Files in dartR

Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

R/gl.run.structure.r R/utils.recalc.maf.r R/gl.report.pa.r R/gl.filter.parent.offspring.r R/gl.set.verbosity.r R/gl.drop.pop.r R/gl.filter.sexlinked.r R/gl.propShared.r R/utils.het.pop.r R/gl.keep.ind.r R/gl.nhybrids.r R/gl.map.structure.r R/gl2related.r R/gl.recalc.metrics.r R/utils.pa.Chao.r R/gl.filter.hwe.r R/gl.write.csv.r R/gl2phylip.r R/gl.evanno.r R/gl.assign.mahalanobis.r R/gl.report.sexlinked.r R/gl.fixed.diff.r R/gl2geno.r R/utils.clumpp.r R/gl.grm.r R/utils.read.dart.r R/gl.filter.locmetric.r R/utils.read.fasta.r R/utils.spautocor.R R/utils.assignment_4.r R/gl.print.history.r R/gl2eigenstrat.r R/gl2fasta.r R/gl.assign.pca.r R/utils.dart2genlight.r R/gl.play.history.r R/gl.edit.recode.pop.r R/utils.dist.binary.r R/gl2bpp.r R/gl.filter.secondaries.r R/gl.amova.r R/utils.reset.flags.r R/gl.collapse.r R/datasets.r R/gl.tree.nj.r R/gl.select.colors.r R/utils.impute.R R/gl.rename.pop.r R/gl2sfs.R R/gl.spatial.autoCorr.r R/gl.He.r R/gl.diagnostics.sim.r R/gl.print.reports.r R/utils.structure.genind2gtypes.r R/gl.report.hwe.r R/gl.merge.pop.r R/utils.check.datatype.R R/gl.subsample.loci.r R/gl.fst.pop.r R/gl.read.vcf.r R/gl.report.rdepth.r R/gl.ld.haplotype.r R/utils.n.var.invariant.r R/gl.genleastcost.r R/gl.report.secondaries.r R/gl2gi.r R/gl.ld.distance.r R/gl.grm.network.r R/utils.recalc.avgpic.r R/gl.blast.r R/utils.assignment_3.r R/gl.join.r R/gl.pcoa.plot.r R/gl.sort.r R/gl.drop.loc.r R/gl.report.maf.r R/gl.filter.allna.r R/utils.hamming.r R/gl2demerelate.r R/gl.list.reports.r R/gl.filter.rdepth.r R/gl.smearplot.r R/gl.sim.create.dispersal.r R/gl.keep.pop.r R/gl.filter.taglength.r R/gl.read.csv.r R/gl.test.heterozygosity.r R/utils.outflank.likelihood.r R/utils.structure.evanno.r R/gl2structure.r R/gl.sim.WF.table.r R/gl.save.r R/zzz.r R/gl.sim.emigration.r R/utils.ld.r R/gl.sim.ind.r R/utils.outflank.plotter.r R/dartR.r R/gl.assign.grm.r R/gl.filter.ld.r R/utils.basic.stats.r R/utils.outflank.r R/gl.report.ld.r R/gl.report.heterozygosity.r R/gl.report.ld.map.r R/gl2hiphop.r R/gl.report.overshoot.r R/gl.filter.callrate.r R/gl.report.reproducibility.r R/utils.structure.run.r R/gl.costdistances.r R/gl.sample.r R/gl.make.recode.pop.r R/gl2plink.r R/gl.alf.r R/gl2snapp.r R/gl.ibd.r R/gl.filter.overshoot.r R/gl.plot.network.r R/gl.random.snp.r R/utils.recalc.freqhomref.r R/gl.filter.reproducibility.r R/gl.report.taglength.r R/utils.recalc.callrate.r R/gl.dist.ind.r R/gl.pcoa.r R/gi2gl.R R/gl.assign.pa.r R/utils.recalc.freqhets.r R/gl.fdsim.r R/gl.report.monomorphs.r R/gl.read.silicodart.r R/gl2shp.R R/gl2treemix.r R/is.fixed.r R/gl2vcf.r R/gl.sim.WF.run.r R/utils.outflank.fst.r R/gl.report.hamming.r R/gl.filter.maf.r R/gl.sfs.R R/gl.sim.offspring.r R/gl.select.shapes.r R/gl.report.bases.r R/utils.flag.start.r R/utils.transpose.R R/gl.report.parent.offspring.r R/gl.filter.hamming.r R/utils.assignment.r R/gl.reassign.pop.r R/gl.read.dart.r R/utils.hwe.r R/gl.read.fasta.r R/gl.impute.r R/gl.report.locmetric.r R/gl.report.diversity.r R/gl.recode.ind.r R/utils.dist.ind.snp.r R/utils.outflank.diploids.r R/gl.edit.recode.ind.r R/gl.filter.heterozygosity.r R/utils.recalc.freqhomsnp.r R/gl.load.r R/gl.plot.structure.r R/gl.drop.ind.r R/gl.filter.pa.r R/utils.jackknife.R R/gl.dist.pop.r R/gl2svdquartets.r R/gl.diagnostics.hwe.r R/gl.recode.pop.r R/gl.outflank.r R/utils.assignment_2.r R/gl.report.callrate.r R/gl.make.recode.ind.r R/gl.basic.stats.r R/gl.Ho.r R/gl2genalex.r R/gl.filter.monomorphs.r R/gl.sim.mutate.r R/gl.keep.loc.r R/gl2gds.r R/gl2genepop.r R/gl.plot.heatmap.r R/gl.percent.freq.r R/gl.hwe.pop.r R/gl2faststructure.r R/gl.define.pop.r R/gl.compliance.check.r R/gl.map.interactive.r R/gl.install.vanilla.dartR.r R/gl2sa.r R/gl2bayescan.r R/utils.sims.r R/gl.LDNe.r R/gl.check.verbosity.r inst/doc/dartRTutorials.pdf inst/doc/dartRTutorials.Rmd tests/testthat.R tests/testthat/test-gl.alf.R vignettes/dartRTutorials.Rmd man/testset_pop_recode.Rd man/gl.recode.ind.Rd man/gl.test.heterozygosity.Rd man/gl.read.silicodart.Rd man/gl.install.vanilla.dartR.Rd man/cbind.dartR.Rd man/gl2gds.Rd man/gl.plot.heatmap.Rd man/gl.LDNe.Rd man/gl2shp.Rd man/gl.filter.allna.Rd man/testset.gs.Rd man/gl.outflank.Rd man/gl.pcoa.plot.Rd man/interactive_reference.Rd man/gl.assign.pa.Rd man/utils.structure.genind2gtypes.Rd man/gl.filter.sexlinked.Rd man/utils.assignment_2.Rd man/utils.recalc.avgpic.Rd man/gl.sfs.Rd man/utils.basic.stats.Rd man/gl2geno.Rd man/gl.spatial.autoCorr.Rd man/utils.read.dart.Rd man/utils.recalc.maf.Rd man/gl.impute.Rd man/gl.list.reports.Rd man/gl.report.secondaries.Rd man/gl.costdistances.Rd man/gl.report.pa.Rd man/gl2svdquartets.Rd man/gl.load.Rd man/sub-dartR-ANY-ANY-ANY-method.Rd man/gl.hwe.pop.Rd man/gl.report.diversity.Rd man/gl2genalex.Rd man/gl.report.heterozygosity.Rd man/platy.Rd man/gl.write.csv.Rd man/gl2vcf.Rd man/gl2bpp.Rd man/gl.ld.distance.Rd man/testset.gl.Rd man/gi2gl.Rd man/gl.fixed.diff.Rd man/utils.dist.binary.Rd man/gl.make.recode.ind.Rd man/gl.fdsim.Rd man/gl.keep.loc.Rd man/zzz.Rd man/gl.sim.mutate.Rd man/possums.gl.Rd man/utils.outflank.plotter.Rd man/gl.percent.freq.Rd man/gl.dist.pop.Rd man/gl.sim.create_dispersal.Rd man/utils.n.var.invariant.Rd man/gl.report.maf.Rd man/gl.filter.taglength.Rd man/gl.set.verbosity.Rd man/utils.recalc.callrate.Rd man/gl.keep.ind.Rd man/gl2treemix.Rd man/gl.collapse.Rd man/gl.define.pop.Rd man/utils.assignment_3.Rd man/gl.report.bases.Rd man/gl.grm.Rd man/utils.recalc.freqhomsnp.Rd man/gl.filter.parent.offspring.Rd man/gl.report.taglength.Rd man/gl.basic.stats.Rd man/utils.hamming.Rd man/gl2faststructure.Rd man/gl.diagnostics.hwe.Rd man/gl.reassign.pop.Rd man/gl.amova.Rd man/utils.check.datatype.Rd man/gl.evanno.Rd man/gl.filter.locmetric.Rd man/utils.outflank.MakeDiploidFSTMat.Rd man/gl.play.history.Rd man/gl.random.snp.Rd man/is.fixed.Rd man/gl.edit.recode.pop.Rd man/gl.sim.ind.Rd man/gl2gi.Rd man/gl.filter.reproducibility.Rd man/gl.report.ld.map.Rd man/gl.report.hwe.Rd man/gl.filter.secondaries.Rd man/gl.print.history.Rd man/gl.read.vcf.Rd man/utils.reset.flags.Rd man/gl.drop.ind.Rd man/utils.het.pop.Rd man/gl2bayescan.Rd man/gl.filter.monomorphs.Rd man/gl.join.Rd man/gl.report.overshoot.Rd man/gl.report.rdepth.Rd man/utils.dist.ind.snp.Rd man/gl.report.locmetric.Rd man/gl.select.shapes.Rd man/gl.ld.haplotype.Rd man/gl.map.interactive.Rd man/gl.compliance.check.Rd man/gl2sfs.Rd man/gl.sample.Rd man/gl.keep.pop.Rd man/gl.map.structure.Rd man/gl.report.parent.offspring.Rd man/gl.filter.callrate.Rd man/gl.run.structure.Rd man/gl.plot.structure.Rd man/gl2genepop.Rd man/gl.assign.mahalanobis.Rd man/gl2plink.Rd man/gl.sim.WF.run.Rd man/gl2eigenstrat.Rd man/gl.filter.pa.Rd man/gl2related.Rd man/utils.spautocor.Rd man/gl.ibd.Rd man/utils.recalc.freqhomref.Rd man/gl.fst.pop.Rd man/gl.sort.Rd man/utils.assignment_4.Rd man/gl.filter.heterozygosity.Rd man/rbind.dartR.Rd man/gl.report.ld.Rd man/utils.dart2genlight.Rd man/gl2fasta.Rd man/gl.assign.grm.Rd man/gl.report.monomorphs.Rd man/gl.smearplot.Rd man/gl2snapp.Rd man/gl.report.sexlinked.Rd man/utils.structure.run.Rd man/utils.recalc.freqhets.Rd man/gl.blast.Rd man/gl.drop.loc.Rd man/gl.read.dart.Rd man/utils.jackknife.Rd man/gl.tree.nj.Rd man/bandicoot.gl.Rd man/gl.edit.recode.ind.Rd man/gl2demerelate.Rd man/utils.flag.start.Rd man/gl.assign.pca.Rd man/testset_SNPs_2Row.Rd man/gl.print.reports.Rd man/gl.filter.hamming.Rd man/gl.select.colors.Rd man/gl.plot.network.Rd man/gl.read.csv.Rd man/gl.sim.offspring.Rd man/gl.report.hamming.Rd man/gl.He.Rd man/utils.assignment.Rd man/gl.diagnostics.sim.Rd man/gl.rename.pop.Rd man/gl.sim.emigration.Rd man/gl.recode.pop.Rd man/gl2sa.Rd man/gl.pcoa.Rd man/gl.report.callrate.Rd man/gl.filter.rdepth.Rd man/gl.dist.ind.Rd man/gl.grm.network.Rd man/gl.filter.overshoot.Rd man/gl.save.Rd man/utils.outflank.Rd man/utils.structure.evanno.Rd man/gl.make.recode.pop.Rd man/gl2hiphop.Rd man/gl.filter.hwe.Rd man/gl.filter.ld.Rd man/gl.nhybrids.Rd man/gl.read.fasta.Rd man/gl2phylip.Rd man/gl.filter.maf.Rd man/gl.genleastcost.Rd man/gl.Ho.Rd man/testset_metadata.Rd man/gl.sim.WF.table.Rd man/gl.drop.pop.Rd man/gl.alf.Rd man/gl.recalc.metrics.Rd man/gl.merge.pop.Rd man/gl.propShared.Rd man/gl.report.reproducibility.Rd man/interactive_sim_run.Rd man/gl2structure.Rd man/gl.subsample.loci.Rd man/gl.check.verbosity.Rd man/theme_dartR.Rd