[med-svn] [r-cran-ape] branch upstream updated (6ea6592 -> 3b7b29e)

[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  6ea6592   Imported Upstream version 3.5
       new  3b7b29e   Imported Upstream version 4.0

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                |  14 +-
 MD5                        | 126 +++++++-------
 NAMESPACE                  |  39 ++++-
 R/CDF.birth.death.R        |   6 +-
 R/DNA.R                    | 202 ++++++++++++++++------
 R/MPR.R                    |   2 +-
 R/SDM.R                    |   2 +-
 R/SlowinskiGuyer.R         |  25 +--
 R/ace.R                    |   6 +-
 R/as.phylo.R               |   2 +-
 R/checkValidPhylo.R        |   9 +-
 R/chronoMPL.R              |   2 +-
 R/clustal.R                |  35 +++-
 R/coalescent.intervals.R   |   2 +-
 R/dist.topo.R              | 124 +++++++------
 R/is.binary.tree.R         |  37 ++--
 R/is.ultrametric.R         |  45 +++--
 R/ltt.plot.R               |   6 +-
 R/makeLabel.R              |   6 +-
 R/multi2di.R               |  54 +++++-
 R/node.dating.R            | 277 +++++++++++++++++++++++++++++
 R/pic.R                    |   2 +-
 R/plot.phylo.R             |  29 +++-
 R/plot.phyloExtra.R        |  32 +++-
 R/read.GenBank.R           |  80 ++++-----
 R/read.dna.R               |  16 +-
 R/read.gff.R               |  22 +++
 R/reconstruct.R            | 421 ++++++++++++++++++++++++++++++++++++++-------
 R/reorder.phylo.R          |  37 +++-
 R/root.R                   | 103 ++++++++---
 R/rtt.R                    |  16 +-
 R/summary.phylo.R          | 116 ++++++++++---
 R/write.dna.R              |   2 +-
 R/yule.R                   |   2 +-
 build/vignette.rds         | Bin 192 -> 194 bytes
 data/hivtree.newick.rda    | Bin 2189 -> 2190 bytes
 data/landplants.newick.rda | Bin 575 -> 0 bytes
 data/opsin.newick.rda      | Bin 445 -> 0 bytes
 inst/doc/MoranI.pdf        | Bin 238263 -> 238589 bytes
 man/AAbin.Rd               |   3 +-
 man/all.equal.DNAbin.Rd    |  65 +++++++
 man/alview.Rd              |   2 +-
 man/ape-internal.Rd        |   6 +
 man/ape-package.Rd         |   4 +
 man/boot.phylo.Rd          |   9 +-
 man/c.phylo.Rd             |  23 +--
 man/checkAlignment.Rd      |   2 +-
 man/clustal.Rd             |  31 +++-
 man/dist.topo.Rd           |  21 ++-
 man/image.DNAbin.Rd        |   5 +-
 man/is.binary.tree.Rd      |  40 +++--
 man/is.ultrametric.Rd      |  39 +++--
 man/landplants.Rd          |  36 ----
 man/mixedFontLabel.Rd      |   2 +-
 man/multi2di.Rd            |  25 ++-
 man/node.dating.Rd         | 107 ++++++++++++
 man/opsin.Rd               |  35 ----
 man/plot.phyloExtra.Rd     |   2 +-
 man/plotTreeTime.Rd        |  44 +++++
 man/read.GenBank.Rd        |  62 +++----
 man/read.dna.Rd            |   4 +-
 man/read.gff.Rd            |  46 +++++
 man/reconstruct.Rd         |  85 ++++++---
 man/reorder.phylo.Rd       |   8 +-
 man/root.Rd                |  64 +++++--
 man/summary.phylo.Rd       |  20 ++-
 src/ape.c                  |   8 +-
 src/dist_dna.c             | 126 +++++++++-----
 src/read_dna.c             |  26 +--
 69 files changed, 2121 insertions(+), 728 deletions(-)
 create mode 100644 R/node.dating.R
 create mode 100644 R/read.gff.R
 delete mode 100644 data/landplants.newick.rda
 delete mode 100644 data/opsin.newick.rda
 create mode 100644 man/all.equal.DNAbin.Rd
 delete mode 100644 man/landplants.Rd
 create mode 100644 man/node.dating.Rd
 delete mode 100644 man/opsin.Rd
 create mode 100644 man/plotTreeTime.Rd
 create mode 100644 man/read.gff.Rd

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