[med-svn] [r-cran-ape] branch master updated (d1f27eb -> f479dbe)

[Dylan Aïssi]

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

      from  d1f27eb   Upload to unstable
       new  5cd32f5   Remove unnecessary comments in debian/rules
       new  6ea6592   Imported Upstream version 3.5
       new  656ee99   Merge tag 'upstream/3.5'
       new  19297fc   Fix vcs-field-uses-insecure-uri
       new  f479dbe   Bump Standards-Version: 3.9.8

The 5 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
 debian/control                 |   8 +-
 debian/rules                   |   2 -
 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 +-
 44 files changed, 1078 insertions(+), 181 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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