[med-svn] [r-cran-phangorn] branch upstream updated (6c56854 -> acb5880)

Andreas Tille tille at debian.org
Thu Sep 7 10:02:47 UTC 2017


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  6c56854   New upstream version 2.1.1
       new  acb5880   New upstream version 2.2.0

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                                        |   15 +-
 MD5                                                |  239 ++--
 NAMESPACE                                          |   26 +-
 NEWS                                               |   21 +
 R/Coalescent.R                                     |   26 +
 R/Densi.R                                          |   50 +
 R/RcppExports.R                                    |    8 +
 R/SH.R                                             |   38 +-
 R/SOWH.R                                           |   49 +
 R/ancestral_pml.R                                  |   83 +-
 R/bootstrap.R                                      |  138 ++
 R/cladePar.R                                       |   27 +
 R/clanistic.R                                      |  129 ++
 R/delta.score.R                                    |   69 +
 R/dist.p.R                                         |   69 +-
 R/distSeq.R                                        |  187 ++-
 R/distTree.R                                       |  117 ++
 R/fitch.R                                          |  270 ++--
 R/hadamard.R                                       |  127 +-
 R/lento.R                                          |   92 ++
 R/modelTest.R                                      |   67 +
 R/neighborNet.R                                    |  475 ++++++-
 R/networx.R                                        | 1333 +++++-------------
 R/parsimony.R                                      |  158 ++-
 R/phangorn-package.R                               |   99 ++
 R/phyDat.R                                         |  245 +++-
 R/phylo.R                                          | 1447 ++++----------------
 R/pmlMix.R                                         |  463 +++++++
 R/pmlPart.R                                        |  933 +++++++++++++
 R/read.nexus.splits.R                              |  483 +++++++
 R/simSeq.R                                         |   88 +-
 R/splits.R                                         |  542 ++++++++
 R/superTree.R                                      |   46 +
 R/treeManipulation.R                               |  168 ++-
 R/treedist.R                                       |  273 ++--
 README.md                                          |    4 +-
 build/vignette.rds                                 |  Bin 376 -> 376 bytes
 inst/doc/Ancestral.R                               |   19 +-
 inst/doc/Ancestral.Rnw                             |    9 +-
 inst/doc/Ancestral.pdf                             |  Bin 245485 -> 261131 bytes
 inst/doc/IntertwiningTreesAndNetworks.R            |  105 +-
 inst/doc/IntertwiningTreesAndNetworks.Rmd          |  144 +-
 inst/doc/IntertwiningTreesAndNetworks.html         |  147 +-
 inst/doc/Networx.html                              |   14 +-
 inst/doc/Trees.R                                   |    4 +-
 inst/doc/Trees.Rnw                                 |    4 +-
 inst/doc/Trees.pdf                                 |  Bin 167906 -> 167923 bytes
 inst/doc/phangorn-specials.R                       |    9 +-
 inst/doc/phangorn-specials.Rnw                     |    3 +-
 inst/doc/phangorn-specials.pdf                     |  Bin 179955 -> 180130 bytes
 inst/extdata/trees/RAxML_bestTree.3moles           |    1 +
 inst/extdata/trees/RAxML_bestTree.AIs              |    1 +
 inst/extdata/trees/RAxML_bestTree.Wang.out         |    1 +
 inst/extdata/trees/RAxML_bestTree.YCh              |    1 +
 inst/extdata/trees/RAxML_bestTree.mtG              |    1 +
 inst/extdata/trees/RAxML_bipartitions.3moles       |    1 +
 inst/extdata/trees/RAxML_bipartitions.AIs          |    1 +
 inst/extdata/trees/RAxML_bipartitions.YCh          |    1 +
 inst/extdata/trees/RAxML_bipartitions.mtG          |    1 +
 .../trees/RAxML_bipartitionsBranchLabels.3moles    |    1 +
 .../trees/RAxML_bipartitionsBranchLabels.AIs       |    1 +
 .../trees/RAxML_bipartitionsBranchLabels.YCh       |    1 +
 .../trees/RAxML_bipartitionsBranchLabels.mtG       |    1 +
 inst/extdata/trees/RAxML_bootstrap.3moles          | 1000 ++++++++++++++
 inst/extdata/trees/RAxML_bootstrap.AIs             |  550 ++++++++
 inst/extdata/trees/RAxML_bootstrap.Wang.out        | 1000 ++++++++++++++
 inst/extdata/trees/RAxML_bootstrap.YCh             |  250 ++++
 inst/extdata/trees/RAxML_bootstrap.mtG             |  100 ++
 inst/extdata/trees/RAxML_distances.Wang.nxs        | 1193 ++++++++++++++++
 inst/extdata/trees/Splits.txt                      |  115 ++
 {vignettes => inst/extdata/trees}/primates.dna     |    0
 man/Ancestors.Rd                                   |   61 +-
 man/CI.Rd                                          |   34 +
 man/Laurasiatherian.Rd                             |   38 +-
 man/NJ.Rd                                          |   58 +-
 man/SH.test.Rd                                     |   49 +-
 man/SOWH.test.Rd                                   |   72 +-
 man/addConfidences.Rd                              |   81 +-
 man/allTrees.Rd                                    |   38 +-
 man/ancestral.pml.Rd                               |  106 +-
 man/as.networx.Rd                                  |  141 ++
 man/as.splits.Rd                                   |  151 +-
 man/bab.Rd                                         |   88 +-
 man/bootstrap.pml.Rd                               |  152 +-
 man/chloroplast.Rd                                 |   35 +-
 man/cladePar.Rd                                    |   79 +-
 man/coalSpeciesTree.Rd                             |   41 +
 man/consensusNet.Rd                                |   65 +-
 man/cophenetic.networx.Rd                          |   25 +-
 man/delta.score.Rd                                 |   69 +-
 man/densiTree.Rd                                   |  105 +-
 man/designTree.Rd                                  |   86 +-
 man/dfactorial.Rd                                  |   41 +-
 man/dist.hamming.Rd                                |   96 +-
 man/dist.p.Rd                                      |   99 +-
 man/distanceHadamard.Rd                            |   46 +-
 man/getClans.Rd                                    |  200 +--
 man/hadamard.Rd                                    |   90 +-
 man/lento.Rd                                       |   77 +-
 man/maxCladeCred.Rd                                |   68 +-
 man/midpoint.Rd                                    |   74 +-
 man/modelTest.Rd                                   |  109 +-
 man/neighborNet.Rd                                 |   55 +-
 man/nni.Rd                                         |   54 +-
 man/parsimony.Rd                                   |  133 +-
 man/phangorn-package.Rd                            |   55 +-
 man/phyDat.Rd                                      |  239 ++--
 man/plot.networx.Rd                                |  154 ---
 man/pml.Rd                                         |  288 ++--
 man/pml.fit.Rd                                     |  131 +-
 man/pmlCluster.Rd                                  |  102 +-
 man/pmlMix.Rd                                      |   80 +-
 man/pmlPart.Rd                                     |  102 +-
 man/read.aa.Rd                                     |   67 +-
 man/read.nexus.splits.Rd                           |   81 ++
 man/simSeq.Rd                                      |   82 +-
 man/splitsNetwork.Rd                               |   80 +-
 man/superTree.Rd                                   |   96 +-
 man/treedist.Rd                                    |  157 ++-
 man/upgma.Rd                                       |   73 +-
 man/writeDist.Rd                                   |   65 +
 man/yeast.Rd                                       |   40 +-
 src/RcppExports.cpp                                |   24 +
 src/dist.c                                         |    2 +-
 src/fitch.c                                        |   99 +-
 src/ml.c                                           |  173 ++-
 src/phangorn.c                                     |   10 +-
 src/phangorn_help.cpp                              |   54 +-
 src/registerDynamicSymbol.c                        |  154 +++
 src/sankoff.c                                      |    2 +-
 src/sprdist.c                                      |   54 +-
 tests/testthat/test_pmlPart.R                      |  167 +++
 tests/testthat/test_treeManipulation.R             |    7 +-
 vignettes/Ancestral.Rnw                            |    9 +-
 vignettes/IntertwiningTreesAndNetworks.Rmd         |  144 +-
 vignettes/Trees.Rnw                                |    4 +-
 vignettes/cophylo.png                              |  Bin 0 -> 13176 bytes
 vignettes/phangorn-specials.Rnw                    |    3 +-
 vignettes/phangorn.bib                             |   44 +
 139 files changed, 14076 insertions(+), 4765 deletions(-)
 create mode 100644 R/delta.score.R
 create mode 100644 R/lento.R
 create mode 100644 R/phangorn-package.R
 create mode 100644 R/pmlMix.R
 create mode 100644 R/pmlPart.R
 create mode 100644 R/read.nexus.splits.R
 create mode 100644 R/splits.R
 create mode 100644 inst/extdata/trees/RAxML_bestTree.3moles
 create mode 100644 inst/extdata/trees/RAxML_bestTree.AIs
 create mode 100644 inst/extdata/trees/RAxML_bestTree.Wang.out
 create mode 100644 inst/extdata/trees/RAxML_bestTree.YCh
 create mode 100644 inst/extdata/trees/RAxML_bestTree.mtG
 create mode 100644 inst/extdata/trees/RAxML_bipartitions.3moles
 create mode 100644 inst/extdata/trees/RAxML_bipartitions.AIs
 create mode 100644 inst/extdata/trees/RAxML_bipartitions.YCh
 create mode 100644 inst/extdata/trees/RAxML_bipartitions.mtG
 create mode 100644 inst/extdata/trees/RAxML_bipartitionsBranchLabels.3moles
 create mode 100644 inst/extdata/trees/RAxML_bipartitionsBranchLabels.AIs
 create mode 100644 inst/extdata/trees/RAxML_bipartitionsBranchLabels.YCh
 create mode 100644 inst/extdata/trees/RAxML_bipartitionsBranchLabels.mtG
 create mode 100644 inst/extdata/trees/RAxML_bootstrap.3moles
 create mode 100644 inst/extdata/trees/RAxML_bootstrap.AIs
 create mode 100644 inst/extdata/trees/RAxML_bootstrap.Wang.out
 create mode 100644 inst/extdata/trees/RAxML_bootstrap.YCh
 create mode 100644 inst/extdata/trees/RAxML_bootstrap.mtG
 create mode 100644 inst/extdata/trees/RAxML_distances.Wang.nxs
 create mode 100644 inst/extdata/trees/Splits.txt
 copy {vignettes => inst/extdata/trees}/primates.dna (100%)
 create mode 100644 man/CI.Rd
 create mode 100644 man/as.networx.Rd
 create mode 100644 man/coalSpeciesTree.Rd
 delete mode 100644 man/plot.networx.Rd
 create mode 100644 man/read.nexus.splits.Rd
 create mode 100644 man/writeDist.Rd
 create mode 100644 src/registerDynamicSymbol.c
 create mode 100644 tests/testthat/test_pmlPart.R
 create mode 100644 vignettes/cophylo.png

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