[med-svn] [r-cran-phangorn] branch upstream updated (ca6513a -> 27047e4)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository r-cran-phangorn.

      from  ca6513a   Imported Upstream version 1.99-13
       new  27047e4   Imported Upstream version 1.99.14

The 1 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
 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 +++++++-
 44 files changed, 1882 insertions(+), 1111 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

-- 
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