[med-svn] [r-cran-phangorn] branch master updated (b82b55e -> df60f7d)

[Alba Crespi]

This is an automated email from the git hooks/post-receive script.

albac-guest pushed a change to branch master
in repository r-cran-phangorn.

      from  b82b55e   Adding explanation of binary files and upload to unstable
       new  82e88f6   Imported Upstream version 1.99.14
       new  df60f7d   Update for new upstream version.

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 DESCRIPTION                     |   16 +-
 MD5                             |   79 +--
 NAMESPACE                       |   28 +-
 NEWS                            |   46 ++
 R/clanistic.R                   |    2 +-
 R/distSeq.R                     |   19 +
 R/distTree.R                    |  554 +++++++++++++++++++++
 R/fitch.R                       |    2 +-
 R/modelTest.R                   |  201 ++++++++
 R/neighborNet.R                 |    9 +-
 R/networx.R                     |   20 +-
 R/parsimony.R                   |   10 +-
 R/phyDat.R                      |   58 ++-
 R/phylo.R                       | 1010 +++++++++++----------------------------
 R/treeManipulation.R            |    1 +
 R/treedist.R                    |   39 +-
 README.md                       |    6 +
 TODO                            |   15 +
 build/vignette.rds              |  Bin 335 -> 335 bytes
 debian/changelog                |    7 +
 debian/control                  |    8 +-
 inst/doc/Networx.R              |   14 +-
 inst/doc/Networx.Rmd            |    2 +-
 inst/doc/Networx.html           |    2 +-
 inst/doc/Trees.R                |    2 +-
 inst/doc/Trees.Rnw              |    2 +-
 man/bootstrap.pml.Rd            |    5 +-
 man/densiTree.Rd                |    3 +
 man/dist.hamming.Rd             |    6 +
 man/modelTest.Rd                |    7 +-
 man/parsimony.Rd                |    4 +-
 man/phyDat.Rd                   |   17 +-
 man/plot.networx.Rd             |    2 +-
 man/pml.fit.Rd                  |    3 +
 man/splitsNetwork.Rd            |    2 +-
 man/treedist.Rd                 |    3 +-
 src/fitch.c                     |   42 +-
 src/ml.c                        |  495 +++++++++++--------
 src/sankoff.c                   |    2 +-
 tests/testthat.R                |    4 +
 tests/testthat/test_parsimony.R |   21 +
 tests/testthat/test_phyDat.R    |   19 +
 tests/testthat/test_treedist.R  |   14 +
 vignettes/Networx.Rmd           |    2 +-
 vignettes/Trees.Rnw             |    2 +-
 vignettes/phangorn.bib          |  203 +++++++-
 46 files changed, 1893 insertions(+), 1115 deletions(-)
 create mode 100644 R/distTree.R
 create mode 100644 R/modelTest.R
 create mode 100644 TODO
 create mode 100644 tests/testthat.R
 create mode 100644 tests/testthat/test_parsimony.R
 create mode 100644 tests/testthat/test_phyDat.R
 create mode 100644 tests/testthat/test_treedist.R

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-cran-phangorn.git