[med-svn] [r-cran-ape] branch master updated (e1e2c07 -> f597f63)

[Dylan Aïssi]

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

      from  e1e2c07   Upload to unstable
       new  2685aff   Imported Upstream version 3.2
       new  bc9fbeb   Merge tag 'upstream/3.2'
       new  a142791   Bump Policy to 3.9.6
       new  f597f63   Updated changelog

The 4 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                |  18 ++--
 MD5                        |  70 +++++++------
 NAMESPACE                  |   4 +
 R/DNA.R                    |  27 ++++-
 R/ace.R                    |   2 +-
 R/def.R                    |  23 +++++
 R/dist.topo.R              |   1 -
 R/is.ultrametric.R         |   2 +-
 R/multi2di.R               |  16 +--
 R/nodepath.R               |  60 ++++++++++++
 R/phymltest.R              |   4 +-
 R/plot.phylo.R             |   4 +-
 R/read.nexus.R             |   8 +-
 R/read.tree.R              |   2 +-
 R/reconstruct.R            | 240 +++++++++++++++++++++++++++++++++++++++++++++
 R/rtt.R                    |   6 +-
 R/scales.R                 |  42 ++++----
 R/vcv.phylo.R              |   2 +-
 R/vcv2phylo.R              | 135 +++++++++++++++++++++++++
 R/write.nexus.data.R       | 176 ++++++++++++++-------------------
 build/vignette.rds         | Bin 192 -> 194 bytes
 data/hivtree.newick.rda    | Bin 2189 -> 2190 bytes
 data/landplants.newick.rda | Bin 575 -> 576 bytes
 data/opsin.newick.rda      | Bin 445 -> 446 bytes
 debian/changelog           |   7 ++
 debian/control             |   4 +-
 inst/doc/MoranI.pdf        | Bin 256526 -> 237986 bytes
 man/all.equal.phylo.Rd     |   4 +-
 man/ape-internal.Rd        |   6 ++
 man/as.alignment.Rd        |  32 +++++-
 man/axisPhylo.Rd           |   8 +-
 man/compar.lynch.Rd        |   2 +-
 man/corClasses.Rd          |   3 +-
 man/def.Rd                 |  63 ++++++++++++
 man/diversi.gof.Rd         |   6 +-
 man/mst.Rd                 |   2 +-
 man/nodepath.Rd            |  31 ++++++
 man/plot.phylo.Rd          |   1 +
 man/reconstruct.Rd         |  81 +++++++++++++++
 man/vcv.phylo.Rd           |   2 +-
 man/vcv2phylo.Rd           |  35 +++++++
 man/write.nexus.data.Rd    |  29 +++---
 42 files changed, 943 insertions(+), 215 deletions(-)
 create mode 100644 R/def.R
 create mode 100644 R/nodepath.R
 create mode 100644 R/reconstruct.R
 create mode 100644 R/vcv2phylo.R
 create mode 100644 man/def.Rd
 create mode 100644 man/nodepath.Rd
 create mode 100644 man/reconstruct.Rd
 create mode 100644 man/vcv2phylo.Rd

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