[med-svn] [r-cran-ape] 02/04: Merge tag 'upstream/3.2'

[Dylan Aïssi]

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

commit bc9fbeb23c4f94d41c2690612718e62f1b0c9731
Merge: e1e2c07 2685aff
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Mon Dec 8 19:09:18 2014 +0100

    Merge tag 'upstream/3.2'
    
    Upstream version 3.2

 DESCRIPTION                |  18 ++--
 MD5                        |  70 +++++++------
 NAMESPACE                  |   4 +
 R/DNA.R                    |  27 ++++-
 R/ace.R                    |   2 +-
 R/def.R                    |  23 +++++
 R/dist.topo.R              |   1 -
 R/is.ultrametric.R         |   2 +-
 R/multi2di.R               |  16 +--
 R/nodepath.R               |  60 ++++++++++++
 R/phymltest.R              |   4 +-
 R/plot.phylo.R             |   4 +-
 R/read.nexus.R             |   8 +-
 R/read.tree.R              |   2 +-
 R/reconstruct.R            | 240 +++++++++++++++++++++++++++++++++++++++++++++
 R/rtt.R                    |   6 +-
 R/scales.R                 |  42 ++++----
 R/vcv.phylo.R              |   2 +-
 R/vcv2phylo.R              | 135 +++++++++++++++++++++++++
 R/write.nexus.data.R       | 176 ++++++++++++++-------------------
 build/vignette.rds         | Bin 192 -> 194 bytes
 data/hivtree.newick.rda    | Bin 2189 -> 2190 bytes
 data/landplants.newick.rda | Bin 575 -> 576 bytes
 data/opsin.newick.rda      | Bin 445 -> 446 bytes
 inst/doc/MoranI.pdf        | Bin 256526 -> 237986 bytes
 man/all.equal.phylo.Rd     |   4 +-
 man/ape-internal.Rd        |   6 ++
 man/as.alignment.Rd        |  32 +++++-
 man/axisPhylo.Rd           |   8 +-
 man/compar.lynch.Rd        |   2 +-
 man/corClasses.Rd          |   3 +-
 man/def.Rd                 |  63 ++++++++++++
 man/diversi.gof.Rd         |   6 +-
 man/mst.Rd                 |   2 +-
 man/nodepath.Rd            |  31 ++++++
 man/plot.phylo.Rd          |   1 +
 man/reconstruct.Rd         |  81 +++++++++++++++
 man/vcv.phylo.Rd           |   2 +-
 man/vcv2phylo.Rd           |  35 +++++++
 man/write.nexus.data.Rd    |  29 +++---
 40 files changed, 934 insertions(+), 213 deletions(-)

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