[med-svn] [r-cran-phangorn] branch upstream updated (27047e4 -> fb6f81b)
Andreas Tille
tille at debian.org
Thu Jul 7 11:12:58 UTC 2016
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 27047e4 Imported Upstream version 1.99.14
new fb6f81b Imported Upstream version 2.0.4
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 | 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(-)
create mode 100644 R/SH.R
create mode 100644 R/ancestral_pml.R
create mode 100644 R/bootstrap.R
delete mode 100644 TODO
create mode 100644 inst/doc/IntertwiningTreesAndNetworks.R
create mode 100644 inst/doc/IntertwiningTreesAndNetworks.Rmd
create mode 100644 inst/doc/IntertwiningTreesAndNetworks.html
create mode 100644 inst/extdata/trees/RAxML_bipartitions.woodmouse
create mode 100644 inst/extdata/trees/RAxML_bootstrap.woodmouse
create mode 100644 inst/extdata/trees/woodmouse.fasta
create mode 100644 inst/extdata/trees/woodmouse.mrbayes.nex.con
create mode 100644 inst/extdata/trees/woodmouse.mrbayes.nex.run1.t
create mode 100644 inst/extdata/trees/woodmouse.mrbayes.nex.run2.t
create mode 100644 inst/extdata/trees/woodmouse.nxs
create mode 100644 man/addConfidences.Rd
create mode 100644 man/cophenetic.networx.Rd
create mode 100644 man/delta.score.Rd
create mode 100644 man/maxCladeCred.Rd
create mode 100644 tests/testthat/test_distances.R
create mode 100644 tests/testthat/test_pml.R
create mode 100644 tests/testthat/test_splits.R
create mode 100644 tests/testthat/test_treeManipulation.R
create mode 100644 vignettes/IntertwiningTreesAndNetworks.Rmd
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