AIc                     Calculates corrected Assignment Index
TajimaD.dosage          Estimates Tajima's D
allele.count            Allelic counts
allelic.richness        Estimates allelic richness
basic.stats             Basic diversity and differentiation statistics
beta.dosage             Estimates pairwise kinships and individual
                        inbreeding coefficients from dosage data
betas                   Estimates betas per population and a bootstrap
                        confidence interval
biall2dos               Converts bi-allelic SNPs from hierfstat format
                        to dosage format
boot.ppbetas            Estimates bootstrap confidence intervals for
                        pairwise betas FST estimates
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
                        continent-island model
cont.isl99              A genetic dataset from a diploid organism in a
                        continent-island model
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 locus
fs.dosage               Estimates F-statistics from dosage data
fstat2dos               Converts a hierfstat genetic data frame to
                        dosage data
g.stats                 Calculates likelihood-ratio G-statistic on
                        contingency table
g.stats.glob            Likelihood ratio G-statistic over loci
genet.dist              Classical genetic distances estimation
genind2hierfstat        Converts genind objects from adegenet into a
                        hierfstat data frame
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 matrix
gtrunchier              Genotypes at 6 microsatellite loci of Galba
                        truncatula from different patches in Western
                        Switzerland
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.WCfst          Estimates pairwise FSTs according to Weir and
                        Cockerham (1984)
pairwise.betas          Estimates pairwise betas according to Weir and
                        Goudet (2017)
pairwise.neifst         Estimates pairwise FSTs according to Nei (1987)
pcoa                    Principal coordinate analysis
pi.dosage               Estimates nucleotide diversity (pi) from dosage
                        data
pop.freq                Allelic frequencies
pp.fst                  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 QuantiNemo
                        (<http://www2.unil.ch/popgen/softwares/quantinemo/>)
                        genotype files extended format (option 2)
read.VCF                Reads a VCF file into a BED object
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 by Hudson ms program, either as
                        Haplotypes or as SNPs.
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
test.between            Tests the significance of the effect of
                        test.lev on genetic differentiation
test.between.within     Tests the significance of the effect of
                        test.lev on genetic differentiation
test.g                  Tests the significance of the effect of level
                        on genetic differentiation
test.within             Tests the significance of the effect of
                        inner.level on genetic differentiation within
                        blocks defined by outer.level
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 over all loci
vec2mat                 Fills a triangular matrix from the inputed
                        vector
wc                      Computes Weir and Cockrham estimates of
                        Fstatistics
write.bayescan          Writes a bayescan file
write.fstat             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
