[med-svn] [r-cran-adegenet] branch master updated (5357240 -> 769af57)
Andreas Tille
tille at debian.org
Sun Oct 22 17:39:01 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository r-cran-adegenet.
from 5357240 Upload to unstable
new b7ca240 Secure URI in watch file
new 456cca3 New upstream version 2.1.0
new be42c06 Updated version 2.1.0 from 'upstream/2.1.0'
new 77df15c New upstream version
new 769af57 Upload to unstable
The 5 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:
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
debian/changelog | 7 +
debian/watch | 4 +-
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 ++++
119 files changed, 3939 insertions(+), 1128 deletions(-)
create mode 100644 R/AIC.snapclust.R
create mode 100644 R/AICc.snapclust.R
create mode 100644 R/BIC.snapclust.R
create mode 100644 R/KIC.snapclust.R
create mode 100644 R/compoplot.R
create mode 100644 R/dist.genlight.R
create mode 100644 R/doc_C_routines.R
create mode 100644 R/export_to_mvmapper.R
rename R/{spca.rtests.R => global_local_tests.R} (100%)
create mode 100644 R/showmekittens.R
create mode 100644 R/snapclust.R
create mode 100644 R/snapclust.choose.k.R
create mode 100644 R/spca_randtest.R
create mode 100644 data/hybridtoy.RData
create mode 100644 data/rupica.RData
delete mode 100644 data/rupica.rda
create mode 100644 man/AIC.snapclust.Rd
create mode 100644 man/AICc.Rd
create mode 100644 man/BIC.snapclust.Rd
create mode 100644 man/KIC.Rd
create mode 100644 man/compoplot.Rd
create mode 100644 man/doc_C_routines.Rd
create mode 100644 man/export_to_mvmapper.Rd
create mode 100644 man/hybridtoy.Rd
create mode 100644 man/showmekittens.Rd
create mode 100644 man/snapclust.Rd
create mode 100644 man/snapclust.choose.k.Rd
create mode 100644 man/spca_randtest.Rd
create mode 100644 src/init.c
create mode 100644 tests/testthat/test-findclust.R
create mode 100644 tests/testthat/test_compoplot.R
create mode 100644 tests/testthat/test_haploGen.R
create mode 100644 tests/testthat/test_snapclust.R
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