[med-svn] [r-cran-ape] branch upstream updated (f30a567 -> 6ea6592)

[Dylan Aïssi]

This is an automated email from the git hooks/post-receive script.

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

      from  f30a567   Imported Upstream version 3.4
       new  6ea6592   Imported Upstream version 3.5

The 1 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                    |   8 +-
 MD5                            |  77 ++++-----
 NAMESPACE                      |   8 +
 R/DNA.R                        | 346 +++++++++++++++++++++++++++++++++++++++--
 R/clustal.R                    |  27 +++-
 R/dist.topo.R                  |  89 +++++------
 R/plot.phylo.R                 |  20 ++-
 R/plot.phyloExtra.R            |  30 ++++
 R/read.nexus.R                 |   2 +-
 R/root.R                       |  29 ++--
 build/vignette.rds             | Bin 194 -> 192 bytes
 data/hivtree.newick.rda        | Bin 2190 -> 2189 bytes
 data/landplants.newick.rda     | Bin 576 -> 575 bytes
 data/opsin.newick.rda          | Bin 446 -> 445 bytes
 inst/doc/MoranI.Rnw            |   2 +-
 inst/doc/MoranI.pdf            | Bin 238529 -> 238263 bytes
 man/AAbin.Rd                   | 101 ++++++++++++
 man/DNAbin.Rd                  |   2 +-
 man/DNAbin2indel.Rd            |   3 +-
 man/LTT.Rd                     |   3 +-
 man/additive.Rd                |   1 -
 man/all.equal.phylo.Rd         |   2 +-
 man/alview.Rd                  |  12 +-
 man/ape-internal.Rd            |   1 +
 man/boot.phylo.Rd              |  48 +++++-
 man/checkAlignment.Rd          |  42 +++++
 man/clustal.Rd                 |   2 +-
 man/def.Rd                     |   2 +-
 man/del.gaps.Rd                |  29 ++--
 man/dist.dna.Rd                |   6 +
 man/diversity.contrast.test.Rd |   2 +-
 man/image.DNAbin.Rd            |   3 +-
 man/makeNodeLabel.Rd           |   2 +-
 man/mcmc.popsize.Rd            |   8 +-
 man/plot.phyloExtra.Rd         |  56 +++++++
 man/read.GenBank.Rd            |   2 +-
 man/root.Rd                    |   2 +-
 man/trans.Rd                   |  52 +++++++
 man/write.nexus.data.Rd        |   4 +-
 src/ape.c                      |   6 +-
 src/dist_dna.c                 | 218 +++++++++++++++++++++++++-
 vignettes/MoranI.Rnw           |   2 +-
 42 files changed, 1074 insertions(+), 175 deletions(-)
 create mode 100644 R/plot.phyloExtra.R
 create mode 100644 man/AAbin.Rd
 create mode 100644 man/checkAlignment.Rd
 create mode 100644 man/plot.phyloExtra.Rd
 create mode 100644 man/trans.Rd

-- 
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