[med-svn] [r-cran-adegenet] 11/12: Updated version 2.0.1 from 'upstream/2.0.1'
Andreas Tille
tille at debian.org
Mon Oct 2 17:04:35 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 f737a13777684f22f7926a7614e762c191db87a7
Merge: 7598d33 268adf1
Author: Andreas Tille <tille at debian.org>
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(+)
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