[med-svn] [r-cran-ape] branch master updated (357a914 -> 598fe7f)

[Dylan Aïssi]

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

      from  357a914   Upload to unstable
       new  c682bf5   Imported Upstream version 3.3
       new  598fe7f   Merge tag 'upstream/3.3'

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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(-)
 create mode 100644 R/binaryPGLMM.R
 create mode 100644 R/corphylo.R
 create mode 100644 man/binaryPGLMM.Rd
 create mode 100644 man/corphylo.Rd

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