[med-svn] [r-cran-ape] 06/06: Merge tag 'upstream/5.0'

[Dylan Aïssi]

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

commit 08bfd4bad63c0a6b1077c68c1c4682b27cdda473
Merge: 56c54b3 8db8fce
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Thu Nov 2 23:16:51 2017 +0100

    Merge tag 'upstream/5.0'
    
    Upstream version 5.0

 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(-)

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