allelefurcation-class   An S4 class containing furcation trees for one
                        allele of a focal marker
as.newick               Convert a furcation tree into Newick format
calc_candidate_regions
                        Determine candidate regions of selection
calc_ehh                EHH and iHH computation for a given focal
                        marker
calc_ehhs               EHHS and iES computation for a given focal
                        marker
calc_furcation          calculate furcation trees around a focal marker
calc_haplen             Calculate length of longest shared haplotypes
                        around a focal marker
calc_pairwise_haplen    Calculate pairwise shared haplotype length
                        between all chromosomes
calc_region_stats       Calculate score statistics for given regions
calc_sfs_tests          Calculate site frequency spectrum test
                        statistics
data2haplohh            Convert data from input file to an object of
                        class haplohh
distribplot             Plot distribution of standardized iHS, Rsb or
                        XP-EHH values
extract_regions         Extract regions from a scan
freqbinplot             Plot of unstandardized iHS within frequency
                        bins
ftree-class             An S4 class to represent a furcation tree on
                        one side of one allele of a focal marker
furcation-class         An S4 class representing the complete furcation
                        pattern around a focal marker.
haplen-class            class for haplotype length
haplohh-class           Class "haplohh"
haplohh2sweepfinder     Translate object of 'haplohh-class' into
                        SweepFinder format
haplohh_cgu_bta12       Example of an 'haplohh' object
ies2xpehh               Compute XP-EHH
ihh2ihs                 Compute iHS
ines2rsb                Compute Rsb
make.example.files      Copy example input files into current working
                        directory
manhattanplot           Manhattan plot of iHS, XP-EHH or Rsb over a
                        genome.
plot.ehh                Plot EHH around a focal marker
plot.ehhs               Plot EHHS around a focal marker
plot.furcation          Plots furcation trees around a focal marker
plot.haplen             Plot the length of extended haplotypes around a
                        focal marker
plot.haplohh            Plot the variants of a haplohh object
rehh-package            rehh: Searching for Footprints of Selection
                        using 'Extended Haplotype Homozygosity' Based
                        Tests
remove.example.files    Remove example files from current working
                        directory.
scan_hh                 Compute iHH, iES and inES over a whole
                        chromosome
scan_hh_full            Compute iHH, iES and inES over a whole
                        chromosome without cut-offs
subset.haplohh          Subsets object of 'haplohh-class'
update_haplohh          Update object of class haplohh
