[med-svn] [r-cran-ape] branch upstream updated (3b7b29e -> 4ef917e)

[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  3b7b29e   Imported Upstream version 4.0
       new  4ef917e   Imported Upstream version 4.1

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          |  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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