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commit f737a13777684f22f7926a7614e762c191db87a7 Merge: 7598d33 268adf1 Author: Andreas Tille <[email protected]> Date: Mon Oct 2 18:59:07 2017 +0200 Updated version 2.0.1 from 'upstream/2.0.1' with Debian dir 161e09c56bfeb09dd8870aa8a5242954328fe221 ChangeLog | 723 ++ DESCRIPTION | 43 + MD5 | 185 + NAMESPACE | 181 + R/HWE.R | 53 + R/Hs.R | 132 + R/PCtest.R | 51 + R/SNPbin.R | 1208 ++++ R/accessors.R | 409 ++ R/adegenet.package.R | 300 + R/auxil.R | 386 ++ R/basicMethods.R | 552 ++ R/chooseCN.R | 288 + R/classes.R | 253 + R/colorplot.R | 76 + R/constructors.R | 329 + R/coords.monmonier.R | 58 + R/dapc.R | 1198 ++++ R/datasets.R | 745 +++ R/dist.genpop.R | 109 + R/export.R | 171 + R/find.clust.R | 357 + R/fstat.R | 97 + R/gengraph.R | 232 + R/genind2genpop.R | 149 + R/glFunctions.R | 774 +++ R/glHandle.R | 461 ++ R/glPlot.R | 42 + R/glSim.R | 227 + R/gstat.randtest.R | 63 + R/handling.R | 663 ++ R/haploGen.R | 723 ++ R/haploPop.R | 946 +++ R/hierarchyMethods.R | 198 + R/hybridize.R | 235 + R/import.R | 1733 +++++ R/inbreeding.R | 122 + R/loadingplot.R | 92 + R/makefreq.R | 118 + R/minorAllele.R | 47 + R/monmonier.R | 666 ++ R/mutations.R | 111 + R/old2new.R | 161 + R/orthobasis.R | 366 + R/pairDist.R | 171 + R/propShared.R | 41 + R/propTyped.R | 140 + R/scale.R | 123 + R/seqTrack.R | 1145 ++++ R/sequences.R | 317 + R/servers.R | 51 + R/setAs.R | 105 + R/simOutbreak.R | 367 + R/snpposi.R | 129 + R/snpzip.R | 340 + R/spca.R | 442 ++ R/spca.rtests.R | 89 + R/strataMethods.R | 686 ++ R/xvalDapc.R | 257 + R/zzz.R | 10 + README.md | 18 + data/H3N2.rda | Bin 0 -> 45216 bytes data/dapcIllus.rda | Bin 0 -> 38831 bytes data/datalist | 8 + data/eHGDP.rda | Bin 0 -> 1126695 bytes data/microbov.rda | Bin 0 -> 28194 bytes data/nancycats.rda | Bin 0 -> 4889 bytes data/rupica.rda | Bin 0 -> 30800 bytes data/sim2pop.rda | Bin 0 -> 6451 bytes data/spcaIllus.rda | Bin 0 -> 16449 bytes inst/CITATION | 26 + inst/dapcServer/server.R | 436 ++ inst/dapcServer/ui.R | 501 ++ inst/files/AFLP.txt | 8 + inst/files/exampleSnpDat.snp | 55 + inst/files/mondata1.rda | Bin 0 -> 1554 bytes inst/files/mondata2.rda | Bin 0 -> 1557 bytes inst/files/nancycats.dat | 247 + inst/files/nancycats.gen | 264 + inst/files/nancycats.gtx | 293 + inst/files/nancycats.str | 475 ++ inst/files/pdH1N1-HA.fasta | 12557 +++++++++++++++++++++++++++++++++++ inst/files/pdH1N1-NA.fasta | 10392 +++++++++++++++++++++++++++++ inst/files/pdH1N1-data.csv | 434 ++ inst/files/usflu.fasta | 2400 +++++++ man/H3N2.Rd | 88 + man/HWE.Rd | 70 + man/Hs.Rd | 45 + man/Hs.test.Rd | 52 + man/SNPbin.Rd | 164 + man/accessors.Rd | 243 + man/adegenet.package.Rd | 210 + man/as-methods.Rd | 75 + man/as.SNPbin.Rd | 56 + man/as.genlight.Rd | 65 + man/ascore.Rd | 94 + man/auxil.Rd | 151 + man/chooseCN.Rd | 96 + man/colorplot.Rd | 65 + man/coords.monmonier.Rd | 49 + man/dapc.Rd | 332 + man/dapcGraphics.Rd | 204 + man/dapcIllus.Rd | 91 + man/df2genind.Rd | 94 + man/dist.genpop.Rd | 121 + man/eHGDP.Rd | 148 + man/fasta2DNAbin.Rd | 61 + man/fasta2genlight.Rd | 96 + man/find.clusters.Rd | 280 + man/gengraph.Rd | 118 + man/genind.Rd | 104 + man/genind2df.Rd | 56 + man/genind2genpop.Rd | 102 + man/genlight.Rd | 348 + man/genpop.Rd | 84 + man/glAux.Rd | 122 + man/glPca.Rd | 184 + man/glPlot.Rd | 65 + man/glSim.Rd | 130 + man/haploGen.Rd | 194 + man/hierarchy-methods.Rd | 80 + man/hybridize.Rd | 104 + man/import2genind.Rd | 85 + man/inbreeding.Rd | 113 + man/isPoly.Rd | 37 + man/loadingplot.Rd | 71 + man/makefreq.Rd | 82 + man/microbov.Rd | 103 + man/minorAllele.Rd | 37 + man/monmonier.Rd | 199 + man/mutations.Rd | 82 + man/nancycats.Rd | 59 + man/new.genind.Rd | 62 + man/new.genpop.Rd | 45 + man/old2new.Rd | 33 + man/pairDist.Rd | 99 + man/population-methods.Rd | 52 + man/propShared.Rd | 49 + man/propTyped.Rd | 48 + man/read.PLINK.Rd | 104 + man/read.fstat.Rd | 48 + man/read.genepop.Rd | 51 + man/read.genetix.Rd | 50 + man/read.snp.Rd | 99 + man/read.structure.Rd | 90 + man/repool.Rd | 47 + man/rupica.Rd | 80 + man/scaleGen.Rd | 93 + man/selpopsize.Rd | 41 + man/seploc.Rd | 78 + man/seppop.Rd | 83 + man/seqTrack.Rd | 270 + man/sequences.Rd | 69 + man/servers.Rd | 39 + man/sim2pop.Rd | 65 + man/snpposi.Rd | 107 + man/snpzip.rd | 109 + man/spca.Rd | 189 + man/spca.rtests.Rd | 65 + man/spcaIllus.Rd | 130 + man/strata-methods.Rd | 169 + man/tab.Rd | 47 + man/truenames.Rd | 36 + man/virClasses.Rd | 18 + man/web.Rd | 41 + man/xvalDapc.Rd | 132 + src/GLfunctions.c | 236 + src/GLfunctions.h | 5 + src/adesub.c | 1152 ++++ src/adesub.h | 44 + src/monmonier-utils.c | 267 + src/sharedAll.c | 159 + src/snpbin.c | 564 ++ src/snpbin.h | 102 + tests/testthat.R | 3 + tests/testthat/test-prop.R | 18 + tests/testthat/test-seppop.R | 63 + tests/testthat/test_accessors.R | 149 + tests/testthat/test_constructors.R | 15 + tests/testthat/test_genlight.R | 106 + tests/testthat/test_hierarchy.R | 50 + tests/testthat/test_import.R | 131 + tests/testthat/test_repool.R | 35 + tests/testthat/test_subset.R | 20 + tests/testthat/test_summary.R | 13 + tests/testthat/test_xval.R | 31 + 186 files changed, 59970 insertions(+) -- 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
