[med-svn] [r-cran-ape] 02/02: Merge tag 'upstream/3.3'

[Dylan Aïssi]

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

commit 598fe7f2f427c37ccdab558243aab3091a21601b
Merge: 357a914 c682bf5
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Thu Jun 18 19:14:38 2015 +0200

    Merge tag 'upstream/3.3'
    
    Upstream version 3.3

 DESCRIPTION                 |  14 +-
 MD5                         |  98 ++++++------
 NAMESPACE                   |   5 +
 R/CDF.birth.death.R         | 174 +++++++++++++++++++++-
 R/DNA.R                     |  29 ++--
 R/PGLS.R                    |   7 +-
 R/ace.R                     |  14 +-
 R/as.bitsplits.R            |  10 +-
 R/as.phylo.R                |   7 +-
 R/binaryPGLMM.R             | 293 ++++++++++++++++++++++++++++++++++++
 R/compar.gee.R              |   7 +-
 R/corphylo.R                | 355 ++++++++++++++++++++++++++++++++++++++++++++
 R/dbd.R                     |   9 +-
 R/dist.topo.R               |  72 +++++----
 R/parafit.R                 |   6 +-
 R/plot.phylo.R              |  38 +++--
 R/read.tree.R               |   8 +-
 R/root.R                    |   8 +-
 R/write.nexus.R             |  15 +-
 R/write.nexus.data.R        |   6 +-
 build/vignette.rds          | Bin 194 -> 192 bytes
 data/hivtree.newick.rda     | Bin 2190 -> 2189 bytes
 data/landplants.newick.rda  | Bin 576 -> 574 bytes
 data/opsin.newick.rda       | Bin 446 -> 444 bytes
 inst/doc/MoranI.pdf         | Bin 237986 -> 238306 bytes
 man/DNAbin.Rd               |   2 +-
 man/LTT.Rd                  |   6 +-
 man/MoranI.Rd               |   4 +-
 man/ace.Rd                  |  14 +-
 man/as.bitsplits.Rd         |   8 +-
 man/binaryPGLMM.Rd          | 268 +++++++++++++++++++++++++++++++++
 man/boot.phylo.Rd           |   3 +-
 man/coalescent.intervals.Rd |   7 +-
 man/collapsed.intervals.Rd  |  13 +-
 man/corphylo.Rd             | 224 ++++++++++++++++++++++++++++
 man/def.Rd                  |   2 +-
 man/del.gaps.Rd             |  32 ++--
 man/dist.topo.Rd            |  18 ++-
 man/is.binary.tree.Rd       |   2 +-
 man/landplants.Rd           |   3 +-
 man/node.depth.Rd           |  10 +-
 man/read.dna.Rd             |   6 +-
 man/read.tree.Rd            |   2 +-
 man/rlineage.Rd             |  53 +++++--
 man/root.Rd                 |  11 ++
 man/seg.sites.Rd            |   5 -
 man/skyline.Rd              |  42 ++----
 man/skylineplot.Rd          |  34 +----
 man/where.Rd                |   3 +-
 man/woodmouse.Rd            |   3 +-
 man/write.dna.Rd            |   6 +-
 src/dist_dna.c              |  24 ++-
 52 files changed, 1653 insertions(+), 327 deletions(-)

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