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commit be42c06abf30d110e1d57c86c9310a70a976ade9 Merge: b7ca240 456cca3 Author: Andreas Tille <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-cran-adegenet.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
