[med-svn] [r-cran-ape] 03/05: Merge tag 'upstream/3.5'

[Dylan Aïssi]

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

commit 656ee99c15d5c4d26d79958e61434087b04c7083
Merge: 5cd32f5 6ea6592
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Fri Jun 3 00:10:14 2016 +0200

    Merge tag 'upstream/3.5'
    
    Upstream version 3.5

 DESCRIPTION                    |   8 +-
 MD5                            |  77 ++++-----
 NAMESPACE                      |   8 +
 R/DNA.R                        | 346 +++++++++++++++++++++++++++++++++++++++--
 R/clustal.R                    |  27 +++-
 R/dist.topo.R                  |  89 +++++------
 R/plot.phylo.R                 |  20 ++-
 R/plot.phyloExtra.R            |  30 ++++
 R/read.nexus.R                 |   2 +-
 R/root.R                       |  29 ++--
 build/vignette.rds             | Bin 194 -> 192 bytes
 data/hivtree.newick.rda        | Bin 2190 -> 2189 bytes
 data/landplants.newick.rda     | Bin 576 -> 575 bytes
 data/opsin.newick.rda          | Bin 446 -> 445 bytes
 inst/doc/MoranI.Rnw            |   2 +-
 inst/doc/MoranI.pdf            | Bin 238529 -> 238263 bytes
 man/AAbin.Rd                   | 101 ++++++++++++
 man/DNAbin.Rd                  |   2 +-
 man/DNAbin2indel.Rd            |   3 +-
 man/LTT.Rd                     |   3 +-
 man/additive.Rd                |   1 -
 man/all.equal.phylo.Rd         |   2 +-
 man/alview.Rd                  |  12 +-
 man/ape-internal.Rd            |   1 +
 man/boot.phylo.Rd              |  48 +++++-
 man/checkAlignment.Rd          |  42 +++++
 man/clustal.Rd                 |   2 +-
 man/def.Rd                     |   2 +-
 man/del.gaps.Rd                |  29 ++--
 man/dist.dna.Rd                |   6 +
 man/diversity.contrast.test.Rd |   2 +-
 man/image.DNAbin.Rd            |   3 +-
 man/makeNodeLabel.Rd           |   2 +-
 man/mcmc.popsize.Rd            |   8 +-
 man/plot.phyloExtra.Rd         |  56 +++++++
 man/read.GenBank.Rd            |   2 +-
 man/root.Rd                    |   2 +-
 man/trans.Rd                   |  52 +++++++
 man/write.nexus.data.Rd        |   4 +-
 src/ape.c                      |   6 +-
 src/dist_dna.c                 | 218 +++++++++++++++++++++++++-
 vignettes/MoranI.Rnw           |   2 +-
 42 files changed, 1074 insertions(+), 175 deletions(-)

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