[med-svn] [r-cran-phangorn] 02/04: Merge tag 'upstream/2.2.0'
Andreas Tille
tille at debian.org
Thu Sep 7 10:02:46 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-phangorn.
commit efb7fd0c036c1561881929cbf54e51a1cc38aacf
Merge: ee011e6 acb5880
Author: Andreas Tille <tille at debian.org>
Date: Thu Sep 7 11:53:01 2017 +0200
Merge tag 'upstream/2.2.0'
Upstream version 2.2.0
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 ++
inst/extdata/trees/primates.dna | 61 +
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, 14137 insertions(+), 4765 deletions(-)
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