[med-svn] [r-cran-phangorn] branch upstream updated (fb6f81b -> 6c56854)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository r-cran-phangorn.

      from  fb6f81b   Imported Upstream version 2.0.4
       new  6c56854   New upstream version 2.1.1

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                                |   22 +-
 MD5                                        |  124 ++--
 NAMESPACE                                  |   26 +-
 NEWS                                       |   36 +
 R/Densi.R                                  |  231 ------
 R/RcppExports.R                            |   11 +
 R/ancestral_pml.R                          |   32 +-
 R/bootstrap.R                              |   55 +-
 R/distSeq.R                                |   97 +--
 R/distTree.R                               |  104 ++-
 R/fitch.R                                  |    3 +-
 R/networx.R                                |  120 +++-
 R/parsimony.R                              |   46 +-
 R/phyDat.R                                 |  388 ++++++-----
 R/phylo.R                                  |   36 +-
 R/sankoff.R                                |    2 -
 R/simSeq.R                                 |   17 +-
 R/superTree.R                              |  135 ++++
 R/treeManipulation.R                       |   65 +-
 R/treedist.R                               |  154 +++-
 R/zzz.R                                    |    5 +
 README.md                                  |    6 +-
 build/vignette.rds                         |  Bin 375 -> 376 bytes
 inst/doc/Ancestral.pdf                     |  Bin 260891 -> 245485 bytes
 inst/doc/IntertwiningTreesAndNetworks.html |    6 +-
 inst/doc/Networx.Rmd                       |    2 +-
 inst/doc/Networx.html                      |   16 +-
 inst/doc/Trees.pdf                         |  Bin 167890 -> 167906 bytes
 inst/doc/phangorn-specials.pdf             |  Bin 180115 -> 179955 bytes
 man/SOWH.test.Rd                           |    2 +-
 man/ancestral.pml.Rd                       |    2 +-
 man/as.splits.Rd                           |    9 +-
 man/densiTree.Rd                           |    7 +-
 man/dist.p.Rd                              |    2 +-
 man/hadamard.Rd                            |   14 +-
 man/maxCladeCred.Rd                        |    2 +-
 man/midpoint.Rd                            |    2 +-
 man/modelTest.Rd                           |    4 +-
 man/nni.Rd                                 |    2 +-
 man/parsimony.Rd                           |    5 +-
 man/phyDat.Rd                              |   19 +-
 man/plot.networx.Rd                        |    2 +-
 man/pml.Rd                                 |    4 +-
 man/pml.fit.Rd                             |   31 +-
 man/simSeq.Rd                              |    5 +-
 man/superTree.Rd                           |   22 +-
 man/treedist.Rd                            |   20 +-
 src/RcppExports.cpp                        |   30 +
 src/dist.c                                 |    9 +-
 src/fitch.c                                |   18 +-
 src/ml.c                                   |   51 +-
 src/phangorn.c                             |   25 +-
 src/phangorn_help.cpp                      |   48 ++
 src/sankoff.c                              |   11 +-
 src/sprdist.c                              | 1047 ++++++++++++++++++++++++++++
 tests/testthat/test_dist_tree.R            |   22 +
 tests/testthat/test_distances.R            |   22 +-
 tests/testthat/test_hadamard.R             |   21 +
 tests/testthat/test_parsimony.R            |   34 +-
 tests/testthat/test_phyDat.R               |   78 ++-
 tests/testthat/test_pml.R                  |   93 ++-
 tests/testthat/test_splits.R               |   39 ++
 tests/testthat/test_superTree.R            |   26 +
 tests/testthat/test_treeManipulation.R     |   31 +-
 tests/testthat/test_treedist.R             |   27 +
 vignettes/Networx.Rmd                      |    2 +-
 vignettes/phangorn.bib                     |   79 +++
 67 files changed, 2681 insertions(+), 925 deletions(-)
 create mode 100644 R/RcppExports.R
 create mode 100644 R/superTree.R
 create mode 100644 src/RcppExports.cpp
 create mode 100644 src/phangorn_help.cpp
 create mode 100644 src/sprdist.c
 create mode 100644 tests/testthat/test_dist_tree.R
 create mode 100644 tests/testthat/test_hadamard.R
 create mode 100644 tests/testthat/test_superTree.R

-- 
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