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 30344e5bfb317f435b6c238495ecf88eb94163c2 Merge: a174223 6c56854 Author: Andreas Tille <[email protected]> Date: Wed Dec 7 09:25:47 2016 +0100 Merge tag 'upstream/2.1.1' Upstream version 2.1.1 DESCRIPTION | 22 +- MD5 | 124 ++-- NAMESPACE | 26 +- NEWS | 36 + R/Densi.R | 231 ------ R/RcppExports.R | 11 + R/ancestral_pml.R | 32 +- R/bootstrap.R | 55 +- R/distSeq.R | 97 +-- R/distTree.R | 104 ++- R/fitch.R | 3 +- R/networx.R | 120 +++- R/parsimony.R | 46 +- R/phyDat.R | 388 ++++++----- R/phylo.R | 36 +- R/sankoff.R | 2 - R/simSeq.R | 17 +- R/superTree.R | 135 ++++ R/treeManipulation.R | 65 +- R/treedist.R | 154 +++- R/zzz.R | 5 + README.md | 6 +- build/vignette.rds | Bin 375 -> 376 bytes inst/doc/Ancestral.pdf | Bin 260891 -> 245485 bytes inst/doc/IntertwiningTreesAndNetworks.html | 6 +- inst/doc/Networx.Rmd | 2 +- inst/doc/Networx.html | 16 +- inst/doc/Trees.pdf | Bin 167890 -> 167906 bytes inst/doc/phangorn-specials.pdf | Bin 180115 -> 179955 bytes man/SOWH.test.Rd | 2 +- man/ancestral.pml.Rd | 2 +- man/as.splits.Rd | 9 +- man/densiTree.Rd | 7 +- man/dist.p.Rd | 2 +- man/hadamard.Rd | 14 +- man/maxCladeCred.Rd | 2 +- man/midpoint.Rd | 2 +- man/modelTest.Rd | 4 +- man/nni.Rd | 2 +- man/parsimony.Rd | 5 +- man/phyDat.Rd | 19 +- man/plot.networx.Rd | 2 +- man/pml.Rd | 4 +- man/pml.fit.Rd | 31 +- man/simSeq.Rd | 5 +- man/superTree.Rd | 22 +- man/treedist.Rd | 20 +- src/RcppExports.cpp | 30 + src/dist.c | 9 +- src/fitch.c | 18 +- src/ml.c | 51 +- src/phangorn.c | 25 +- src/phangorn_help.cpp | 48 ++ src/sankoff.c | 11 +- src/sprdist.c | 1047 ++++++++++++++++++++++++++++ tests/testthat/test_dist_tree.R | 22 + tests/testthat/test_distances.R | 22 +- tests/testthat/test_hadamard.R | 21 + tests/testthat/test_parsimony.R | 34 +- tests/testthat/test_phyDat.R | 78 ++- tests/testthat/test_pml.R | 93 ++- tests/testthat/test_splits.R | 39 ++ tests/testthat/test_superTree.R | 26 + tests/testthat/test_treeManipulation.R | 31 +- tests/testthat/test_treedist.R | 27 + vignettes/Networx.Rmd | 2 +- vignettes/phangorn.bib | 79 +++ 67 files changed, 2681 insertions(+), 925 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
