Files in dartR.base

Analysing 'SNP' and 'Silicodart' Data - Basic Functions

R/gl.filter.excess.het.r R/utils.recalc.maf.r R/gl.report.pa.r R/gl.set.verbosity.r R/gl.drop.pop.r R/gl.set.wd.r R/gl.propShared.r R/utils.het.pop.r R/gl.keep.ind.r R/utils.dartR.class.def.r R/gl2related.r R/gl.recalc.metrics.r R/utils.plot.save.r R/utils.pa.Chao.r R/gl.filter.hwe.r R/gl.write.csv.r R/gl2phylip.r R/gl.fixed.diff.r R/gl2paup.parsimony.r R/gl2geno.r R/utils.read.dart.r R/gl.filter.locmetric.r R/utils.read.fasta.r R/utils.het.report.r R/gl.print.history.r R/gl2eigenstrat.r R/gl2fasta.r R/utils.dart2genlight.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/gl2paup.svdquartets.r R/utils.reset.flags.r R/gl.tree.nj.r R/gl.select.colors.r R/gl.report.allna.r R/gl.rename.pop.r R/gl.He.r R/gl.report.fstat.r R/gl.report.allelerich.r R/gl.report.hwe.r R/gl.filter.factorloadings.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/utils.n.var.invariant.r R/gl.dist.phylo.r R/gl.subsample.loc.r R/gl.report.secondaries.r R/gl2gi.r R/gl.check.wd.r R/gl2gapit.r R/utils.recalc.avgpic.r R/gl.report.basics.r R/gl.join.r R/gl.pcoa.plot.r R/gl.sort.r R/gl.drop.loc.r R/gl.report.polyploid_heterozygosity.r R/gl.report.maf.r R/gl.filter.allna.r R/utils.hamming.r R/gl2demerelate.r R/gl.filter.rdepth.r R/gl.smearplot.r R/gl.keep.pop.r R/gl.filter.taglength.r R/utils.plink.run.r R/gl.sim.genotypes.r R/gl.read.csv.r R/gl.test.heterozygosity.r R/gl2structure.r R/gl.save.r R/utils.is.fixed.r R/zzz.r R/gl.filter.ld.r R/gl.report.excess.het.r R/utils.basic.stats.r R/utils.vcfr2genlight.polyploid.R R/gl.mahal.assign.r R/gl.report.ld.r R/gl.report.heterozygosity.r R/gl2hapmap.r R/utils.collapse.matrix.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/gl.read.PLINK.r R/gl.sample.r R/gl.make.recode.pop.r R/gl.report.shannon.r R/gl2plink.r R/gl.alf.r R/gl2snapper.r R/gl.filter.overshoot.r R/gl.random.snp.r R/utils.recalc.freqhomref.r R/gl.filter.reproducibility.r R/utils.stats.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.allele.freq.r R/utils.recalc.freqhets.r R/gl.tree.fitch.r R/gl.fdsim.r R/gl.colors.r R/gl.report.monomorphs.r R/gl.sim.crosses.r R/gl.read.silicodart.r R/gl2treemix.r R/gl2vcf.r R/gl.report.hamming.r R/gl.filter.maf.r R/gl.select.shapes.r R/gl.report.bases.r R/gl.report.factorloadings.r R/utils.flag.start.r R/gl.randomize.snps.r R/utils.transpose.r R/gl.filter.hamming.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/gl2bayesAss.R R/gl.edit.recode.ind.r R/theme_dartR.r R/gl.filter.heterozygosity.r R/utils.recalc.freqhomsnp.r R/gl.load.r R/gl.drop.ind.r R/gl.filter.pa.r R/utils.jackknife.R R/gl.dist.pop.r R/gl.diagnostics.hwe.r R/gl.recode.pop.r R/gl.report.callrate.r R/gl.make.recode.ind.r R/utils.read.ped.r R/gl.Ho.r R/gl2genalex.r R/gl.report.replicates.r R/gl.filter.monomorphs.r R/gl.keep.loc.r R/gl.add.indmetrics.r R/gl2gds.r R/gl2genepop.r R/gl.plot.heatmap.r R/gl.hwe.pop.r R/gl2faststructure.r R/utils.impute.r R/gl.define.pop.r R/gl.compliance.check.r R/gl.map.interactive.r R/gl2sa.r R/gl.subsample.ind.r R/gl2bayescan.r R/gl.check.verbosity.r man/gl.recode.ind.Rd man/gl.test.heterozygosity.Rd man/gl.read.silicodart.Rd man/cbind.dartR.Rd man/gl.sim.genotypes.Rd man/gl2gds.Rd man/gl.plot.heatmap.Rd man/gl.filter.allna.Rd man/gl.report.basics.Rd man/gl.pcoa.plot.Rd man/utils.recalc.avgpic.Rd man/utils.basic.stats.Rd man/gl2geno.Rd man/gl.allele.freq.Rd man/utils.read.dart.Rd man/utils.read.ped.Rd man/gl.filter.excess.het.Rd man/utils.recalc.maf.Rd man/gl.impute.Rd man/utils.impute.Rd man/gl.report.secondaries.Rd man/gl.colors.Rd man/utils.vcfr2genlight.polyploid.Rd man/gl.report.pa.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.tree.fitch.Rd man/gl.report.heterozygosity.Rd man/gl.write.csv.Rd man/gl2vcf.Rd man/gl2bpp.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/gl.report.allelerich.Rd man/zzz.Rd man/utils.is.fixed.Rd man/gl.dist.pop.Rd man/gl2snapper.Rd man/utils.n.var.invariant.Rd man/gl.report.maf.Rd man/gl.filter.taglength.Rd man/gl2paup.parsimony.Rd man/gl.report.allna.Rd man/gl.set.verbosity.Rd man/utils.recalc.callrate.Rd man/gl.keep.ind.Rd man/gl2treemix.Rd man/gl.define.pop.Rd man/gl.report.bases.Rd man/gl.subsample.loc.Rd man/utils.recalc.freqhomsnp.Rd man/gl.report.taglength.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.filter.locmetric.Rd man/gl.edit.recode.pop.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/utils.plot.save.Rd man/gl.read.vcf.Rd man/gl.prop.shared.Rd man/utils.reset.flags.Rd man/gl.drop.ind.Rd man/utils.het.pop.Rd man/utils.transpose.Rd man/gl2bayescan.Rd man/gl.filter.monomorphs.Rd man/gl.join.Rd man/utils.read.fasta.Rd man/gl.report.overshoot.Rd man/gl.report.rdepth.Rd man/utils.dist.ind.snp.Rd man/gl.filter.factorloadings.Rd man/gl.report.locmetric.Rd man/gl.report.fstat.Rd man/gl.select.shapes.Rd man/gl.map.interactive.Rd man/gl.compliance.check.Rd man/gl.read.PLINK.Rd man/gl.randomize.snps.Rd man/gl.sample.Rd man/gl.keep.pop.Rd man/gl.filter.callrate.Rd man/gl2genepop.Rd man/gl.subsample.ind.Rd man/gl2plink.Rd man/gl2eigenstrat.Rd man/gl.filter.pa.Rd man/gl2related.Rd man/utils.recalc.freqhomref.Rd man/gl.fst.pop.Rd man/gl.sort.Rd man/gl.filter.heterozygosity.Rd man/rbind.dartR.Rd man/gl.report.ld.Rd man/utils.dart2genlight.Rd man/gl2fasta.Rd man/gl.report.monomorphs.Rd man/gl.smearplot.Rd man/utils.recalc.freqhets.Rd man/gl.report.replicates.Rd man/gl.drop.loc.Rd man/gl.read.dart.Rd man/utils.jackknife.Rd man/utils.plink.run.Rd man/gl.tree.nj.Rd man/gl.add.indmetrics.Rd man/gl.edit.recode.ind.Rd man/gl2demerelate.Rd man/utils.flag.start.Rd man/gl.filter.hamming.Rd man/gl.select.colors.Rd man/gl.read.csv.Rd man/utils.collapse.matrix.Rd man/gl.report.hamming.Rd man/gl.He.Rd man/gl.set.wd.Rd man/gl.rename.pop.Rd man/gl.recode.pop.Rd man/gl2sa.Rd man/gl.pcoa.Rd man/gl2paup.svdquartets.Rd man/gl.report.callrate.Rd man/gl.filter.rdepth.Rd man/gl.dist.ind.Rd man/gl.filter.overshoot.Rd man/gl.dist.phylo.Rd man/gl.save.Rd man/gl.sim.cross.Rd man/gl.make.recode.pop.Rd man/gl2hiphop.Rd man/gl.report.factorloadings.Rd man/gl.filter.hwe.Rd man/gl.filter.ld.Rd man/gl.read.fasta.Rd man/gl2phylip.Rd man/gl.check.wd.Rd man/gl.report.shannon.Rd man/gl.filter.maf.Rd man/gl.Ho.Rd man/gl.drop.pop.Rd man/gl.alf.Rd man/gl.recalc.metrics.Rd man/gl.merge.pop.Rd man/gl.report.reproducibility.Rd man/gl2bayesAss.Rd man/gl2structure.Rd man/gl.subsample.loci.Rd man/gl.report.excess.het.Rd man/gl.check.verbosity.Rd man/theme_dartR.Rd man/gl.mahal.assign.Rd man/gl.report.polyploid_heterozygosity.Rd