b/R/cophyloplot.R
index 29e5b3c..56d4b1d 100644
--- a/R/cophyloplot.R
+++ b/R/cophyloplot.R
@@ -1,4 +1,4 @@
-## cophyloplot.R (2012-02-14)
+## cophyloplot.R (2014-04-07)
## Plots two phylogenetic trees face to
## face with the links between the tips
@@ -34,7 +34,7 @@ cophyloplot <-
y <- rotate(y, click - length(res$a[, 1]))
}
}
- on.exit(print("done"))
+ on.exit(cat("done\n"))
}
else plotCophylo2(x, y, assoc = assoc, use.edge.length = use.edge.length,
space = space, length.line = length.line, gap = gap,
@@ -152,17 +152,19 @@ plotCophylo2 <-
decx[i] <- decy[i] <- 0
}
- segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + decx[i] + gap,
- a[lsa[x$tip.label == assoc[i, 1]], 2],
- a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left,
- a[lsa[x$tip.label == assoc[i, 1]], 2],
- col = colors[i], lwd = lwidths[i], lty = ltype[i])
+ if (length.line) { # added by EP (2014-04-07)
+ segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + decx[i] + gap,
+ a[lsa[x$tip.label == assoc[i, 1]], 2],
+ a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left,
+ a[lsa[x$tip.label == assoc[i, 1]], 2],
+ col = colors[i], lwd = lwidths[i], lty = ltype[i])
- segments(b2[lsb[y$tip.label == assoc[i, 2]], 1] - (decy[i] + gap),
- b2[lsb[y$tip.label == assoc[i, 2]], 2],
- b2[lsb[y$tip.label == assoc[i, 2]], 1] - (gap + right),
- b2[lsb[y$tip.label == assoc[i, 2]], 2],
- col = colors[i], lwd = lwidths[i], lty = ltype[i])
+ segments(b2[lsb[y$tip.label == assoc[i, 2]], 1] - (decy[i] + gap),
+ b2[lsb[y$tip.label == assoc[i, 2]], 2],
+ b2[lsb[y$tip.label == assoc[i, 2]], 1] - (gap + right),
+ b2[lsb[y$tip.label == assoc[i, 2]], 2],
+ col = colors[i], lwd = lwidths[i], lty = ltype[i])
+ }
segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left,
a[lsa[x$tip.label == assoc[i, 1]], 2],
diff --git a/R/dist.topo.R b/R/dist.topo.R
index ce49a81..d2907df 100644
--- a/R/dist.topo.R
+++ b/R/dist.topo.R
@@ -1,4 +1,4 @@
-## dist.topo.R (2014-03-07)
+## dist.topo.R (2014-05-16)
## Topological Distances, Tree Bipartitions,
## Consensus Trees, and Bootstrapping Phylogenies
@@ -97,7 +97,7 @@ dist.topo <- function(x, y, method = "PH85")
prop.part <- function(..., check.labels = TRUE)
{
obj <- list(...)
- if (length(obj) == 1 && class(obj[[1]]) != "phylo")
+ if (length(obj) == 1 && !inherits(obj[[1]], "phylo")) # fix by Steve Walker (2014-03-31)
obj <- obj[[1]]
ntree <- length(obj)
if (ntree == 1) check.labels <- FALSE
diff --git a/R/plot.phylo.R b/R/plot.phylo.R
index 8950bed..3106dc6 100644
--- a/R/plot.phylo.R
+++ b/R/plot.phylo.R
@@ -1,4 +1,4 @@
-## plot.phylo.R (2014-03-03)
+## plot.phylo.R (2014-05-07)
## Plot Phylogenies
@@ -14,7 +14,7 @@ plot.phylo <-
edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"),
adj = NULL, srt = 0, no.margin = FALSE, root.edge = FALSE,
label.offset = 0, underscore = FALSE, x.lim = NULL,
- y.lim = NULL, direction = "rightwards", lab4ut = "horizontal",
+ y.lim = NULL, direction = "rightwards", lab4ut = NULL,
tip.color = "black", plot = TRUE, rotate.tree = 0,
open.angle = 0, node.depth = 1, ...)
{
@@ -97,11 +97,11 @@ plot.phylo <-
## 'z' is the tree in postorder order used in calls to .C
z <- reorder(x, order = "postorder")
- if (phyloORclado) {
- if (is.null(node.pos)) {
- node.pos <- 1
- if (type == "cladogram" && !use.edge.length) node.pos <- 2
- }
+if (phyloORclado) {
+ if (is.null(node.pos))
+ node.pos <-
+ if (type == "cladogram" && !use.edge.length) 2 else 1
+
if (node.pos == 1)
yy <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
else {
@@ -120,10 +120,11 @@ plot.phylo <-
} else {
xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
}
- } else {
+} else {
twopi <- 2 * pi
rotate.tree <- twopi * rotate.tree/360
- switch(type, "fan" = {
+
+ if (type != "unrooted") { # for "fan" and "radial" trees (open.angle)
## if the tips are not in the same order in tip.label
## and in edge[, 2], we must reorder the angles: we
## use `xx' to store temporarily the angles
@@ -133,6 +134,9 @@ plot.phylo <-
theta <- double(Ntip)
theta[TIPS] <- xx
theta <- c(theta, numeric(Nnode))
+ }
+
+ switch(type, "fan" = {
theta <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, theta)
if (use.edge.length) {
r <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
@@ -153,16 +157,15 @@ plot.phylo <-
xx <- XY$M[, 1] - min(XY$M[, 1])
yy <- XY$M[, 2] - min(XY$M[, 2])
}, "radial" = {
- X <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
- X[X == 1] <- 0
- ## radius:
- X <- 1 - X/Ntip
- ## angle (1st compute the angles for the tips):
- yy <- c((1:Ntip)*twopi/Ntip, rep(0, Nnode))
- Y <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
- xx <- X * cos(Y + rotate.tree)
- yy <- X * sin(Y + rotate.tree)
- })}
+ r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
+ r[r == 1] <- 0
+ r <- 1 - r/Ntip
+ theta <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, theta) + rotate.tree
+ xx <- r * cos(theta)
+ yy <- r * sin(theta)
+ })
+}
+
if (phyloORclado) {
if (!horizontal) {
tmp <- yy
@@ -174,13 +177,18 @@ plot.phylo <-
if (direction == "upwards") yy <- yy + x$root.edge
}
}
+
if (no.margin) par(mai = rep(0, 4))
+
+ if (show.tip.label) nchar.tip.label <- nchar(x$tip.label)
+ max.yy <- max(yy)
+
if (is.null(x.lim)) {
if (phyloORclado) {
if (horizontal) {
x.lim <- c(0, NA)
pin1 <- par("pin")[1] # width of the device in inches
- strWi <- strwidth(x$tip.label, "inches") # id. for the tip labels
+ strWi <- strwidth(x$tip.label, "inches", cex = cex) # id. for the tip labels
## 1.04 comes from that we are using a regular axis system
## with 4% on both sides of the range of x:
xx.tips <- xx[1:Ntip] * 1.04
@@ -188,25 +196,26 @@ plot.phylo <-
## user coordinates to inches:
alp <- try(uniroot(function(a) max(a*xx.tips + strWi) - pin1,
c(0, 1e6))$root, silent = TRUE)
- ## if the above fails, give 1/3 of the device for the tip labels:
+ ## if the above fails, give 1/3 of the plot for the tip labels:
if (is.character(alp)) tmp <- max(xx.tips)*1.5 else {
tmp <- if (show.tip.label) max(xx.tips + strWi/alp) else max(xx.tips)
}
+ if (show.tip.label) tmp <- tmp + label.offset
x.lim[2] <- tmp
} else x.lim <- c(1, Ntip)
} else switch(type, "fan" = {
if (show.tip.label) {
- offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
- x.lim <- c(min(xx) - offset, max(xx) + offset)
- } else x.lim <- c(min(xx), max(xx))
+ offset <- max(nchar.tip.label * 0.018 * max.yy * cex)
+ x.lim <- range(xx) + c(-offset, offset)
+ } else x.lim <- range(xx)
}, "unrooted" = {
if (show.tip.label) {
- offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
+ offset <- max(nchar.tip.label * 0.018 * max.yy * cex)
x.lim <- c(0 - offset, max(xx) + offset)
} else x.lim <- c(0, max(xx))
}, "radial" = {
if (show.tip.label) {
- offset <- max(nchar(x$tip.label) * 0.03 * cex)
+ offset <- max(nchar.tip.label * 0.03 * cex)
x.lim <- c(-1 - offset, 1 + offset)
} else x.lim <- c(-1, 1)
})
@@ -214,10 +223,10 @@ plot.phylo <-
x.lim <- c(0, x.lim)
if (phyloORclado && !horizontal) x.lim[1] <- 1
if (type %in% c("fan", "unrooted") && show.tip.label)
- x.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
+ x.lim[1] <- -max(nchar.tip.label * 0.018 * max.yy * cex)
if (type == "radial")
x.lim[1] <-
- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.03 * cex)
+ if (show.tip.label) -1 - max(nchar.tip.label * 0.03 * cex)
else -1
}
## mirror the xx:
@@ -227,7 +236,7 @@ plot.phylo <-
if (horizontal) y.lim <- c(1, Ntip) else {
y.lim <- c(0, NA)
pin2 <- par("pin")[2] # height of the device in inches
- strWi <- strwidth(x$tip.label, "inches")
+ strWi <- strwidth(x$tip.label, "inches", cex = cex)
## 1.04 comes from that we are using a regular axis system
## with 4% on both sides of the range of x:
yy.tips <- yy[1:Ntip] * 1.04
@@ -239,21 +248,22 @@ plot.phylo <-
if (is.character(alp)) tmp <- max(yy.tips)*1.5 else {
tmp <- if (show.tip.label) max(yy.tips + strWi/alp) else max(yy.tips)
}
+ if (show.tip.label) tmp <- tmp + label.offset
y.lim[2] <- tmp
}
} else switch(type, "fan" = {
if (show.tip.label) {
- offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
- y.lim <- c(min(yy) - offset, max(yy) + offset)
- } else y.lim <- c(min(yy), max(yy))
+ offset <- max(nchar.tip.label * 0.018 * max.yy * cex)
+ y.lim <- c(min(yy) - offset, max.yy + offset)
+ } else y.lim <- c(min(yy), max.yy)
}, "unrooted" = {
if (show.tip.label) {
- offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
- y.lim <- c(0 - offset, max(yy) + offset)
- } else y.lim <- c(0, max(yy))
+ offset <- max(nchar.tip.label * 0.018 * max.yy * cex)
+ y.lim <- c(0 - offset, max.yy + offset)
+ } else y.lim <- c(0, max.yy)
}, "radial" = {
if (show.tip.label) {
- offset <- max(nchar(x$tip.label) * 0.03 * cex)
+ offset <- max(nchar.tip.label * 0.03 * cex)
y.lim <- c(-1 - offset, 1 + offset)
} else y.lim <- c(-1, 1)
})
@@ -261,9 +271,9 @@ plot.phylo <-
y.lim <- c(0, y.lim)
if (phyloORclado && horizontal) y.lim[1] <- 1
if (type %in% c("fan", "unrooted") && show.tip.label)
- y.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
+ y.lim[1] <- -max(nchar.tip.label * 0.018 * max.yy * cex)
if (type == "radial")
- y.lim[1] <- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.018 * max(yy) * cex) else -1
+ y.lim[1] <- if (show.tip.label) -1 - max(nchar.tip.label * 0.018 * max.yy * cex) else -1
}
## mirror the yy:
if (phyloORclado && direction == "downwards") yy <- y.lim[2] - yy # fix by Klaus
@@ -337,31 +347,71 @@ if (plot) {
if (phyloORclado)
text(xx[1:Ntip] + lox, yy[1:Ntip] + loy, x$tip.label, adj = adj,
font = font, srt = srt, cex = cex, col = tip.color)
+ else {
+ angle <- if (type == "unrooted") XY$axe else atan2(yy[1:Ntip], xx[1:Ntip]) # in radians
+
+ lab4ut <-
+ if (is.null(lab4ut)) {
+ if (type == "unrooted") "horizontal" else "axial"
+ } else match.arg(lab4ut, c("horizontal", "axial"))
- if (type == "unrooted") {
if (lab4ut == "horizontal") {
y.adj <- x.adj <- numeric(Ntip)
- sel <- abs(XY$axe) > 0.75 * pi
+ sel <- abs(angle) > 0.75 * pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] * 1.05
- sel <- abs(XY$axe) > pi/4 & abs(XY$axe) < 0.75 * pi
- x.adj[sel] <- -strwidth(x$tip.label)[sel] * (2 * abs(XY$axe)[sel] / pi - 0.5)
- sel <- XY$axe > pi / 4 & XY$axe < 0.75 * pi
+ sel <- abs(angle) > pi/4 & abs(angle) < 0.75 * pi
+ x.adj[sel] <- -strwidth(x$tip.label)[sel] * (2 * abs(angle)[sel] / pi - 0.5)
+ sel <- angle > pi / 4 & angle < 0.75 * pi
y.adj[sel] <- strheight(x$tip.label)[sel] / 2
- sel <- XY$axe < -pi / 4 & XY$axe > -0.75 * pi
+ sel <- angle < -pi / 4 & angle > -0.75 * pi
y.adj[sel] <- -strheight(x$tip.label)[sel] * 0.75
text(xx[1:Ntip] + x.adj * cex, yy[1:Ntip] + y.adj * cex,
x$tip.label, adj = c(adj, 0), font = font,
srt = srt, cex = cex, col = tip.color)
} else { # if lab4ut == "axial"
- adj <- abs(XY$axe) > pi/2
- srt <- 180 * XY$axe / pi
- srt[adj] <- srt[adj] - 180
- adj <- as.numeric(adj)
+### adj <- abs(XY$axe) > pi/2
+### srt <- 180 * XY$axe / pi
+### srt[adj] <- srt[adj] - 180
+### adj <- as.numeric(adj)
+### xx.tips <- xx[1:Ntip]
+### yy.tips <- yy[1:Ntip]
+### if (label.offset) {
+### xx.tips <- xx.tips + label.offset * cos(XY$axe)
+### yy.tips <- yy.tips + label.offset * sin(XY$axe)
+### }
+### ## `srt' takes only a single value, so can't vectorize this:
+### ## (and need to 'elongate' these vectors:)
+### font <- rep(font, length.out = Ntip)
+### tip.color <- rep(tip.color, length.out = Ntip)
+### cex <- rep(cex, length.out = Ntip)
+### for (i in 1:Ntip)
+### text(xx.tips[i], yy.tips[i], cex = cex[i],
+### x$tip.label[i], adj = adj[i], font = font[i],
+### srt = srt[i], col = tip.color[i])
+### }
+### }
+### if (type %in% c("fan", "radial")) {
xx.tips <- xx[1:Ntip]
yy.tips <- yy[1:Ntip]
+### angle <- atan2(yy.tips, xx.tips) # in radians
if (label.offset) {
- xx.tips <- xx.tips + label.offset * cos(XY$axe)
- yy.tips <- yy.tips + label.offset * sin(XY$axe)
+ xx.tips <- xx.tips + label.offset * cos(angle)
+ yy.tips <- yy.tips + label.offset * sin(angle)
+ }
+### s <- xx.tips < 0
+### angle <- angle * 180/pi # switch to degrees
+### angle[s] <- angle[s] + 180
+### adj <- as.numeric(s)
+ if (type == "unrooted"){
+ adj <- abs(angle) > pi/2
+ angle <- angle * 180/pi # switch to degrees
+ angle[adj] <- angle[adj] - 180
+ adj <- as.numeric(adj)
+ } else {
+ s <- xx.tips < 0
+ angle <- angle * 180/pi
+ angle[s] <- angle[s] + 180
+ adj <- as.numeric(s)
}
## `srt' takes only a single value, so can't vectorize this:
## (and need to 'elongate' these vectors:)
@@ -369,32 +419,10 @@ if (plot) {
tip.color <- rep(tip.color, length.out = Ntip)
cex <- rep(cex, length.out = Ntip)
for (i in 1:Ntip)
- text(xx.tips[i], yy.tips[i], cex = cex[i],
- x$tip.label[i], adj = adj[i], font = font[i],
- srt = srt[i], col = tip.color[i])
- }
- }
- if (type %in% c("fan", "radial")) {
- xx.tips <- xx[1:Ntip]
- yy.tips <- yy[1:Ntip]
- angle <- atan2(yy.tips, xx.tips) # in radians
- if (label.offset) {
- xx.tips <- xx.tips + label.offset * cos(angle)
- yy.tips <- yy.tips + label.offset * sin(angle)
+ text(xx.tips[i], yy.tips[i], x$tip.label[i], font = font[i],
+ cex = cex[i], srt = angle[i], adj = adj[i],
+ col = tip.color[i])
}
- s <- xx.tips < 0
- angle <- angle * 180/pi # switch to degrees
- angle[s] <- angle[s] + 180
- adj <- as.numeric(s)
- ## `srt' takes only a single value, so can't vectorize this:
- ## (and need to 'elongate' these vectors:)
- font <- rep(font, length.out = Ntip)
- tip.color <- rep(tip.color, length.out = Ntip)
- cex <- rep(cex, length.out = Ntip)
- for (i in 1:Ntip)
- text(xx.tips[i], yy.tips[i], x$tip.label[i], font = font[i],
- cex = cex[i], srt = angle[i], adj = adj[i],
- col = tip.color[i])
}
}
if (show.node.label)
@@ -426,14 +454,20 @@ phylogram.plot <- function(edge, Ntip, Nnode, xx, yy, horizontal,
## un trait vertical a chaque noeud...
x0v <- xx[nodes]
y0v <- y1v <- numeric(Nnode)
+
## store the index of each node in the 1st column of edge:
NodeInEdge1 <- vector("list", Nnode)
- for (i in nodes) {
- ii <- i - Ntip
- j <- NodeInEdge1[[ii]] <- which(edge[, 1] == i)
+ e1 <- edge[, 1]
+ for (i in seq_along(e1)) {
+ j <- e1[i] - Ntip
+ NodeInEdge1[[j]] <- c(NodeInEdge1[[j]], i)
+ }
+
+ for (i in 1:Nnode) {
+ j <- NodeInEdge1[[i]]
tmp <- range(yy[edge[j, 2]])
- y0v[ii] <- tmp[1]
- y1v[ii] <- tmp[2]
+ y0v[i] <- tmp[1]
+ y1v[i] <- tmp[2]
}
## ... et un trait horizontal partant de chaque tip et chaque noeud
## vers la racine
diff --git a/R/read.GenBank.R b/R/read.GenBank.R
index 23bf4db..d490215 100644
--- a/R/read.GenBank.R
+++ b/R/read.GenBank.R
@@ -1,8 +1,8 @@
-## read.GenBank.R (2012-02-17)
+## read.GenBank.R (2014-04-02)
## Read DNA Sequences from GenBank via Internet
-## Copyright 2002-2012 Emmanuel Paradis
+## Copyright 2002-2014 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
@@ -25,7 +25,7 @@ read.GenBank <-
"&rettype=gb&retmode=text", sep = "")
X <- c(X, scan(file = URL, what = "", sep = "\n", quiet = TRUE))
}
- FI <- grep("^ {0,}ORIGIN", X) + 1
+ FI <- which(X == "ORIGIN ") + 1 # fix by Sofia Sal Bregua (2014-04-02)
LA <- which(X == "//") - 1
obj <- vector("list", N)
for (i in 1:N) {
diff --git a/R/read.nexus.R b/R/read.nexus.R
index ac567c2..a3b7d4d 100644
--- a/R/read.nexus.R
+++ b/R/read.nexus.R
@@ -1,8 +1,8 @@
-## read.nexus.R (2012-09-28)
+## read.nexus.R (2014-04-09)
## Read Tree File in Nexus Format
-## Copyright 2003-2012 Emmanuel Paradis and 2010 Klaus Schliep
+## Copyright 2003-2014 Emmanuel Paradis and 2010 Klaus Schliep
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
@@ -23,29 +23,29 @@
clado.build <- function(tp)
{
add.internal <- function() {
- edge[j, 1] <<- current.node
- node <<- node + 1
- edge[j, 2] <<- current.node <<- node
+ edge[j, 1L] <<- current.node
+ node <<- node + 1L
+ edge[j, 2L] <<- current.node <<- node
index[node] <<- j # set index
- j <<- j + 1
+ j <<- j + 1L
}
add.terminal <- function() {
- edge[j, 1] <<- current.node
- edge[j, 2] <<- tip
+ edge[j, 1L] <<- current.node
+ edge[j, 2L] <<- tip
index[tip] <<- j # set index
tip.label[tip] <<- tpc[k]
- k <<- k + 1
- tip <<- tip + 1
- j <<- j + 1
+ k <<- k + 1L
+ tip <<- tip + 1L
+ j <<- j + 1L
}
go.down <- function() {
l <- index[current.node]
node.label[current.node - nb.tip] <<- tpc[k]
- k <<- k + 1
- current.node <<- edge[l, 1]
+ k <<- k + 1L
+ current.node <<- edge[l, 1L]
}
if (!length(grep(",", tp))) {
- obj <- list(edge = matrix(c(2, 1), 1, 2), Nnode = 1)
+ obj <- list(edge = matrix(c(2L, 1L), 1L, 2L), Nnode = 1L)
tp <- unlist(strsplit(tp, "[\\(\\);]"))
obj$tip.label <- tp[2]
if (tp[3] != "") obj$node.label <- tp[3]
@@ -60,24 +60,24 @@ clado.build <- function(tp)
skeleton <- tsp[tsp == "(" | tsp == ")" | tsp == "," | tsp == ";"]
nsk <- length(skeleton)
nb.node <- length(skeleton[skeleton == ")"])
- nb.tip <- length(skeleton[skeleton == ","]) + 1
+ nb.tip <- length(skeleton[skeleton == ","]) + 1L
## We will assume there is an edge at the root;
## if so, it will be removed and put in a vector
nb.edge <- nb.node + nb.tip
node.label <- character(nb.node)
tip.label <- character(nb.tip)
- edge <- matrix(NA, nb.edge, 2)
- current.node <- node <- nb.tip + 1 # node number
- edge[nb.edge, 1] <- 0 # see comment above
- edge[nb.edge, 2] <- node #
+ edge <- matrix(NA_integer_, nb.edge, 2L)
+ current.node <- node <- nb.tip + 1L # node number
+ edge[nb.edge, 1L] <- 0L # see comment above
+ edge[nb.edge, 2L] <- node #
- index <- numeric(nb.edge + 1)
+ index <- numeric(nb.edge + 1L)
index[node] <- nb.edge
## j: index of the line number of edge
## k: index of the line number of tpc
## tip: tip number
- j <- k <- tip <- 1
+ j <- k <- tip <- 1L
for (i in 2:nsk) {
if (skeleton[i] == "(") add.internal() # add an internal branch (on top)
if (skeleton[i] == ",") {
diff --git a/build/vignette.rds b/build/vignette.rds
index 4ce6254..9aeb3b1 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/data/hivtree.newick.rda b/data/hivtree.newick.rda
index 94b996f..36d30f0 100644
Binary files a/data/hivtree.newick.rda and b/data/hivtree.newick.rda differ
diff --git a/data/landplants.newick.rda b/data/landplants.newick.rda
index 2ad392d..ff9b2af 100644
Binary files a/data/landplants.newick.rda and b/data/landplants.newick.rda differ
diff --git a/data/opsin.newick.rda b/data/opsin.newick.rda
index 2561a99..42c5688 100644
Binary files a/data/opsin.newick.rda and b/data/opsin.newick.rda differ
diff --git a/inst/doc/MoranI.pdf b/inst/doc/MoranI.pdf
index 75ecbf2..2d44754 100644
Binary files a/inst/doc/MoranI.pdf and b/inst/doc/MoranI.pdf differ
diff --git a/man/ace.Rd b/man/ace.Rd
index 1461ff0..c61b7f6 100644
--- a/man/ace.Rd
+++ b/man/ace.Rd
@@ -27,7 +27,7 @@ ace(x, phy, type = "continuous", method = if (type == "continuous")
"REML" else "ML", CI = TRUE,
model = if (type == "continuous") "BM" else "ER",
scaled = TRUE, kappa = 1, corStruct = NULL, ip = 0.1,
- use.expm = FALSE, use.eigen = TRUE)
+ use.expm = FALSE, use.eigen = TRUE, marginal = FALSE)
\method{print}{ace}(x, digits = 4, ...)
\method{logLik}{ace}(object, ...)
\method{deviance}{ace}(object, ...)
@@ -66,6 +66,10 @@ ace(x, phy, type = "continuous", method = if (type == "continuous")
\item{use.eigen}{a logical (relevant if \code{type = "d"}); if
\code{TRUE} then the probability matrix is computed with an eigen
decomposition instead of a matrix exponential (see details).}
+ \item{marginal}{a logical (relevant if \code{type = "d"}). By default,
+ the joint reconstruction of the ancestral states are done. Set this
+ option to \code{TRUE} if you want the marginal reconstruction (see
+ details.)}
\item{digits}{the number of digits to be printed.}
\item{object}{an object of class \code{"ace"}.}
\item{k}{a numeric value giving the penalty per estimated parameter;
@@ -119,6 +123,20 @@ ace(x, phy, type = "continuous", method = if (type == "continuous")
3)}). If a short-cut is used, the number of states is determined from
the data.
+ By default, the likelihood of the different ancestral states of
+ discrete characters are computed with a joint estimation procedure
+ using a procedure similar to the one described in Pupko et al. (2000).
+ If \code{marginal = TRUE}, a marginal estimation procedure is used
+ (this was the only choice until ape 3.1-1). With this second method,
+ the likelihood values at a given node are computed using only the
+ information from the tips (and branches) descending from this node.
+ With the joint estimation, all information is used for each node. The
+ difference between these two methods is further explained in
+ Felsenstein (2004, pp. 259-260) and in Yang (2006, pp. 121-126). The
+ present implementation of the joint estimation uses a ``two-pass''
+ algorithm which is much faster than stochastic mapping while the
+ estimates of both methods are very close.
+
With discrete characters it is necessary to compute the exponential of
the rate matrix. The only possibility until \pkg{ape} 3.0-7) was the
function \code{\link{matexpo}} in \pkg{ape}. If \code{use.expm = TRUE}
@@ -164,6 +182,9 @@ ace(x, phy, type = "continuous", method = if (type == "continuous")
Felsenstein, J. (1985) Phylogenies and the comparative
method. \emph{American Naturalist}, \bold{125}, 1--15.
+ Felsenstein, J. (2004) \emph{Inferring Phylogenies}. Sunderland:
+ Sinauer Associates.
+
Lebl, J. (2013) \emph{Notes on Diffy Qs: Differential Equations for
Engineers}. \url{http://www.jirka.org/diffyqs/}.
@@ -177,17 +198,27 @@ ace(x, phy, type = "continuous", method = if (type == "continuous")
characters. \emph{Proceedings of the Royal Society of London. Series
B. Biological Sciences}, \bold{255}, 37--45.
+ Pupko, T., Pe'er, I, Shamir, R., and Graur, D. (2000) A fast algorithm
+ for joint reconstruction of ancestral amino acid sequences.
+ \emph{Molecular Biology and Evolution}, \bold{17}, 890--896.
+
Schluter, D., Price, T., Mooers, A. O. and Ludwig, D. (1997)
Likelihood of ancestor states in adaptive radiation. \emph{Evolution},
\bold{51}, 1699--1711.
+
+ Yang, Z. (2006) \emph{Computational Molecular Evolution}. Oxford:
+ Oxford University Press.
}
\author{Emmanuel Paradis, Ben Bolker}
\seealso{
- \code{\link{MPR}}, \code{\link{corBrownian}}, \code{\link{corGrafen}},
- \code{\link{corMartins}}, \code{\link{compar.ou}}, \code{\link[stats]{anova}}
+ \code{\link{MPR}}, \code{\link{corBrownian}}, \code{\link{compar.ou}},
+ \code{\link[stats]{anova}}
+
+ Reconstruction of ancestral sequences can be done with the package
+ \pkg{phangorn} (see function \code{?ancestral.pml}).
}
\examples{
-### Just some random data...
+### Some random data...
data(bird.orders)
x <- rnorm(23)
### Compare the three methods for continuous characters:
diff --git a/man/plot.phylo.Rd b/man/plot.phylo.Rd
index 3c3a0da..eb9d551 100644
--- a/man/plot.phylo.Rd
+++ b/man/plot.phylo.Rd
@@ -13,7 +13,7 @@
cex = par("cex"), adj = NULL, srt = 0, no.margin = FALSE,
root.edge = FALSE, label.offset = 0, underscore = FALSE,
x.lim = NULL, y.lim = NULL, direction = "rightwards",
- lab4ut = "horizontal", tip.color = "black", plot = TRUE,
+ lab4ut = NULL, tip.color = "black", plot = TRUE,
rotate.tree = 0, open.angle = 0, node.depth = 1, ...)
\method{plot}{multiPhylo}(x, layout = 1, ...)
}
@@ -88,11 +88,12 @@
tree. Four values are possible: "rightwards" (the default),
"leftwards", "upwards", and "downwards".}
\item{lab4ut}{(= labels for unrooted trees) a character string
- specifying the display of tip labels for unrooted trees: either
- \code{"horizontal"} where all labels are horizontal (the default),
- or \code{"axial"} where the labels are displayed in the axis of the
- corresponding terminal branches. This option has an effect only if
- \code{type = "unrooted"}.}
+ specifying the display of tip labels for unrooted trees (can be
+ abbreviated): either \code{"horizontal"} where all labels are
+ horizontal (the default if \code{type = "u"}), or \code{"axial"}
+ where the labels are displayed in the axis of the corresponding
+ terminal branches. This option has an effect if \code{type = "u"},
+ \code{"f"}, or \code{"r"}.}
\item{tip.color}{the colours used for the tip labels, eventually
recycled (see examples).}
\item{plot}{a logical controlling whether to draw the tree. If
@@ -101,8 +102,8 @@
\item{rotate.tree}{for "fan", "unrooted", or "radial" trees: the
rotation of the whole tree in degrees (negative values are
accepted).}
- \item{open.angle}{if \code{type = "f"}, the angle in degrees left
- blank. Use a non-zero value if you want to call
+ \item{open.angle}{if \code{type = "f"} or \code{"r"}, the angle in
+ degrees left blank. Use a non-zero value if you want to call
\code{\link{axisPhylo}} after the tree is plotted.}
\item{node.depth}{an integer value (1 or 2) used if branch lengths are
not used to plot the tree; 1: the node depths are proportional to
diff --git a/src/bionjs.c b/src/bionjs.c
index 1a9c66c..4619ffb 100644
--- a/src/bionjs.c
+++ b/src/bionjs.c
@@ -1,6 +1,6 @@
-/* bionjs.c 2013-09-26 */
+/* bionjs.c 2014-03-21 */
-/* Copyright 2011-2012 Andrei-Alin Popescu */
+/* Copyright 2011-2014 Andrei-Alin Popescu */
/* This file is part of the R-package `ape'. */
/* See the file ../COPYING for licensing issues. */
@@ -209,11 +209,20 @@ void C_bionjs(double *D, int *N, int *edge1, int *edge2, double *edge_length, in
//if we stil have incomplete distances
if(sw==1)
{
- lamb=0.5+(1/(2*(s[give_index(OTU1,OTU2,n)]-2)*v[give_index(OTU2,OTU1,n)]))*lambSum;
+ if(v[give_index(OTU2,OTU1,n)]!=0.0)
+ lamb=0.5+(1.0/(2*(s[give_index(OTU1,OTU2,n)]-2)*v[give_index(OTU2,OTU1,n)]))*lambSum;
+ else
+ lamb=0.5;
+ if(lamb<0.0)lamb=0.0;
+ if(lamb>1.0)lamb=1.0;
}else{
- lamb=0.5+(1/(2*(n-2)*v[give_index(OTU2,OTU1,n)]))*lambSum;
- }
-
+ if(v[give_index(OTU2,OTU1,n)]!=0.0)
+ lamb=0.5+(1.0/(2*(n-2)*v[give_index(OTU1,OTU2,n)]))*lambSum;
+ else
+ lamb=0.5;
+ if(lamb<0.0)lamb=0.0;
+ if(lamb>1.0)lamb=1.0;
+ }
//although s was updated above, s[otu1,otu2] has remained unchanged
//so it is safe to use it here
//if complete distanes, use N-2, else use S
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-cran-ape.git
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