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commit d4b85778d7452656863bff0a18f6702fab5872fc Merge: 2250f32 fb6f81b Author: Andreas Tille <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-cran-phangorn.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
