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

codemeta.json

dartR.Rproj

data/bandicoot.rda

data/possums.gl.rda

data/testset.gl.rda

data/testset.gs.rda

docs/404.html

docs/LICENSE.html

docs/articles/dartRTutorials.html

docs/articles/index.html

docs/authors.html

docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js

docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js.map

docs/deps/bootstrap-5.1.0/bootstrap.min.css

docs/deps/data-deps.txt

docs/deps/jquery-3.6.0/jquery-3.6.0.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.map

docs/index.html

docs/link.svg

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/Rplot002.png

docs/reference/Rplot003.png

docs/reference/Rplot004.png

docs/reference/Rplot005.png

docs/reference/Rplot006.png

docs/reference/Rplot007.png

docs/reference/Rplot008.png

docs/reference/Rplot009.png

docs/reference/Rplot010.png

docs/reference/bandicoot.gl.html

docs/reference/gi2gl.html

docs/reference/gl.He.html

docs/reference/gl.Ho.html

docs/reference/gl.LDNe.html

docs/reference/gl.alf-1.png

docs/reference/gl.alf.html

docs/reference/gl.amova.html

docs/reference/gl.assign.mahalanobis.html

docs/reference/gl.assign.pa.html

docs/reference/gl.assign.pca.html

docs/reference/gl.basic.stats.html

docs/reference/gl.blast.html

docs/reference/gl.check.verbosity.html

docs/reference/gl.collapse.html

docs/reference/gl.compliance.check.html

docs/reference/gl.costdistances.html

docs/reference/gl.define.pop.html

docs/reference/gl.diagnostics.hwe-1.png

docs/reference/gl.diagnostics.hwe-2.png

docs/reference/gl.diagnostics.hwe.html

docs/reference/gl.diagnostics.sim.html

docs/reference/gl.dist.ind-1.png

docs/reference/gl.dist.ind-2.png

docs/reference/gl.dist.ind-3.png

docs/reference/gl.dist.ind.html

docs/reference/gl.dist.pop-1.png

docs/reference/gl.dist.pop-2.png

docs/reference/gl.dist.pop-3.png

docs/reference/gl.dist.pop.html

docs/reference/gl.drop.ind.html

docs/reference/gl.drop.loc.html

docs/reference/gl.drop.pop.html

docs/reference/gl.edit.recode.ind.html

docs/reference/gl.edit.recode.pop.html

docs/reference/gl.evanno.html

docs/reference/gl.fdsim.html

docs/reference/gl.filter.allna.html

docs/reference/gl.filter.callrate-1.png

docs/reference/gl.filter.callrate-2.png

docs/reference/gl.filter.callrate-3.png

docs/reference/gl.filter.callrate-4.png

docs/reference/gl.filter.callrate-5.png

docs/reference/gl.filter.callrate-6.png

docs/reference/gl.filter.callrate.html

docs/reference/gl.filter.hamming-1.png

docs/reference/gl.filter.hamming.html

docs/reference/gl.filter.heterozygosity-1.png

docs/reference/gl.filter.heterozygosity.html

docs/reference/gl.filter.hwe.html

docs/reference/gl.filter.locmetrics.html

docs/reference/gl.filter.maf-1.png

docs/reference/gl.filter.maf.html

docs/reference/gl.filter.monomorphs.html

docs/reference/gl.filter.overshoot.html

docs/reference/gl.filter.pa.html

docs/reference/gl.filter.parent.offspring-1.png

docs/reference/gl.filter.parent.offspring-2.png

docs/reference/gl.filter.parent.offspring-3.png

docs/reference/gl.filter.parent.offspring.html

docs/reference/gl.filter.rdepth-1.png

docs/reference/gl.filter.rdepth-2.png

docs/reference/gl.filter.rdepth-3.png

docs/reference/gl.filter.rdepth.html

docs/reference/gl.filter.reproducibility-1.png

docs/reference/gl.filter.reproducibility-2.png

docs/reference/gl.filter.reproducibility-3.png

docs/reference/gl.filter.reproducibility-4.png

docs/reference/gl.filter.reproducibility.html

docs/reference/gl.filter.secondaries.html

docs/reference/gl.filter.sexlinked-1.png

docs/reference/gl.filter.sexlinked-2.png

docs/reference/gl.filter.sexlinked.html

docs/reference/gl.filter.taglength-1.png

docs/reference/gl.filter.taglength-2.png

docs/reference/gl.filter.taglength-3.png

docs/reference/gl.filter.taglength-4.png

docs/reference/gl.filter.taglength.html

docs/reference/gl.fixed.diff.html

docs/reference/gl.fst.pop.html

docs/reference/gl.genleastcost.html

docs/reference/gl.grm-1.png

docs/reference/gl.grm.html

docs/reference/gl.grm.network-1.png

docs/reference/gl.grm.network.html

docs/reference/gl.hwe.pop-1.png

docs/reference/gl.hwe.pop.html

docs/reference/gl.ibd-1.png

docs/reference/gl.ibd-2.png

docs/reference/gl.ibd-3.png

docs/reference/gl.ibd.html

docs/reference/gl.impute-1.png

docs/reference/gl.impute-2.png

docs/reference/gl.impute.html

docs/reference/gl.install.vanilla.dartR.html

docs/reference/gl.join.html

docs/reference/gl.keep.ind.html

docs/reference/gl.keep.loc.html

docs/reference/gl.keep.pop.html

docs/reference/gl.list.reports.html

docs/reference/gl.load.html

docs/reference/gl.make.recode.ind.html

docs/reference/gl.make.recode.pop.html

docs/reference/gl.map.interactive.html

docs/reference/gl.map.structure.html

docs/reference/gl.merge.pop.html

docs/reference/gl.nhybrids.html

docs/reference/gl.outflank-1.png

docs/reference/gl.outflank.html

docs/reference/gl.pcoa.html

docs/reference/gl.pcoa.plot-1.png

docs/reference/gl.pcoa.plot-10.png

docs/reference/gl.pcoa.plot-2.png

docs/reference/gl.pcoa.plot-3.png

docs/reference/gl.pcoa.plot-4.png

docs/reference/gl.pcoa.plot-5.png

docs/reference/gl.pcoa.plot-6.png

docs/reference/gl.pcoa.plot-7.png

docs/reference/gl.pcoa.plot-8.png

docs/reference/gl.pcoa.plot-9.png

docs/reference/gl.pcoa.plot.html

docs/reference/gl.percent.freq.html

docs/reference/gl.play.history.html

docs/reference/gl.plot.heatmap-1.png

docs/reference/gl.plot.heatmap-2.png

docs/reference/gl.plot.heatmap-3.png

docs/reference/gl.plot.heatmap-4.png

docs/reference/gl.plot.heatmap.html

docs/reference/gl.plot.multiSpaAC-1.png

docs/reference/gl.plot.multiSpaAC-2.png

docs/reference/gl.plot.multiSpaAC-3.png

docs/reference/gl.plot.multiSpaAC-4.png

docs/reference/gl.plot.multiSpaAC.html

docs/reference/gl.plot.network-1.png

docs/reference/gl.plot.network-2.png

docs/reference/gl.plot.network.html

docs/reference/gl.plot.structure.html

docs/reference/gl.print.history-1.png

docs/reference/gl.print.history-2.png

docs/reference/gl.print.history.html

docs/reference/gl.print.reports.html

docs/reference/gl.propShared.html

docs/reference/gl.random.snp-1.png

docs/reference/gl.random.snp-2.png

docs/reference/gl.random.snp-3.png

docs/reference/gl.random.snp.html

docs/reference/gl.read.csv.html

docs/reference/gl.read.dart.html

docs/reference/gl.read.silicodart.html

docs/reference/gl.read.vcf.html

docs/reference/gl.reassign.pop.html

docs/reference/gl.recalc.metrics.html

docs/reference/gl.recode.ind.html

docs/reference/gl.recode.pop.html

docs/reference/gl.rename.pop.html

docs/reference/gl.report.bases-1.png

docs/reference/gl.report.bases-2.png

docs/reference/gl.report.bases.html

docs/reference/gl.report.callrate-1.png

docs/reference/gl.report.callrate-2.png

docs/reference/gl.report.callrate-3.png

docs/reference/gl.report.callrate-4.png

docs/reference/gl.report.callrate-5.png

docs/reference/gl.report.callrate-6.png

docs/reference/gl.report.callrate.html

docs/reference/gl.report.diversity-1.png

docs/reference/gl.report.diversity.html

docs/reference/gl.report.hamming-1.png

docs/reference/gl.report.hamming-2.png

docs/reference/gl.report.hamming.html

docs/reference/gl.report.heterozygosity-1.png

docs/reference/gl.report.heterozygosity-2.png

docs/reference/gl.report.heterozygosity-3.png

docs/reference/gl.report.heterozygosity-4.png

docs/reference/gl.report.heterozygosity.html

docs/reference/gl.report.hwe-1.png

docs/reference/gl.report.hwe-2.png

docs/reference/gl.report.hwe.html

docs/reference/gl.report.ld.html

docs/reference/gl.report.ld.map.html

docs/reference/gl.report.locmetric-1.png

docs/reference/gl.report.locmetric-2.png

docs/reference/gl.report.locmetric.html

docs/reference/gl.report.maf-1.png

docs/reference/gl.report.maf.html

docs/reference/gl.report.monomorphs.html

docs/reference/gl.report.overshoot.html

docs/reference/gl.report.pa.html

docs/reference/gl.report.parent.offspring-1.png

docs/reference/gl.report.parent.offspring-2.png

docs/reference/gl.report.parent.offspring-3.png

docs/reference/gl.report.parent.offspring.html

docs/reference/gl.report.rdepth-1.png

docs/reference/gl.report.rdepth-2.png

docs/reference/gl.report.rdepth.html

docs/reference/gl.report.reproducibility-1.png

docs/reference/gl.report.reproducibility-2.png

docs/reference/gl.report.reproducibility.html

docs/reference/gl.report.secondaries-1.png

docs/reference/gl.report.secondaries-2.png

docs/reference/gl.report.secondaries.html

docs/reference/gl.report.sexlinked-1.png

docs/reference/gl.report.sexlinked-2.png

docs/reference/gl.report.sexlinked.html

docs/reference/gl.report.taglength-1.png

docs/reference/gl.report.taglength.html

docs/reference/gl.run.structure.html

docs/reference/gl.save.html

docs/reference/gl.select.colors-1.png

docs/reference/gl.select.colors-2.png

docs/reference/gl.select.colors-3.png

docs/reference/gl.select.colors-4.png

docs/reference/gl.select.colors-5.png

docs/reference/gl.select.colors-6.png

docs/reference/gl.select.colors-7.png

docs/reference/gl.select.colors.html

docs/reference/gl.select.shapes-1.png

docs/reference/gl.select.shapes-2.png

docs/reference/gl.select.shapes.html

docs/reference/gl.set.verbosity.html

docs/reference/gl.sim.WF.run.html

docs/reference/gl.sim.WF.table.html

docs/reference/gl.sim.create_dispersal.html

docs/reference/gl.sim.emigration.html

docs/reference/gl.sim.ind-1.png

docs/reference/gl.sim.ind.html

docs/reference/gl.sim.mutate.html

docs/reference/gl.sim.offspring.html

docs/reference/gl.smearplot-1.png

docs/reference/gl.smearplot-2.png

docs/reference/gl.smearplot.html

docs/reference/gl.spatial.autoCorr-1.png

docs/reference/gl.spatial.autoCorr.html

docs/reference/gl.subsample.loci.html

docs/reference/gl.test.heterozygosity-1.png

docs/reference/gl.test.heterozygosity-2.png

docs/reference/gl.test.heterozygosity.html

docs/reference/gl.tree.nj-1.png

docs/reference/gl.tree.nj-2.png

docs/reference/gl.tree.nj.html

docs/reference/gl.write.csv.html

docs/reference/gl2bayescan.html

docs/reference/gl2demerelate.html

docs/reference/gl2eigenstrat.html

docs/reference/gl2fasta-1.png

docs/reference/gl2fasta-2.png

docs/reference/gl2fasta.html

docs/reference/gl2faststructure.html

docs/reference/gl2gds.html

docs/reference/gl2genalex.html

docs/reference/gl2genepop.html

docs/reference/gl2geno.html

docs/reference/gl2gi.html

docs/reference/gl2hiphop.html

docs/reference/gl2phylip.html

docs/reference/gl2plink.html

docs/reference/gl2related.html

docs/reference/gl2sa.html

docs/reference/gl2sfs.html

docs/reference/gl2shp.html

docs/reference/gl2snapp.html

docs/reference/gl2structure.html

docs/reference/gl2svdquartets.html

docs/reference/gl2treemix.html

docs/reference/gl2vcf.html

docs/reference/index.html

docs/reference/interactive_reference.html

docs/reference/interactive_sim_run.html

docs/reference/is.fixed.html

docs/reference/libs/Proj4Leaflet-1.0.1/proj4leaflet.js

docs/reference/libs/htmlwidgets-1.5.4/htmlwidgets.js

docs/reference/libs/leaflet-1.3.1/images/layers-2x.png

docs/reference/libs/leaflet-1.3.1/images/layers.png

docs/reference/libs/leaflet-1.3.1/images/marker-icon-2x.png

docs/reference/libs/leaflet-1.3.1/images/marker-icon.png

docs/reference/libs/leaflet-1.3.1/images/marker-shadow.png

docs/reference/libs/leaflet-1.3.1/leaflet.css

docs/reference/libs/leaflet-1.3.1/leaflet.js

docs/reference/libs/leaflet-binding-2.1.1/leaflet.js

docs/reference/libs/leaflet-providers-1.9.0/leaflet-providers_1.9.0.js

docs/reference/libs/leaflet-providers-plugin-2.1.1/leaflet-providers-plugin.js

docs/reference/libs/leafletfix-1.0.0/leafletfix.css

docs/reference/libs/proj4-2.6.2/proj4.min.js

docs/reference/libs/rstudio_leaflet-1.3.1/images/1px.png

docs/reference/libs/rstudio_leaflet-1.3.1/rstudio_leaflet.css

docs/reference/platy-1.png

docs/reference/platy.html

docs/reference/platypus.gl.html

docs/reference/possums.gl.html

docs/reference/testset.gl.html

docs/reference/testset.gs.html

docs/reference/testset_SNPs_2Row.html

docs/reference/testset_metadata.html

docs/reference/testset_pop_recode.html

docs/reference/theme_dartR.html

docs/reference/utils.basic.stats.html

docs/reference/utils.check.datatype.html

docs/reference/utils.dart2genlight.html

docs/reference/utils.dist.binary.html

docs/reference/utils.dist.ind.snp.html

docs/reference/utils.flag.start.html

docs/reference/utils.hamming.html

docs/reference/utils.het.pop.html

docs/reference/utils.jackknife.html

docs/reference/utils.n.var.invariant.html

docs/reference/utils.outflank.MakeDiploidFSTMat.html

docs/reference/utils.outflank.html

docs/reference/utils.outflank.plotter.html

docs/reference/utils.read.dart.html

docs/reference/utils.recalc.avgpic.html

docs/reference/utils.recalc.callrate.html

docs/reference/utils.recalc.freqhets.html

docs/reference/utils.recalc.freqhomref.html

docs/reference/utils.recalc.freqhomsnp.html

docs/reference/utils.recalc.maf.html

docs/reference/utils.reset.flags.html

docs/reference/utils.spautocorr.html

docs/reference/utils.structure.evanno.html

docs/reference/utils.structure.genind2gtypes.html

docs/reference/utils.structure.run.html

docs/reference/zzz.html

docs/search.json

docs/sitemap.xml

gl.read.vcf.r

inst/CITATION

inst/extdata/dispersal_table.csv

inst/extdata/landscape.sim.rdata

inst/extdata/locus_1.fas

inst/extdata/platy.csv

inst/extdata/platy_ind.csv

inst/extdata/platy_test.csv

inst/extdata/ref_variables.csv

inst/extdata/sim_variables.csv

inst/extdata/test.vcf

inst/extdata/testset_SNPs_2Row.csv

inst/extdata/testset_SilicoDArT.csv

inst/extdata/testset_ind_recode.csv

inst/extdata/testset_metadata.csv

inst/extdata/testset_metadata_silicodart.csv

inst/extdata/testset_pop_recode.csv

man/bandicoot.gl.Rd man/cbind.dartR.Rd

man/figures/ACT.png

man/figures/DArT-removebg-preview.png

man/figures/DArT_logo.png

man/figures/Figure_1.png

man/figures/Monash.png

man/figures/UC.png

man/figures/csiro_logo.png

man/figures/dartRlogo.png

man/figures/monashlogo_white.png

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

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 Sept. 7, 2024, 4:15 a.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

green-striped-gecko/dartR
Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Files in green-striped-gecko/dartR
Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

R Package Documentation

Browse R Packages

We want your feedback!

green-striped-gecko/dartR Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Files in green-striped-gecko/dartR Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

R Package Documentation

Browse R Packages

We want your feedback!

green-striped-gecko/dartR
Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Files in green-striped-gecko/dartR
Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis