[med-svn] [r-cran-phylobase] 05/06: Updated version 0.8.4 from 'upstream/0.8.4'
Andreas Tille
tille at debian.org
Mon Oct 2 20:43:25 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-phylobase.
commit 6bf89adf00abf1d87f6c3ee748cdedad5ef18555
Merge: 71b6f0e 7b6b9ef
Author: Andreas Tille <tille at debian.org>
Date: Mon Oct 2 22:34:10 2017 +0200
Updated version 0.8.4 from 'upstream/0.8.4'
with Debian dir 055534cc9379f72dc03dc2728899da803d089e62
DESCRIPTION | 37 ++
MD5 | 145 +++++
NAMESPACE | 97 ++++
NEWS.md | 298 ++++++++++
R/MRCA-methods.R | 73 +++
R/RcppExports.R | 79 +++
R/addData-methods.R | 98 ++++
R/ancestors.R | 234 ++++++++
R/checkdata.R | 318 +++++++++++
R/edgeLength-methods.R | 310 ++++++++++
R/extractTree.R | 37 ++
R/formatData.R | 213 +++++++
R/getNode-methods.R | 206 +++++++
R/internal-constructors.R | 87 +++
R/labels-methods.R | 298 ++++++++++
R/multiphylo4-class.R | 53 ++
R/nodeId-methods.R | 100 ++++
R/oldclasses-class.R | 13 +
R/pdata.R | 149 +++++
R/phylo4-accessors.R | 177 ++++++
R/phylo4-class.R | 35 ++
R/phylo4-methods.R | 178 ++++++
R/phylo4d-accessors.R | 82 +++
R/phylo4d-class.R | 39 ++
R/phylo4d-methods.R | 414 ++++++++++++++
R/phylobase-package.R | 137 +++++
R/phylobase.options.R | 54 ++
R/phylomats-class.R | 136 +++++
R/print-methods.R | 126 +++++
R/readNCL.R | 435 ++++++++++++++
R/reorder-methods.R | 149 +++++
R/root-methods.R | 64 +++
R/setAs-methods.R | 321 +++++++++++
R/shortestPath-methods.R | 67 +++
R/subset-methods.R | 429 ++++++++++++++
R/summary-methods.R | 251 +++++++++
R/tbind.R | 44 ++
R/tdata-methods.R | 212 +++++++
R/treePlot.R | 784 ++++++++++++++++++++++++++
R/treestruc.R | 87 +++
R/zzz.R | 16 +
build/vignette.rds | Bin 0 -> 233 bytes
data/geospiza.rda | Bin 0 -> 1541 bytes
data/geospiza_raw.rda | Bin 0 -> 1212 bytes
data/owls4.rda | Bin 0 -> 345 bytes
inst/doc/phylobase.Rnw | 674 ++++++++++++++++++++++
inst/doc/phylobase.pdf | Bin 0 -> 203197 bytes
inst/nexmlfiles/comp_analysis.xml | 135 +++++
inst/nexusfiles/ExContData.Rdata | Bin 0 -> 4596 bytes
inst/nexusfiles/MultiLineTrees.nex | 89 +++
inst/nexusfiles/NastyLabels.nex | 56 ++
inst/nexusfiles/NastyLabels2.nex | 52 ++
inst/nexusfiles/co1.nex | 13 +
inst/nexusfiles/minNex.nex | 56 ++
inst/nexusfiles/minSeq.nex | 12 +
inst/nexusfiles/newick.tre | 1 +
inst/nexusfiles/noStateLabels.nex | 36 ++
inst/nexusfiles/shorebird_underscore.nex | 321 +++++++++++
inst/nexusfiles/testSubsetTaxa.nex | 26 +
inst/nexusfiles/test_min.nex | 20 +
inst/nexusfiles/treeRoundingError.nex | 35 ++
inst/nexusfiles/treeWithContinuousData.nex | 365 ++++++++++++
inst/nexusfiles/treeWithDiscAndContData.nex | 413 ++++++++++++++
inst/nexusfiles/treeWithDiscreteData.nex | 354 ++++++++++++
inst/nexusfiles/treeWithPolyExcludedData.nex | 465 +++++++++++++++
inst/nexusfiles/treeWithSpecialCharacters.nex | 35 ++
inst/nexusfiles/treeWithUnderscoreLabels.nex | 354 ++++++++++++
man/MRCA.Rd | 47 ++
man/addData-methods.Rd | 79 +++
man/ancestors.Rd | 110 ++++
man/checkPhylo4.Rd | 59 ++
man/edgeLength-methods.Rd | 150 +++++
man/edges-accessors.Rd | 73 +++
man/extractTree.Rd | 45 ++
man/formatData.Rd | 88 +++
man/geospiza.Rd | 29 +
man/getNode-methods.Rd | 104 ++++
man/labels-methods.Rd | 165 ++++++
man/multiPhylo-class.Rd | 21 +
man/nTips-methods.Rd | 41 ++
man/nodeId-methods.Rd | 46 ++
man/owls4.Rd | 22 +
man/pdata-class.Rd | 26 +
man/pdata.Rd | 33 ++
man/phylo4-class.Rd | 26 +
man/phylo4-methods.Rd | 119 ++++
man/phylo4d-accessors.Rd | 77 +++
man/phylo4d-class.Rd | 33 ++
man/phylo4d-methods.Rd | 290 ++++++++++
man/phyloXXYY.Rd | 50 ++
man/phylobase-package.Rd | 73 +++
man/phylobase.options.Rd | 39 ++
man/phylobubbles.Rd | 61 ++
man/phylomat-class.Rd | 59 ++
man/plotOneTree.Rd | 66 +++
man/print-methods.Rd | 101 ++++
man/readNexus.Rd | 180 ++++++
man/reorder-methods.Rd | 58 ++
man/root-methods.Rd | 47 ++
man/setAs-methods.Rd | 69 +++
man/shortestPath-methods.Rd | 40 ++
man/subset-methods.Rd | 184 ++++++
man/summary-methods.Rd | 100 ++++
man/tdata-methods.Rd | 114 ++++
man/tip.data.plot.Rd | 48 ++
man/treePlot-methods.Rd | 117 ++++
man/treeStructure-methods.Rd | 59 ++
src/Makevars | 2 +
src/Makevars.win | 6 +
src/RcppExports.cpp | 222 ++++++++
src/ancestors.c | 53 ++
src/checkPhylo4.cpp | 415 ++++++++++++++
src/descendants.c | 53 ++
src/phyloXX.c | 97 ++++
src/phylobase_init.c | 74 +++
src/reorderBinary.c | 66 +++
src/reorderRobust.c | 62 ++
tests/misctests.R | 112 ++++
tests/phylo4dtests.R | 29 +
tests/phylosubtest.R | 16 +
tests/phylotorture.R | 129 +++++
tests/plottest.R | 54 ++
tests/roundtrip.R | 41 ++
tests/test-all.R | 3 +
tests/testprune.R | 20 +
tests/testthat/test.badnex.R | 15 +
tests/testthat/test.checkdata.R | 70 +++
tests/testthat/test.class-phylo4.R | 119 ++++
tests/testthat/test.class-phylo4d.R | 317 +++++++++++
tests/testthat/test.formatData.R | 480 ++++++++++++++++
tests/testthat/test.methods-oldclasses.R | 8 +
tests/testthat/test.methods-phylo4.R | 641 +++++++++++++++++++++
tests/testthat/test.pdata.R | 21 +
tests/testthat/test.phylo4.R | 11 +
tests/testthat/test.phylobase.options.R | 32 ++
tests/testthat/test.prune.R | 18 +
tests/testthat/test.readNCL.R | 585 +++++++++++++++++++
tests/testthat/test.setAs-Methods.R | 183 ++++++
tests/testthat/test.subset.R | 133 +++++
tests/testthat/test.tbind.R | 8 +
tests/testthat/test.treePlot.R | 42 ++
tests/testthat/test.treestruc.R | 30 +
tests/testthat/test.treewalk.R | 275 +++++++++
vignettes/auto/developer.el | 19 +
vignettes/auto/phylobase.el | 21 +
vignettes/phylobase.Rnw | 674 ++++++++++++++++++++++
146 files changed, 18898 insertions(+)
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