├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── a.R ├── ae.R ├── allele_counts.R ├── alleles.R ├── as_data_frame.R ├── bad_parents.R ├── column_class.R ├── cov2dist.R ├── dest.R ├── dist2cov.R ├── dist_amova.R ├── dist_bray.R ├── dist_cavalli.R ├── dist_cgd.R ├── dist_euclidean.R ├── dist_jaccard.R ├── dist_nei.R ├── dist_ss.R ├── distance_to_covariance.R ├── exclusion_probability.R ├── fis.R ├── frequencies.R ├── frequency_matrix.R ├── fst.R ├── gendist_nei_test.R ├── genetic_autocorrealtion.R ├── genetic_distance.R ├── genetic_diversity.R ├── genetic_relatedness.R ├── genetic_structure.R ├── genotype_counts.R ├── genotype_frequencies.R ├── geom_frequencies.R ├── geom_locus.R ├── geom_strata.R ├── geom_strata_label.R ├── gst.R ├── gst_prime.R ├── gstudio-package.R ├── harmonic_mean.R ├── he.R ├── hes.R ├── hi.R ├── ho.R ├── hos.R ├── ht.R ├── hwe.R ├── indices.R ├── is_frequency.R ├── is_heterozygote.R ├── is_na.R ├── kronecker_delta.R ├── lag_matrix.R ├── locus.R ├── make_loci.R ├── make_population.R ├── make_populations.R ├── mate.R ├── maximum_allele_size.R ├── migrate.R ├── minus_mom.R ├── mixed_mating.R ├── multilocus_assignment.R ├── multilocus_diversity.R ├── optimal_sampling.R ├── parent_finder.R ├── partition.R ├── paternity.R ├── pe.R ├── permute_ci.R ├── permute_matrix.R ├── pies_on_map.R ├── ploidy.R ├── plot.R ├── population_graph.R ├── rarefaction.R ├── read012.R ├── read_population.R ├── rel_lynch.R ├── rel_nason.R ├── rel_queller.R ├── rel_ritland.R ├── spiderplot_data.R ├── strata_coordinates.R ├── strata_distance.R ├── subsample_loci.R ├── to_dfdist.R ├── to_fixed_locus.R ├── to_genepop.R ├── to_mv.R ├── to_mv_freq.R ├── to_structure.R ├── transition_probability.R └── write_population.R ├── README.md ├── data ├── aflp_arapat.rda ├── arapat.rda ├── cornus.rda └── cornus_florida.rda ├── inst └── extdata │ ├── data_2_column.csv │ ├── data_aflp.csv │ ├── data_separated.csv │ ├── data_snp.csv │ ├── data_structure.str │ ├── data_zymelike.csv │ ├── genepop.txt │ ├── grid.csv │ └── snp_prob.csv ├── man ├── A.Rd ├── Ae.Rd ├── Dest.Rd ├── Fis.Rd ├── Fst.Rd ├── Gst.Rd ├── Gst_prime.Rd ├── He.Rd ├── Hes.Rd ├── Hi.Rd ├── Ho.Rd ├── Hos.Rd ├── Ht.Rd ├── Pe.Rd ├── aflp_arapat.Rd ├── allele_counts.Rd ├── alleles.Rd ├── arapat.Rd ├── as.data.frame.locus.Rd ├── as.list.locus.Rd ├── as.locus.Rd ├── bad_parents.Rd ├── c.locus.Rd ├── column_class.Rd ├── cornus.Rd ├── cornus_florida.Rd ├── cov2dist.Rd ├── data_2_column.Rd ├── data_aflp.Rd ├── data_separated.Rd ├── data_snp.Rd ├── data_zymelike.Rd ├── dist2cov.Rd ├── dist_amova.Rd ├── dist_bray.Rd ├── dist_cavalli.Rd ├── dist_cgd.Rd ├── dist_euclidean.Rd ├── dist_jaccard.Rd ├── dist_nei.Rd ├── dist_ss.Rd ├── distance_to_covariance.Rd ├── exclusion_probability.Rd ├── frequencies.Rd ├── frequency_matrix.Rd ├── from012.Rd ├── genetic_autocorrelation.Rd ├── genetic_distance.Rd ├── genetic_diversity.Rd ├── genetic_relatedness.Rd ├── genetic_structure.Rd ├── genotype_counts.Rd ├── genotype_frequencies.Rd ├── geom_frequencies.Rd ├── geom_locus.Rd ├── geom_strata.Rd ├── geom_strata_label.Rd ├── grid.csv.Rd ├── gstudio-package.Rd ├── harmonic_mean.Rd ├── hwe.Rd ├── indices.Rd ├── is.locus.Rd ├── is.na.locus.Rd ├── is_frequency.Rd ├── is_heterozygote.Rd ├── kronecker_delta.Rd ├── lag_matrix.Rd ├── locus-operator-index.Rd ├── locus-operator-minus.Rd ├── locus-operator-plus.Rd ├── locus.Rd ├── make_loci.Rd ├── make_population.Rd ├── make_populations.Rd ├── mate.Rd ├── maximum_allele_size.Rd ├── migrate.Rd ├── minus_mom.Rd ├── mixed_mating.Rd ├── multilocus_assignment.Rd ├── multilocus_diversity.Rd ├── optimal_sampling.Rd ├── parent_finder.Rd ├── partition.Rd ├── paternity.Rd ├── permute_ci.Rd ├── permute_matrix.Rd ├── ploidy.Rd ├── plot.locus.Rd ├── population_graph.Rd ├── print.locus.Rd ├── rarefaction.Rd ├── read_population.Rd ├── rel_lynch.Rd ├── rel_nason.Rd ├── rel_queller.Rd ├── rel_ritland.Rd ├── rep.locus.Rd ├── snp_prob.csv.Rd ├── spiderplot_data.Rd ├── strata_coordinates.Rd ├── strata_distance.Rd ├── subsample_loci.Rd ├── summary.locus.Rd ├── to_dfdist.Rd ├── to_fixed_locus.Rd ├── to_genepop.Rd ├── to_mv.Rd ├── to_mv_freq.Rd ├── to_structure.Rd ├── transition_probability.Rd └── write_population.Rd └── tests ├── testthat.R └── testthat ├── .gitignore ├── test-A.R ├── test-Ae.R ├── test-Pe.R ├── test-alleles.R ├── test-as_data_frame.R ├── test-bad_parents.R ├── test-column_class.R ├── test-dest.R ├── test-dist_amova.R ├── test-dist_bray.R ├── test-dist_cavalli.R ├── test-dist_cgd.R ├── test-dist_euclidean.R ├── test-dist_jaccard.R ├── test-dist_nei.R ├── test-dist_ss.R ├── test-f_statistics.R ├── test-frequencies.R ├── test-frequency_matrix.R ├── test-fst.R ├── test-genetic_distance.R ├── test-genetic_diversity.R ├── test-genetic_relatedness.R ├── test-genetic_structure.R ├── test-genotype_counts.R ├── test-genotype_frequencies.R ├── test-geom_frequencies.R ├── test-geom_locus.R ├── test-geom_strata.R ├── test-gst.R ├── test-gst_prime.R ├── test-he.R ├── test-hi.R ├── test-ho.R ├── test-ht.R ├── test-indices.R ├── test-is_heterozygote.R ├── test-is_na.R ├── test-kronecker_delta.R ├── test-lab_matrix.R ├── test-locus.R ├── test-make_loci.R ├── test-make_population.R ├── test-make_populations.R ├── test-mate.R ├── test-maximum_allele_size.R ├── test-minus_mom.R ├── test-mixed_mating.R ├── test-multilocus_assignment.R ├── test-multilocus_diversity.R ├── test-parent_finder.R ├── test-partition.R ├── test-paternity.R ├── test-permute_ci.R ├── test-pies_on_map.R ├── test-ploidy.R ├── test-plot.R ├── test-rarefaction.R ├── test-read_population.R ├── test-rel_lynch.R ├── test-rel_nason.R ├── test-rel_queller.R ├── test-rel_ritland.R ├── test-strata_coordinates.R ├── test-strata_distance.R ├── test-to_fixed_locus.R ├── test-to_genepop.R ├── test-to_mv.R ├── test-to_structure.R ├── test-transition_probability.R └── test-write_population.R /.Rbuildignore: 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