[med-svn] [r-cran-ape] branch upstream updated (4ef917e -> 8db8fce)

[Dylan Aïssi]

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a change to branch upstream
in repository r-cran-ape.

      from  4ef917e   Imported Upstream version 4.1
       new  8db8fce   New upstream version 5.0

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               |  15 +-
 MD5                       | 156 ++++++++++---------
 NAMESPACE                 |  11 +-
 R/CADM.global.R           |   1 +
 R/CADM.post.R             |   3 +-
 R/CDF.birth.death.R       |   7 +-
 R/DNA.R                   | 104 +++++++++++--
 R/PGLS.R                  |  12 +-
 R/RcppExports.R           |  15 ++
 R/ace.R                   |  10 +-
 R/alex.R                  |   5 +-
 R/apetools.R              | 103 ++++++++++++-
 R/as.phylo.R              |  14 +-
 R/biplot.pcoa.R           |  44 ++++--
 R/chronoMPL.R             |   8 +-
 R/collapse.singles.R      |  42 +++--
 R/dist.topo.R             |  87 +++++++----
 R/drop.tip.R              |  20 +--
 R/evonet.R                | 122 ++++++++++++++-
 R/is.compatible.R         |   4 +-
 R/ladderize.R             |   8 +-
 R/makeLabel.R             |   4 +-
 R/mrca.R                  |  47 +++---
 R/nodelabels.R            |  27 +++-
 R/pcoa.R                  |   4 +
 R/phydataplot.R           |  24 +--
 R/pic.R                   |  12 +-
 R/plot.phylo.R            | 132 ++++++++--------
 R/plotPhyloCoor.R         |  97 +++---------
 R/read.nexus.R            | 237 +++++++++++++++++-----------
 R/read.tree.R             | 333 ++++++++++++++++++++++++----------------
 R/reorder.phylo.R         |  24 ++-
 R/subtreeplot.R           |   9 +-
 R/which.edge.R            |  65 ++++++--
 R/write.nexus.R           |   4 +-
 R/write.tree.R            |  13 +-
 build/vignette.rds        | Bin 194 -> 194 bytes
 data/hivtree.newick.rda   | Bin 2190 -> 2189 bytes
 inst/doc/MoranI.Rnw       |  28 ++--
 inst/doc/MoranI.pdf       | Bin 238354 -> 238497 bytes
 man/AAbin.Rd              |  28 +++-
 man/LTT.Rd                |   3 +-
 man/add.scale.bar.Rd      |   2 +-
 man/ape-internal.Rd       |  15 +-
 man/ape-package.Rd        |  11 +-
 man/apetools.Rd           |   6 +
 man/boot.phylo.Rd         |   4 +-
 man/carnivora.Rd          |  19 +--
 man/checkAlignment.Rd     |   1 +
 man/chiroptera.Rd         |   2 +-
 man/chronoMPL.Rd          |   1 +
 man/collapse.singles.Rd   |  17 +-
 man/dist.topo.Rd          |   3 +-
 man/drop.tip.Rd           |  10 +-
 man/evonet.Rd             |  49 +++++-
 man/image.DNAbin.Rd       |  16 +-
 man/mrca.Rd               |   5 +-
 man/multi2di.Rd           |   2 +-
 man/nodelabels.Rd         |   5 +-
 man/pcoa.Rd               |   7 +-
 man/phydataplot.Rd        |  11 +-
 man/plot.phylo.Rd         |   2 +-
 man/rTraitCont.Rd         |   4 +-
 man/read.tree.Rd          |  21 ++-
 man/reorder.phylo.Rd      |  26 +++-
 man/richness.yule.test.Rd |   2 +-
 man/rtree.Rd              |   3 +-
 man/speciesTree.Rd        |  17 +-
 man/trans.Rd              |   2 +-
 man/write.nexus.Rd        |   3 +
 man/write.tree.Rd         |   6 +
 src/RcppExports.cpp       |  45 ++++++
 src/ape.c                 |  32 ++--
 src/bipartition.c         | 276 ++++++++++++++++-----------------
 src/dist_dna.c            |   5 +-
 src/pic.c                 |   6 +-
 src/plot_phylo.c          |  17 +-
 src/prop_part.cpp         |  82 ++++++++++
 src/reorder_Rcpp.cpp      |  93 +++++++++++
 src/tree_build.c          | 384 +++++++++++++++++++++++++++++++++++++++++-----
 vignettes/MoranI.Rnw      |  28 ++--
 81 files changed, 2176 insertions(+), 946 deletions(-)
 create mode 100644 R/RcppExports.R
 create mode 100644 src/RcppExports.cpp
 create mode 100644 src/prop_part.cpp
 create mode 100644 src/reorder_Rcpp.cpp

-- 
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