[med-svn] [r-cran-adegenet] branch upstream updated (268adf1 -> 456cca3)
Andreas Tille
tille at debian.org
Sun Oct 22 17:39:05 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository r-cran-adegenet.
from 268adf1 New upstream version 2.0.1
new 456cca3 New upstream version 2.1.0
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:
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(-)
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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