allele.counts           This counts the number of alleles at a locus.
bins                    Example heterozygosity bins from fsthet.
calc.actual.fst         This calcualtes global Fsts from a genepop
                        dataframe.
calc.allele.freq        This calculates allele frequencies.
calc.betahat            This calculates beta-hat, the Fst value used in
                        Lositan.
calc.exp.het            This calculates expected heterozygosities.
calc.fst                This calculates Fst.
calc.theta              This calculates theta.
ci.means                This calculates the average confidence
                        intervals from multiple bootstrap outputs.
cis                     Example dataframe of smoothed quantiles from
                        fsthet
cis.list                Example list of CI matrices from bootstrap
                        output from numerical simulations
fhetboot                This is a wrapper to run the bootstrapping and
                        plot the confidence intervals and significant
                        loci.
find.outliers           This identifies all of the SNPs outside of the
                        smoothed quantiles in the dataset.
find.quantiles          Generates quantiles from binned Fst values
fst.boot                This is the major bootstrapping function to
                        calculate confidence intervals.
fst.boot.means          Calculates mean values within the bins.
fst.boot.onecol         This bootstraps across all individuals to
                        calculate a bootstrapped Fst for a
                        randomly-sampled locus.
fst.options.print       This prints the options for choosing an Fst
                        calculation.
fsthet                  This is a wrapper to generate and plot the
                        smoothed quantiles and identify outliers.
fsts                    Example fst calculations from a genepop file.
fsts.beta               Example fst calculations from a genepop file.
fsts.betahat            Example fst calculations from a genepop file.
fsts.theta              Example fst calculations from a genepop file.
gpop                    Example genepop file from numerical simulations
make.bins               This sorts Fst values into a designated number
                        of overlapping heterozygosity bins.
my.read.genepop         This reads a genepop file into R
p.boot                  Calculates mean values within the bins.
plotting.cis            This plots a dataframe of fsts with
                        bootstrapped confidence intervals.
quant.out               Example fsthet output based on numerical
                        simulations
remove.spaces           This removes spaces from a character vector
var.fst                 This calculates Cockerham & Weir's Beta.
