Files in green-striped-gecko/dartR

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

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check-beta.yaml

.github/workflows/R-CMD-check-dev.yaml

.github/workflows/R-CMD-check-dev_Arthur.yaml

.github/workflows/R-CMD-check-dev_Bernd.yaml

.github/workflows/R-CMD-check-dev_Carlo.yaml

.github/workflows/R-CMD-check-dev_Luis.yaml

.github/workflows/R-CMD-check.yaml

.github/workflows/check-standard.yml

.github/workflows/pkgdown.yaml

.github/workflows/render_markdown.yaml

.gitignore

CONTRIBUTING.md

DESCRIPTION

NAMESPACE

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

_pkgdown.yml

code_of_conduct.md

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pkgdown.yaml

tests/testthat.R tests/testthat/test-gl.alf.R vignettes/dartRTutorials.Rmd vignettes/dartRTutorials.pdf

vignettes/figures/dartRlogo.png

green-striped-gecko/dartR documentation built on Jan. 31, 2024, 10:14 a.m.