[med-svn] [r-cran-ape] 02/03: Merge tag 'upstream/3.1-2'

[Dylan Aïssi]

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

commit 9ad91d1ad224cd91a843c581f402b55457b84748
Merge: f51147b 8ab7815
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Tue May 27 19:16:15 2014 +0200

    Merge tag 'upstream/3.1-2'
    
    Upstream version 3.1-2

 COPYING                    | 340 +++++++++++++++++++++++++++++++++++++++++++++
 DESCRIPTION                |   8 +-
 MD5                        |  43 +++---
 NEWS                       |  46 ++++++
 R/CDF.birth.death.R        |   4 +-
 R/DNA.R                    |   6 +-
 R/SlowinskiGuyer.R         |   1 -
 R/ace.R                    |  44 ++++--
 R/all.equal.phylo.R        |  12 +-
 R/chronos.R                |  11 +-
 R/cophyloplot.R            |  26 ++--
 R/dist.topo.R              |   4 +-
 R/plot.phylo.R             | 194 +++++++++++++++-----------
 R/read.GenBank.R           |   6 +-
 R/read.nexus.R             |  42 +++---
 build/vignette.rds         | Bin 192 -> 192 bytes
 data/hivtree.newick.rda    | Bin 2189 -> 2189 bytes
 data/landplants.newick.rda | Bin 574 -> 575 bytes
 data/opsin.newick.rda      | Bin 445 -> 445 bytes
 inst/doc/MoranI.pdf        | Bin 126448 -> 256525 bytes
 man/ace.Rd                 |  39 +++++-
 man/plot.phylo.Rd          |  17 +--
 src/bionjs.c               |  21 ++-
 23 files changed, 676 insertions(+), 188 deletions(-)

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