[med-svn] [r-cran-ape] 02/02: Merge tag 'upstream/3.4'

[Dylan Aïssi]

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

commit 09deb2346f7e3aad59e7e7b5e66bd408b521b0cb
Merge: ef8a147 f30a567
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Sat Dec 5 22:57:37 2015 +0100

    Merge tag 'upstream/3.4'
    
    Upstream version 3.4

 DESCRIPTION                |  11 +-
 MD5                        |  81 +++++++------
 NAMESPACE                  |  23 +++-
 R/CDF.birth.death.R        |  11 +-
 R/DNA.R                    |  34 +++++-
 R/as.phylo.R               |  33 +++---
 R/balance.R                |   6 +-
 R/checkValidPhylo.R        |  93 +++++++++++++++
 R/clustal.R                |  33 +++++-
 R/collapse.singles.R       | 101 +++++++++-------
 R/drop.tip.R               |  11 +-
 R/ladderize.R              |   5 +-
 R/makeLabel.R              |  44 ++++++-
 R/nodelabels.R             |  28 +++--
 R/parafit.R                |   1 +
 R/phydataplot.R            |  89 ++++++++++++--
 R/plot.phylo.R             | 106 ++++++++++-------
 R/reorder.phylo.R          |   8 +-
 R/root.R                   | 287 ++++++++++++++++-----------------------------
 R/rtt.R                    |  82 ++++++-------
 build/vignette.rds         | Bin 192 -> 194 bytes
 data/hivtree.newick.rda    | Bin 2189 -> 2190 bytes
 data/landplants.newick.rda | Bin 574 -> 576 bytes
 data/opsin.newick.rda      | Bin 444 -> 446 bytes
 inst/doc/MoranI.pdf        | Bin 238306 -> 238529 bytes
 man/DNAbin2indel.Rd        |  28 +++++
 man/LTT.Rd                 |   3 +
 man/alex.Rd                |   2 +-
 man/alview.Rd              |  32 +++++
 man/ape-internal.Rd        |   1 +
 man/as.phylo.Rd            |  10 +-
 man/checkValidPhylo.Rd     |  29 +++++
 man/clustal.Rd             |  20 +++-
 man/collapse.singles.Rd    |  36 +++++-
 man/image.DNAbin.Rd        |   2 +-
 man/label2table.Rd         |  47 ++++++++
 man/makeLabel.Rd           |   2 +-
 man/makeNodeLabel.Rd       |   2 +-
 man/mixedFontLabel.Rd      |   2 +-
 man/phydataplot.Rd         |  70 ++++++++++-
 man/plot.phylo.Rd          |  11 +-
 man/rlineage.Rd            |   1 +
 src/ape.c                  |   6 +-
 src/dist_dna.c             | 149 ++++++++++++++---------
 44 files changed, 1035 insertions(+), 505 deletions(-)

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