[med-svn] [r-cran-ape] 02/03: Merge tag 'upstream/4.0'

[Dylan Aïssi]

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

commit 485ea020c1252688a1f81d71a4893ee82b689f54
Merge: bd01c59 3b7b29e
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Sat Dec 3 22:57:07 2016 +0100

    Merge tag 'upstream/4.0'
    
    Upstream version 4.0

 DESCRIPTION                |  14 +-
 MD5                        | 126 +++++++-------
 NAMESPACE                  |  39 ++++-
 R/CDF.birth.death.R        |   6 +-
 R/DNA.R                    | 202 ++++++++++++++++------
 R/MPR.R                    |   2 +-
 R/SDM.R                    |   2 +-
 R/SlowinskiGuyer.R         |  25 +--
 R/ace.R                    |   6 +-
 R/as.phylo.R               |   2 +-
 R/checkValidPhylo.R        |   9 +-
 R/chronoMPL.R              |   2 +-
 R/clustal.R                |  35 +++-
 R/coalescent.intervals.R   |   2 +-
 R/dist.topo.R              | 124 +++++++------
 R/is.binary.tree.R         |  37 ++--
 R/is.ultrametric.R         |  45 +++--
 R/ltt.plot.R               |   6 +-
 R/makeLabel.R              |   6 +-
 R/multi2di.R               |  54 +++++-
 R/node.dating.R            | 277 +++++++++++++++++++++++++++++
 R/pic.R                    |   2 +-
 R/plot.phylo.R             |  29 +++-
 R/plot.phyloExtra.R        |  32 +++-
 R/read.GenBank.R           |  80 ++++-----
 R/read.dna.R               |  16 +-
 R/read.gff.R               |  22 +++
 R/reconstruct.R            | 421 ++++++++++++++++++++++++++++++++++++++-------
 R/reorder.phylo.R          |  37 +++-
 R/root.R                   | 103 ++++++++---
 R/rtt.R                    |  16 +-
 R/summary.phylo.R          | 116 ++++++++++---
 R/write.dna.R              |   2 +-
 R/yule.R                   |   2 +-
 build/vignette.rds         | Bin 192 -> 194 bytes
 data/hivtree.newick.rda    | Bin 2189 -> 2190 bytes
 data/landplants.newick.rda | Bin 575 -> 0 bytes
 data/opsin.newick.rda      | Bin 445 -> 0 bytes
 inst/doc/MoranI.pdf        | Bin 238263 -> 238589 bytes
 man/AAbin.Rd               |   3 +-
 man/all.equal.DNAbin.Rd    |  65 +++++++
 man/alview.Rd              |   2 +-
 man/ape-internal.Rd        |   6 +
 man/ape-package.Rd         |   4 +
 man/boot.phylo.Rd          |   9 +-
 man/c.phylo.Rd             |  23 +--
 man/checkAlignment.Rd      |   2 +-
 man/clustal.Rd             |  31 +++-
 man/dist.topo.Rd           |  21 ++-
 man/image.DNAbin.Rd        |   5 +-
 man/is.binary.tree.Rd      |  40 +++--
 man/is.ultrametric.Rd      |  39 +++--
 man/landplants.Rd          |  36 ----
 man/mixedFontLabel.Rd      |   2 +-
 man/multi2di.Rd            |  25 ++-
 man/node.dating.Rd         | 107 ++++++++++++
 man/opsin.Rd               |  35 ----
 man/plot.phyloExtra.Rd     |   2 +-
 man/plotTreeTime.Rd        |  44 +++++
 man/read.GenBank.Rd        |  62 +++----
 man/read.dna.Rd            |   4 +-
 man/read.gff.Rd            |  46 +++++
 man/reconstruct.Rd         |  85 ++++++---
 man/reorder.phylo.Rd       |   8 +-
 man/root.Rd                |  64 +++++--
 man/summary.phylo.Rd       |  20 ++-
 src/ape.c                  |   8 +-
 src/dist_dna.c             | 126 +++++++++-----
 src/read_dna.c             |  26 +--
 69 files changed, 2121 insertions(+), 728 deletions(-)

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