Files in EricArcher/strataG
Summaries and Population Structure Analyses of Genetic Data

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/LDgenepop.R R/RcppExports.R R/TiTvRatio.R R/alleleFreqFormat.R R/alleleFreqs.R R/alleleSplit.R R/allelicRichness.R R/arlequin.R R/as.array.gtypes.R R/as.data.frame.gtypes.R R/as.matrix.gtypes.R R/as.multidna.R R/baseFreqs.R R/clumpp.R R/createConsensus.R R/df2gtypes.R R/dupGenotypes.R R/evanno.R R/expandHaplotypes.R R/fasta.R R/fastsimcoal.R R/fastsimcoal.input.R R/fixedDifferences.R R/fixedSites.R R/freq2GenData.R R/fusFs.R R/gelato.R R/genepop.R R/gtypes.accessors.R R/gtypes.class.R R/gtypes2genind.R R/gtypes2loci.R R/gtypes2phyDat.R R/heterozygosity.R R/hweTest.R R/initialize.gtypes.R R/is.gtypes.R R/iupacCode.R R/jackHWE.R R/labelHaplotypes.R R/ldNe.R R/lowFreqSubs.R R/mRatio.R R/maf.R R/mafft.R R/maverickRun.R R/mega.R R/mostDistantSequences.R R/mostRepresentativeSequences.R R/neiDa.R R/nucleotideDivergence.R R/nucleotideDiversity.R R/numAlleles.R R/numGenotyped.R R/numMissing.R R/numericSNPmat.R R/permuteStrata.R R/phase.R R/popGenEqns.R R/popStructStat.R R/popStructTest.R R/privateAlleles.R R/propUniqueAlleles.R R/qaqc.R R/readGenData.R R/removeSequences.R R/sequence2gtypes.R R/sequenceLikelihoods.R R/sharedLoci.R R/show.gtypes.R R/simGammaHaps.R R/strataG-internal.R R/strataG-package.R R/strataGUI.R R/strataSplit.R R/stratify.R R/structure.R R/structurePlot.R R/summarizeLoci.R R/summarizeSamples.R R/summarizeSeqs.R R/summary.gtypes.R
R/sysdata.rda
R/tajimasD.R R/theta.R R/trimNs.R R/validIupacCodes.R R/variableSites.R R/write.gtypes.R R/write.nexus.snapp.R README.md
appveyor.yml
data/bowhead.snp.position.rda
data/bowhead.snps.rda
data/dloop.g.rda
data/dolph.haps.rda
data/dolph.msats.rda
data/dolph.seqs.rda
data/dolph.strata.rda
data/msats.g.rda
inst/CITATION
inst/extdata/dolph.seqs.fasta
inst/shiny/app.R inst/shiny/global.R inst/shiny/load.data/server.load.R inst/shiny/load.data/server.load.display.gtypes.R inst/shiny/load.data/server.load.ui.R inst/shiny/load.data/server.load.ui.sidepanel.csv.R inst/shiny/load.data/server.load.ui.sidepanel.rdata.R inst/shiny/load.data/ui.load.R inst/shiny/popstruct/server.popstruct.R inst/shiny/popstruct/server.popstruct.ui.R inst/shiny/popstruct/ui.popstruct.R inst/shiny/qaqc/server.qaqc.01.loci.missing.R inst/shiny/qaqc/server.qaqc.02.loci.hmzg.R inst/shiny/qaqc/server.qaqc.03.samples.missing.R inst/shiny/qaqc/server.qaqc.04.samples.hmzg.R inst/shiny/qaqc/server.qaqc.05.dups.R inst/shiny/qaqc/server.qaqc.06.hwe.jack.R inst/shiny/qaqc/server.qaqc.07.ld.R inst/shiny/qaqc/server.qaqc.08.reports.R inst/shiny/qaqc/server.qaqc.R inst/shiny/qaqc/server.qaqc.haploid.R inst/shiny/qaqc/server.qaqc.summaries.R inst/shiny/qaqc/ui.qaqc.R inst/shiny/qaqc/ui.qaqc.diploid.R inst/shiny/qaqc/ui.qaqc.haploid.R inst/shiny/setup/server.setup.R inst/shiny/setup/ui.setup.R
man/.gitignore
man/LDgenepop.Rd man/TiTvRatio.Rd man/alleleFreqFormat.Rd man/alleleFreqs.Rd man/alleleSplit.Rd man/allelicRichness.Rd man/arlequin.Rd man/as.array.gtypes.Rd man/as.data.frame.gtypes.Rd man/as.matrix-gtypes-method.Rd man/as.multidna.Rd man/baseFreqs.Rd man/bowhead.snp.position.Rd man/bowhead.snps.Rd man/clumpp.Rd man/createConsensus.Rd man/df2gtypes.Rd man/dloop.g.Rd man/dolph.haps.Rd man/dolph.msats.Rd man/dolph.seqs.Rd man/dolph.strata.Rd man/dupGenotypes.Rd man/evanno.Rd man/expandHaplotypes.Rd man/fasta.Rd man/fastsimcoal.Rd man/fastsimcoal.input.Rd man/fixedDifferences.Rd man/fixedSites.Rd man/freq2GenData.Rd man/fusFs.Rd man/gelato.Rd man/genepop.Rd man/gtypes-class.Rd man/gtypes.accessors.Rd man/gtypes2genind.Rd man/gtypes2loci.Rd man/gtypes2phyDat.Rd man/heterozygosity.Rd man/hweTest.Rd man/initialize-gtypes-method.Rd man/is.gtypes.Rd man/iupacCode.Rd man/jackHWE.Rd man/labelHaplotypes.Rd man/ldNe.Rd man/lowFreqSubs.Rd man/mRatio.Rd man/maf.Rd man/mafft.Rd man/maverickRun.Rd man/mega.Rd man/mostDistantSequences.Rd man/mostRepresentativeSequences.Rd man/msats.g.Rd man/neiDa.Rd man/nucleotideDivergence.Rd man/nucleotideDiversity.Rd man/numAlleles.Rd man/numGenotyped.Rd man/numMissing.Rd man/numericSNPmat.Rd man/permuteStrata.Rd man/phase.Rd man/popGenEqns.Rd man/popStructStat.Rd man/popStructTest.Rd man/privateAlleles.Rd man/propUniqueAlleles.Rd man/qaqc.Rd man/readGenData.Rd man/removeSequences.Rd man/sequence2gtypes.Rd man/sequenceLikelihoods.Rd man/sharedLoci.Rd man/show-gtypes-method.Rd man/simGammaHaps.Rd man/strataG-internal.Rd man/strataG-package.Rd man/strataGUI.Rd man/strataSplit.Rd man/stratify.Rd man/structure.Rd man/structurePlot.Rd man/summarizeLoci.Rd man/summarizeSamples.Rd man/summarizeSeqs.Rd man/summary-gtypes-method.Rd man/tajimasD.Rd man/theta.Rd man/trimNs.Rd man/validIupacCodes.Rd man/variableSites.Rd man/write.gtypes.Rd man/write.nexus.snapp.Rd
src/.gitignore
src/Hstats_C.cpp
src/RcppExports.cpp
src/init.c
src/misc.funcs.cpp
src/statChi2_C.cpp
src/statFis_C.cpp
src/statFst_C.cpp
src/statGst_C.cpp
src/statJostD_C.cpp
src/statPhist_C.cpp
tests/testthat.R tests/testthat/test-popStructStats.R vignettes/external.programs.Rmd
vignettes/external.programs.html
vignettes/gtypes.R vignettes/gtypes.Rmd
vignettes/gtypes.html
vignettes/msats.csv
vignettes/population.structure.R vignettes/population.structure.Rmd
vignettes/population.structure.html
vignettes/qaqc.R vignettes/qaqc.Rmd
vignettes/qaqc.html
vignettes/sequences.R vignettes/sequences.Rmd
vignettes/sequences.html
vignettes/summaries.R vignettes/summaries.Rmd
vignettes/summaries.html
EricArcher/strataG documentation built on July 31, 2017, 11:17 p.m.