bandicoot.gl            A genlight object created via the read.dart
                        functions
dart2genlight           Convert DarT to genlight
gi2gl                   Converts a genind object to genlight object
gl.Ho                   A very simple function to report observed
                        Heterozygosity
gl.Hs                   A very simple function to report expected
                        Heterozygosity
gl.alf                  Calculates allele frequency of the first and
                        second allele for each loci #' A very simple
                        function to report allele frequencies
gl.amova                Performs and AMOVA using genlight data.
gl.assign               Assign an individual of unknown provenance to
                        population
gl.basic.stats          Calculates basic statistics for each loci (Hs,
                        Ho, Fis etc.)
gl.collapse             Collapse a distance matrix by amalgamating
                        populations
gl.collapse.pval        Collapse a fixed distance matrix by
                        amalgamating populations for which fixed
                        differences are not significant
gl.collapse.recursive   Recursively collapse a distance matrix by
                        amalgamating populations
gl.costdistances        Calculates cost distances for a given landscape
                        (resistance matrix)
gl.define.pop           Define a new population in a genelight
                        {adegenet} object on the basis of specified
                        individuals
gl.dist.heatmap         Represent a distance matrix as a heatmap
gl.dist.pop             Calculate a distance matrix for populations
                        defined in an {adegenet} genlight object
gl.diversity            Calculate diversity indices for SNPs
gl.drop.ind             Remove specified individuals from a genelight
                        {adegenet} object
gl.drop.loc             Remove specified loci from a genelight
                        {adegenet} object
gl.drop.pop             Remove specified populations from a genelight
                        {adegenet} object
gl.edit.recode.ind      Create or edit a individual (=specimen) names
                        and create an recode_ind file
gl.edit.recode.pop      Create or edit a population re-assignment table
gl.filter.callrate      Filter loci or specimens in a genlight
                        {adegenet} object based on call rate
gl.filter.cloneid       Filter for CloneID to select only unique SNPs
gl.filter.hamming       Filters loci in a genlight object based on
                        pairwise Hamming distance between sequence tags
gl.filter.hwe           Filters loci that show significant departure
                        from Hardy-Weinberg Equilibrium
gl.filter.maf           Filter loci on the basis of minor allele
                        frequency (MAF) in a genlight adegenet object
gl.filter.monomorphs    Remove monomorphic loci, including those with
                        all NAs
gl.filter.repavg        Filter loci in a genlight {adegenet} object
                        based on average repeatability of alleles at a
                        locus
gl.filter.secondaries   Filter loci that represent secondary SNPs in a
                        genlight {adegenet} object
gl.fixed.diff           Generate a matrix of fixed differences from a
                        genelight or genind object {adegenet}
gl.fst.pop              Calculate a pairwise fst values for populations
                        in a genlight object
gl.gene.freq            Calculate a statistic for each locus by group
                        An internal function essentially to convey
                        readability to rather contorted R code.  It
                        takes as input a genlight {adegenet} object
                        with an index variable (say, population) and
                        calculates the selected statistic for each
                        locus, broken down by the groups defined by the
                        index variable.
gl.genleastcost         Least-cost path analysis based on a friction
                        matrix
gl.grm                  Calculates the genomic relatedness matrix
gl.grm.network          Represents a genomic relatedness matrix as a
                        network
gl.hwe.pop              Filter function to facilitate analysing of dart
                        data
gl.ibd                  Isolation by distance
gl.keep.ind             Remove all but the specified individuals from a
                        genelight {adegenet} object
gl.keep.pop             Remove all but specified populations from a
                        genelight {adegenet} object
gl.make.recode.ind      Create a proforma recode_ind file for
                        reassigning individual (=specimen) names
gl.make.recode.pop      Create a proforma recode_pop_table file for
                        reassigning population names
gl.map.interactive      Creates an interactive map (based on latlong)
                        from a genlight object
gl.merge.pop            Merge two or more populations in a genelight
                        {adegenet} object into one population
gl.nhybrids             Create an input file for the program NewHybrids
                        and run it if NewHybrids is installed
gl.outflank             Function to identify loci under selection per
                        population using the outflank method of
                        Whitlock and Lotterhos (2015)
gl.pcoa                 PCoA ordination (glPca)
gl.pcoa.plot            Bivariate plot of the results of a PCoA
                        ordination
gl.pcoa.plot.3d         3D interactive plot of the results of a PCoA
                        ordination
gl.pcoa.pop             PCoA ordination of populations
gl.pcoa.scree           Produce a plot of eigenvalues, standardized as
                        percentages, derived from a PCoA
gl.percent.freq         Generate percentage allele frequencies by locus
                        and population
gl.plot                 Plotting genlight object
gl.read.dart            Import DarT data into R and conver it to a
                        genlight object
gl.read.dart.2row       Import SNP data from DArT and convert to
                        genlight {agegenet} format (gl)
gl.read.silicodart      Import presence/absence data from SilicoDArT
                        and convert to genind {agegenet} format
gl.recalc.metrics       Recalculate locus metrics when individuals or
                        populations are deleted from a genlight
                        {adegenet} object
gl.recode.ind           Recode individual (=specimen) labels in a
                        genelight or genind object {adegenet}
gl.recode.pop           Recode population assignments in a genelight
                        object {adegenet}
gl.report.bases         Summary of base pair frequencies
gl.report.callrate      Report summary of Call Rate for loci or
                        individuals
gl.report.hamming       Calculates the pairwise Hamming distance
                        between DArT trimmed DNA sequences
gl.report.heterozygosity
                        Reports hetrozygosity
gl.report.hwe           Reports departure from Hardy-Weinberg
                        Equilibrium
gl.report.ld            Calculates pairwise population based Linkage
                        Disequilibirum across all loci using the
                        specifyied number of cores
gl.report.maf           Report minor allele frequency (MAF) for each
                        locus in a genlight adegenet object
gl.report.monomorphs    Report monomorphic loci, including those with
                        all NAs
gl.report.pa            Report number of private alleles possessed by
                        an individual of unknown provenance
gl.report.pa.pop        Report private alleles (and fixed alleles) per
                        pair of populations
gl.report.repavg        Report summary of RepAvg, reproducibility
                        averaged over both alleles for each locus in a
                        genlight adegenet object
gl.report.secondaries   Report loci containing secondary SNPs in a
                        genlight {adegenet} object
gl.sexlinkage           Identify loci that are sex linked in specimens
                        in a genlight {adegenet} object
gl.sim.ind              Simulates individuals based on the allele
                        frequencies provided via a genlight object.
gl.sim.offspring        Simulates a specified number of offsprings
                        based on alleles provided by potential
                        father(s) and mother(s)
gl.subsample.loci       Subsample n loci from a genlight object and
                        return as a genlight object
gl.tree.nj              Output an nj tree to summarize genetic
                        similarity among populations
gl.utils.fdsim          Estimate the rate of false positives in a fixed
                        difference analysis
gl.write.csv            Write out data from a gl object adegenet to csv
                        file
gl2demerelate           Create a dataframe suitable for input to
                        package {Demerelate} from a genlight {adegenet}
                        object
gl2fasta                Concatenates DArT trimmed sequences and outputs
                        a fastA file.
gl2faststructure        Export DArT genlight object {adegenet} to
                        faststructure format (to run faststructure
                        elsewhere)
gl2gds                  Convert a genlight object to nexus format PAUP
                        SVDquartets
gl2gi                   Converts a genlight object to genind object
gl2phylip               Create a Phylip input distance matrix from a
                        genlight (SNP) or genind (SilicoDarT)
                        {adegenet} object
gl2plink                Converts a genlight object to plink file format
gl2sa                   Convert genlight objects to the format used in
                        the SNPassoc package
gl2shp                  Convert genlight objects to ESRI shapefiles or
                        kml files
gl2snapp                Convert a genlight object to nexus format
                        suitable for phylogenetic analysis by SNAPP
                        (via BEAUti)
gl2structure            Converts genlight objects to STRUCTURE formated
                        files
gl2svdquartets          Convert a genlight object to nexus format PAUP
                        SVDquartets
gl2treemix              Convert a genlight object to a treemix input
                        file
is.fixed                Test to see if two populations are fixed at a
                        given locus
platy                   Example data set as text file to be imported
                        into a genlight object
possums.gl              A simulated genlight object created to run a
                        landscape genetic example
prob.hwe                Exact SNP test of Hardy-Weinberg Equilibrium
read.dart               Import DarT data to R
testset.gl              A genlight object created via the read.dart
                        functions
testset_SNPs_2Row       Testfile in DArT format (as provided by DArT)
testset_metadata        Metadata file. Can be integrated via the
                        dart2genlight function.
testset_pop_recode      Recode file to be used with the function.
util.outflank           OutFLANK: An Fst outlier approach by Mike
                        Whitlock and Katie Lotterhos, University of
                        British Columbia.
util.outflank.MakeDiploidFSTMat
                        Creates OutFLANK input file from individual
                        genotype info.
util.outflank.plotter   Plotting functions for Fst distributions after
                        OutFLANK This function takes the output of
                        OutFLANK as input with the OFoutput parameter.
                        It plots a histogram of the FST (by default,
                        the uncorrected FSTs used by OutFLANK) of loci
                        and overlays the inferred null histogram.
utils.hamming           Calculates the Hamming distance between two
                        DArT trimmed DNA sequences
utils.hwe               Calculates departure from Hardy-Weinberg
                        Equilibrium. Utility script not meant for end
                        users.
utils.recalc.avgpic     A utility script to recalculate the
                        OneRatioRef, OneRatioSnp, PICRef, PICSnp, and
                        AvgPIC by locus after some populations have
                        been deleted.
utils.recalc.callrate   A utility script to recalculate the callrate by
                        locus after some populations have been deleted
utils.recalc.freqhets   A utility script to recalculate the the
                        frequency of the heterozygous SNPs by locus
                        after some populations have been deleted
utils.recalc.freqhomref
                        A utility script to recalculate the the
                        frequency of the homozygous reference SNP by
                        locus after some populations have been deleted
utils.recalc.freqhomsnp
                        A utility script to recalculate the the
                        frequency of the homozygous alternate SNP by
                        locus after some populations have been deleted
utils.recalc.maf        A utility script to recalculate the the minor
                        allele frequency by locus, typically after some
                        populations have been deleted
