[med-svn] [r-cran-ape] branch master updated (e6f81fc -> 08bfd4b)

[Dylan Aïssi]

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

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

      from  e6f81fc   Add OMICtools ref
       new  85c3396   d/upstream/metadata: Add references to registries
       new  75c3cf3   cme fix dpkg-control
       new  78a3334   Remove trailing whitespace characters in d/changelog
       new  56c54b3   Bump Standards-Version: 4.1.1 (no changes needed)
       new  8db8fce   New upstream version 5.0
       new  08bfd4b   Merge tag 'upstream/5.0'

The 6 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
 debian/changelog          |   9 +-
 debian/control            |  30 ++--
 debian/upstream/metadata  |   6 +-
 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 ++--
 84 files changed, 2203 insertions(+), 964 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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