| AIc | Calculates corrected Assignment Index |
| allele.count | Allelic counts |
| allelic.richness | Estimates allelic richness |
| basic.stats | Basic diversity and differentiation statistics |
| beta.dosage | Estimates pairwise kinships and individual inbreeding... |
| betas | Estimates betas per population and a bootstrap confidence... |
| biall2dos | Converts bi-allelic SNPs from hierfstat format to dosage... |
| boot.ppbetas | Estimates bootstrap confidence intervals for pairwise betas... |
| boot.ppfis | Performs bootstrapping over loci of population's Fis |
| boot.ppfst | Performs bootstrapping over loci of pairwise Fst |
| boot.vc | Bootstrap confidence intervals for variance components |
| cont.isl | A genetic dataset from a diploid organism in a... |
| cont.isl99 | A genetic dataset from a diploid organism in a... |
| crocrussula | Genotypes and sex of 140 shrews Crocidura russula |
| diploid | A genetic dataset from a diploid organism |
| exhier | Example data set with 4 levels, one diploid and one haploid... |
| fs.dosage | Estimates F-statistics from dosage data |
| fstat2dos | Converts a hierfstat genetic data frame to dosage data |
| genet.dist | Classical genetic distances estimation |
| genind2hierfstat | Converts genind objects from adegenet into a hierfstat data... |
| genot2al | Separates diploid genotypes in its constituant alleles |
| getal | Converts diploid genotypic data into allelic data |
| getal.b | Converts diploid genotypic data into allelic data |
| grm2kinship | Converts a Genetic Relationship Matrix (GRM) to a kinship... |
| g.stats | Calculates likelihood-ratio G-statistic on contingency table |
| g.stats.glob | Likelihood ratio G-statistic over loci |
| gtrunchier | Genotypes at 6 microsatellite loci of Galba truncatula from... |
| hierfstat | General information on the hierfstat package |
| ind.count | individual counts |
| indpca | PCA on a matrix of individuals genotypes frequencies |
| kinship2dist | Converts a kinship matrix to a distance matrix |
| kinship2grm | Converts a kinship matrix to a Genetic Relation Matrix (GRM) |
| kinshipShift | Shifts a kinship matrix |
| mat2vec | Creates a vector from a matrix |
| matching | Estimates matching between pairs of individuals |
| ms2bed | Import the output of the 'ms' program in a 'BED' object |
| ms2dos | Import 'ms' output |
| nb.alleles | Number of different alleles |
| pairwise.betas | Estimates pairwise betas according to Weir and Goudet (2017) |
| pairwise.neifst | Estimates pairwise FSTs according to Nei (1987) |
| pairwise.WCfst | Estimates pairwise FSTs according to Weir and Cockerham... |
| pcoa | Principal coordinate analysis |
| pi.dosage | Estimates nucleotide diversity (pi) from dosage data |
| pop.freq | Allelic frequencies |
| ppfst | fst per pair |
| pp.sigma.loc | wrapper to return per locus variance components |
| print.pp.fst | print function for pp.fst |
| qn2.read.fstat | Read QuantiNemo extended format for genotype files Read... |
| read.fstat | Reads data from a FSTAT file |
| read.fstat.data | Reads data from a FSTAT file |
| read.ms | Read data generated by Hudson ms program Read data generated... |
| read.VCF | Reads a VCF file into a BED object |
| samp.between | Shuffles a sequence among groups defined by the input vector |
| samp.between.within | Shuffles a sequence |
| samp.within | Shuffles a sequence within groups defined by the input vector |
| sexbias.test | Test for sex biased dispersal |
| sim.freq | Simulates frequencies, for internal use only |
| sim.genot | Simulates genotypes in an island model at equilibrium |
| sim.genot.metapop.t | Simulate genetic data from a metapopulation model |
| sim.genot.t | Simulate data from a non equilibrium continent-island model |
| subsampind | Subsample a FSTAT data frame |
| TajimaD.dosage | Estimates Tajima's D |
| test.between | Tests the significance of the effect of test.lev on genetic... |
| test.between.within | Tests the significance of the effect of test.lev on genetic... |
| test.g | Tests the significance of the effect of level on genetic... |
| test.within | Tests the significance of the effect of inner.level on... |
| theta.Watt.dosage | Estimates theta_{Watterson} from dosage data |
| varcomp | Estimates variance components for each allele of a locus |
| varcomp.glob | Estimate variance components and hierarchical F-statistics... |
| vec2mat | Fills a triangular matrix from the inputed vector |
| wc | Computes Weir and Cockrham estimates of Fstatistics |
| write.bayescan | Writes a bayescan file |
| writefstat | Write an Fstat data file |
| write.ped | Write ped file for analyses with PLINK |
| write.struct | Write structure file |
| yangex | Example data set from Yang (1998) appendix |
