[med-svn] [r-cran-phangorn] 02/08: Merge tag 'upstream/2.1.1'

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-cran-phangorn.

commit 30344e5bfb317f435b6c238495ecf88eb94163c2
Merge: a174223 6c56854
Author: Andreas Tille <tille at debian.org>
Date:   Wed Dec 7 09:25:47 2016 +0100

    Merge tag 'upstream/2.1.1'
    
    Upstream version 2.1.1

 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(-)

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