[med-svn] [r-cran-phangorn] 02/07: Merge tag 'upstream/2.0.4'
Andreas Tille
tille at debian.org
Thu Jul 7 11:12:57 UTC 2016
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 d4b85778d7452656863bff0a18f6702fab5872fc
Merge: 2250f32 fb6f81b
Author: Andreas Tille <tille at debian.org>
Date: Thu Jul 7 13:05:04 2016 +0200
Merge tag 'upstream/2.0.4'
Upstream version 2.0.4
DESCRIPTION | 26 +-
MD5 | 169 +-
NAMESPACE | 54 +-
NEWS | 110 +-
R/Coalescent.R | 2 +-
R/Densi.R | 144 +-
R/SH.R | 51 +
R/ancestral_pml.R | 102 ++
R/bootstrap.R | 238 +++
R/cladePar.R | 2 +-
R/clanistic.R | 26 +-
R/dist.p.R | 2 +-
R/distSeq.R | 98 +-
R/distTree.R | 96 +-
R/fitch.R | 178 +-
R/hadamard.R | 8 +-
R/modelTest.R | 89 +-
R/networx.R | 893 +++++++---
R/parsimony.R | 76 +-
R/phyDat.R | 173 +-
R/phylo.R | 2092 ++++++++++++-----------
R/sankoff.R | 10 +-
R/simSeq.R | 12 +-
R/treeManipulation.R | 286 +---
R/treedist.R | 484 +++++-
README.md | 10 +-
TODO | 15 -
build/vignette.rds | Bin 335 -> 375 bytes
inst/doc/Ancestral.R | 15 +-
inst/doc/Ancestral.Rnw | 1 +
inst/doc/Ancestral.pdf | Bin 237029 -> 260891 bytes
inst/doc/IntertwiningTreesAndNetworks.R | 123 ++
inst/doc/IntertwiningTreesAndNetworks.Rmd | 190 ++
inst/doc/IntertwiningTreesAndNetworks.html | 249 +++
inst/doc/Networx.R | 9 +-
inst/doc/Networx.Rmd | 40 +-
inst/doc/Networx.html | 167 +-
inst/doc/Trees.R | 155 +-
inst/doc/Trees.Rnw | 144 +-
inst/doc/Trees.pdf | Bin 138040 -> 167890 bytes
inst/doc/phangorn-specials.R | 19 +-
inst/doc/phangorn-specials.Rnw | 37 +-
inst/doc/phangorn-specials.pdf | Bin 157302 -> 180115 bytes
inst/extdata/trees/RAxML_bipartitions.woodmouse | 1 +
inst/extdata/trees/RAxML_bootstrap.woodmouse | 1000 +++++++++++
inst/extdata/trees/woodmouse.fasta | 30 +
inst/extdata/trees/woodmouse.mrbayes.nex.con | 9 +
inst/extdata/trees/woodmouse.mrbayes.nex.run1.t | 1021 +++++++++++
inst/extdata/trees/woodmouse.mrbayes.nex.run2.t | 1021 +++++++++++
inst/extdata/trees/woodmouse.nxs | 517 ++++++
man/Ancestors.Rd | 9 +-
man/addConfidences.Rd | 73 +
man/allTrees.Rd | 60 +-
man/ancestral.pml.Rd | 4 +-
man/as.splits.Rd | 15 +-
man/bootstrap.pml.Rd | 34 +-
man/consensusNet.Rd | 7 +-
man/cophenetic.networx.Rd | 25 +
man/delta.score.Rd | 57 +
man/dfactorial.Rd | 56 +-
man/dist.hamming.Rd | 31 +-
man/dist.p.Rd | 6 +-
man/distanceHadamard.Rd | 4 +-
man/lento.Rd | 3 +-
man/maxCladeCred.Rd | 72 +
man/midpoint.Rd | 3 +-
man/modelTest.Rd | 24 +-
man/neighborNet.Rd | 2 +-
man/nni.Rd | 2 +-
man/parsimony.Rd | 5 +-
man/phangorn-package.Rd | 84 +-
man/phyDat.Rd | 21 +-
man/plot.networx.Rd | 47 +-
man/pml.Rd | 44 +-
man/pml.fit.Rd | 8 +-
man/simSeq.Rd | 2 +-
man/superTree.Rd | 2 +-
man/treedist.Rd | 46 +-
src/Makevars | 4 +-
src/dist.c | 2 +-
src/fitch.c | 66 +-
src/ml.c | 331 ++--
src/phangorn.c | 111 +-
src/sankoff.c | 2 +-
tests/testthat/test_distances.R | 18 +
tests/testthat/test_parsimony.R | 5 +-
tests/testthat/test_pml.R | 61 +
tests/testthat/test_splits.R | 23 +
tests/testthat/test_treeManipulation.R | 35 +
tests/testthat/test_treedist.R | 73 +-
vignettes/Ancestral.Rnw | 1 +
vignettes/IntertwiningTreesAndNetworks.Rmd | 190 ++
vignettes/Networx.Rmd | 40 +-
vignettes/Trees.RData | Bin 51886 -> 164438 bytes
vignettes/Trees.Rnw | 144 +-
vignettes/phangorn-specials.Rnw | 37 +-
vignettes/phangorn.bib | 316 +++-
97 files changed, 9830 insertions(+), 2569 deletions(-)
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