[med-svn] [r-cran-ape] branch master updated (badaf97 -> b91b106)

[Dylan Aïssi]

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

      from  badaf97   Upload to unstable
       new  4ef917e   Imported Upstream version 4.1
       new  b91b106   Merge tag 'upstream/4.1'

The 2 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          |  12 +--
 MD5                  |  40 ++++-----
 NAMESPACE            |   2 +-
 R/DNA.R              |  47 ++++++-----
 R/apetools.R         |  83 ++++++++++++++++++
 R/chronos.R          |   7 +-
 R/drop.tip.R         |  83 ++++++------------
 R/multi2di.R         |   6 +-
 R/nj.R               |   6 +-
 R/node.dating.R      | 232 ++++++++++++++++++++++++++++++---------------------
 R/read.GenBank.R     |  11 ++-
 R/read.dna.R         |  49 +++++++++--
 R/read.nexus.R       |   8 +-
 inst/doc/MoranI.pdf  | Bin 238589 -> 238354 bytes
 man/apetools.Rd      |  47 +++++++++++
 man/as.bitsplits.Rd  |   2 +-
 man/c.phylo.Rd       |   2 +-
 man/is.compatible.Rd |   1 +
 man/node.dating.Rd   |  15 ++--
 man/read.dna.Rd      | 111 ++++++++++++++++++------
 man/read.nexus.Rd    |  10 ++-
 src/read_dna.c       |  11 ++-
 22 files changed, 524 insertions(+), 261 deletions(-)
 create mode 100644 R/apetools.R
 create mode 100644 man/apetools.Rd

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