[med-svn] [r-cran-adegenet] 03/05: Updated version 2.1.0 from 'upstream/2.1.0'
Andreas Tille
tille at debian.org
Sun Oct 22 17:39:04 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-adegenet.
commit be42c06abf30d110e1d57c86c9310a70a976ade9
Merge: b7ca240 456cca3
Author: Andreas Tille <tille at debian.org>
Date: Sun Oct 22 19:33:06 2017 +0200
Updated version 2.1.0 from 'upstream/2.1.0'
with Debian dir 5dc6e37d00465dfd6fd7c989e1d7b2925e2aa787
ChangeLog | 46 +++
DESCRIPTION | 39 +--
MD5 | 200 ++++++-----
NAMESPACE | 36 +-
R/AIC.snapclust.R | 23 ++
R/AICc.snapclust.R | 37 ++
R/BIC.snapclust.R | 25 ++
R/KIC.snapclust.R | 36 ++
R/SNPbin.R | 88 ++++-
R/adegenet.package.R | 86 +++--
R/auxil.R | 37 +-
R/basicMethods.R | 28 +-
R/chooseCN.R | 28 +-
R/compoplot.R | 199 +++++++++++
R/constructors.R | 8 +-
R/dapc.R | 301 ++++++----------
R/datasets.R | 36 ++
R/dist.genlight.R | 33 ++
R/dist.genpop.R | 2 +-
R/doc_C_routines.R | 15 +
R/export_to_mvmapper.R | 271 +++++++++++++++
R/find.clust.R | 130 +++++--
R/gengraph.R | 4 +-
R/glFunctions.R | 12 +-
R/glHandle.R | 9 +-
R/{spca.rtests.R => global_local_tests.R} | 0
R/handling.R | 10 +-
R/haploGen.R | 4 +-
R/import.R | 153 +++++----
R/inbreeding.R | 49 +--
R/monmonier.R | 4 +-
R/seqTrack.R | 2 +-
R/showmekittens.R | 45 +++
R/snapclust.R | 465 +++++++++++++++++++++++++
R/snapclust.choose.k.R | 107 ++++++
R/snpposi.R | 7 +-
R/spca.R | 550 ++++++++++++++++++++----------
R/spca_randtest.R | 92 +++++
R/xvalDapc.R | 29 +-
R/zzz.R | 11 +-
README.md | 6 +
data/H3N2.rda | Bin 45216 -> 45128 bytes
data/dapcIllus.rda | Bin 38831 -> 38791 bytes
data/datalist | 1 +
data/eHGDP.rda | Bin 1126695 -> 1126522 bytes
data/hybridtoy.RData | Bin 0 -> 2723 bytes
data/microbov.rda | Bin 28194 -> 28203 bytes
data/nancycats.rda | Bin 4889 -> 4833 bytes
data/rupica.RData | Bin 0 -> 34264 bytes
data/rupica.rda | Bin 30800 -> 0 bytes
data/sim2pop.rda | Bin 6451 -> 6432 bytes
data/spcaIllus.rda | Bin 16449 -> 16388 bytes
man/AIC.snapclust.Rd | 23 ++
man/AICc.Rd | 26 ++
man/BIC.snapclust.Rd | 23 ++
man/H3N2.Rd | 5 +-
man/Hs.Rd | 7 +-
man/Hs.test.Rd | 7 +-
man/KIC.Rd | 26 ++
man/adegenet.package.Rd | 79 +++--
man/auxil.Rd | 17 +-
man/chooseCN.Rd | 11 +-
man/compoplot.Rd | 74 ++++
man/dapcGraphics.Rd | 37 +-
man/dapcIllus.Rd | 7 +-
man/df2genind.Rd | 42 +--
man/doc_C_routines.Rd | 26 ++
man/eHGDP.Rd | 1 -
man/export_to_mvmapper.Rd | 122 +++++++
man/fasta2DNAbin.Rd | 6 +-
man/find.clusters.Rd | 230 +++++++------
man/genind2df.Rd | 7 +-
man/genind2genpop.Rd | 7 +-
man/genlight.Rd | 8 +
man/glAux.Rd | 2 +-
man/glPca.Rd | 2 +-
man/hierarchy-methods.Rd | 7 +-
man/hybridize.Rd | 7 +-
man/hybridtoy.Rd | 42 +++
man/import2genind.Rd | 7 +-
man/makefreq.Rd | 7 +-
man/microbov.Rd | 1 -
man/minorAllele.Rd | 7 +-
man/nancycats.Rd | 1 -
man/new.genind.Rd | 5 +-
man/new.genpop.Rd | 5 +-
man/old2new.Rd | 3 +-
man/population-methods.Rd | 1 -
man/read.PLINK.Rd | 9 +-
man/read.fstat.Rd | 7 +-
man/read.genepop.Rd | 7 +-
man/read.genetix.Rd | 7 +-
man/read.snp.Rd | 11 +-
man/read.structure.Rd | 7 +-
man/repool.Rd | 7 +-
man/rupica.Rd | 1 -
man/scaleGen.Rd | 5 +-
man/seploc.Rd | 2 +-
man/showmekittens.Rd | 25 ++
man/sim2pop.Rd | 7 +-
man/snapclust.Rd | 140 ++++++++
man/snapclust.choose.k.Rd | 33 ++
man/spca.Rd | 167 ++++++---
man/spcaIllus.Rd | 7 +-
man/spca_randtest.Rd | 51 +++
man/strata-methods.Rd | 31 +-
man/tab.Rd | 1 -
man/web.Rd | 5 +-
man/xvalDapc.Rd | 12 +-
src/init.c | 32 ++
tests/testthat/test-findclust.R | 27 ++
tests/testthat/test_accessors.R | 26 ++
tests/testthat/test_compoplot.R | 28 ++
tests/testthat/test_genlight.R | 2 +-
tests/testthat/test_haploGen.R | 5 +
tests/testthat/test_import.R | 180 +++++++---
tests/testthat/test_snapclust.R | 62 ++++
117 files changed, 3930 insertions(+), 1126 deletions(-)
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