[med-svn] [r-cran-ape] branch upstream updated (c682bf5 -> f30a567)

[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  c682bf5   Imported Upstream version 3.3
       new  f30a567   Imported Upstream version 3.4

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                |  11 +-
 MD5                        |  81 +++++++------
 NAMESPACE                  |  23 +++-
 R/CDF.birth.death.R        |  11 +-
 R/DNA.R                    |  34 +++++-
 R/as.phylo.R               |  33 +++---
 R/balance.R                |   6 +-
 R/checkValidPhylo.R        |  93 +++++++++++++++
 R/clustal.R                |  33 +++++-
 R/collapse.singles.R       | 101 +++++++++-------
 R/drop.tip.R               |  11 +-
 R/ladderize.R              |   5 +-
 R/makeLabel.R              |  44 ++++++-
 R/nodelabels.R             |  28 +++--
 R/parafit.R                |   1 +
 R/phydataplot.R            |  89 ++++++++++++--
 R/plot.phylo.R             | 106 ++++++++++-------
 R/reorder.phylo.R          |   8 +-
 R/root.R                   | 287 ++++++++++++++++-----------------------------
 R/rtt.R                    |  82 ++++++-------
 build/vignette.rds         | Bin 192 -> 194 bytes
 data/hivtree.newick.rda    | Bin 2189 -> 2190 bytes
 data/landplants.newick.rda | Bin 574 -> 576 bytes
 data/opsin.newick.rda      | Bin 444 -> 446 bytes
 inst/doc/MoranI.pdf        | Bin 238306 -> 238529 bytes
 man/DNAbin2indel.Rd        |  28 +++++
 man/LTT.Rd                 |   3 +
 man/alex.Rd                |   2 +-
 man/alview.Rd              |  32 +++++
 man/ape-internal.Rd        |   1 +
 man/as.phylo.Rd            |  10 +-
 man/checkValidPhylo.Rd     |  29 +++++
 man/clustal.Rd             |  20 +++-
 man/collapse.singles.Rd    |  36 +++++-
 man/image.DNAbin.Rd        |   2 +-
 man/label2table.Rd         |  47 ++++++++
 man/makeLabel.Rd           |   2 +-
 man/makeNodeLabel.Rd       |   2 +-
 man/mixedFontLabel.Rd      |   2 +-
 man/phydataplot.Rd         |  70 ++++++++++-
 man/plot.phylo.Rd          |  11 +-
 man/rlineage.Rd            |   1 +
 src/ape.c                  |   6 +-
 src/dist_dna.c             | 149 ++++++++++++++---------
 44 files changed, 1035 insertions(+), 505 deletions(-)
 create mode 100644 R/checkValidPhylo.R
 create mode 100644 man/DNAbin2indel.Rd
 create mode 100644 man/alview.Rd
 create mode 100644 man/checkValidPhylo.Rd
 create mode 100644 man/label2table.Rd

-- 
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