[,dartR,ANY,ANY,ANY-method
                        indexing dartR objects correctly...
cbind.dartR             adjust cbind for dartR
gl.He                   Estimates expected Heterozygosity
gl.Ho                   Estimates observed Heterozygosity
gl.add.indmetrics       Adds metadata into a genlight object
gl.alf                  Calculates allele frequency of the first and
                        second allele for each locus A very simple
                        function to report allele frequencies
gl.allele.freq          Generates percentage allele frequencies by
                        locus and population
gl.amova                Performs AMOVA using genlight data
gl.check.verbosity      Checks the current global verbosity
gl.check.wd             Checks the global working directory
gl.colors               Returns a list of colors for use in plots
gl.compliance.check     Checks a genlight object to see if it complies
                        with dartR expectations and amends it to comply
                        if necessary @family environment
gl.define.pop           Defines a new population in a genlight object
                        for specified individuals
gl.diagnostics.hwe      Provides descriptive stats and plots to
                        diagnose potential problems with Hardy-Weinberg
                        proportions @family matched report
gl.dist.ind             Calculates a distance matrix for individuals
                        defined in a genlight object
gl.dist.phylo           Generates a distance matrix from a SNP genlight
                        object taking into account a substitution model
gl.dist.pop             Calculates a distance matrix for populations
                        with SNP or Silicodart genotypes in a genlight
                        object
gl.drop.ind             Removes specified individuals from a dartR
                        genlight object
gl.drop.loc             Removes specified loci from a dartR genlight
                        object
gl.drop.pop             Removes specified populations from a dartR
                        genlight object
gl.edit.recode.ind      Creates or edits individual (=specimen) names,
                        creates a recode_ind file and applies the
                        changes to a genlight object @family data
                        manipulation
gl.edit.recode.pop      Creates or edits and applies a population
                        re-assignment table
gl.fdsim                Estimates the rate of false positives in a
                        fixed difference analysis
gl.filter.allna         Filters loci that are all NA across individuals
                        and/or populations with all NA across loci
gl.filter.callrate      Filters loci or specimens in a genlight
                        {adegenet} object based on call rate
gl.filter.excess.het    Filters excessively-heterozygous loci from a
                        genlight object
gl.filter.factorloadings
                        Filters loci based on factor loadings for a PCA
                        or PCoA
gl.filter.hamming       Filters loci based on pairwise Hamming distance
                        between sequence tags
gl.filter.heterozygosity
                        Filters individuals with average heterozygosity
                        greater than a specified upper threshold or
                        less than a specified lower threshold @family
                        matched filter
gl.filter.hwe           Filters loci that show significant departure
                        from Hardy-Weinberg Equilibrium @family matched
                        filter
gl.filter.ld            Filters loci based on linkage disequilibrium
                        (LD)
gl.filter.locmetric     Filters loci on the basis of numeric
                        information stored in other$loc.metrics in a
                        genlight {adegenet} object
gl.filter.maf           Filters loci on the basis of minor allele
                        frequency (MAF) or minor allele count (MAC)
gl.filter.monomorphs    Filters monomorphic loci, including those with
                        all NAs
gl.filter.overshoot     Filters loci for which the SNP has been trimmed
                        from the sequence tag along with the adaptor
gl.filter.pa            Filters loci that contain private (and fixed
                        alleles) between two populations
gl.filter.rdepth        Filters loci based on counts of sequence tags
                        scored at a locus (read depth) @family matched
                        filter
gl.filter.reproducibility
                        Filters loci in a genlight {adegenet} object
                        based on average repeatability of alleles at a
                        locus @family matched filter
gl.filter.secondaries   Filters loci that represent secondary SNPs in a
                        genlight object
gl.filter.taglength     Filters loci in a genlight {adegenet} object
                        based on sequence tag length @family matched
                        filter
gl.fixed.diff           Generates a matrix of fixed differences and
                        associated statistics for populations taken
                        pairwise
gl.fst.pop              Calculates a pairwise Fst values for
                        populations in a genlight object This script
                        calculates pairwise Fst values based on the
                        implementation in the StAMPP package
                        (?stamppFst). It allows to run bootstrap to
                        estimate probability of Fst values to be
                        different from zero. For detailed information
                        please check the help pages (?stamppFst).
gl.hwe.pop              Performs Hardy-Weinberg tests over loci and
                        populations
gl.impute               Imputes missing data
gl.join                 Combines two dartR genlight objects
gl.keep.ind             Removes all but the specified individuals from
                        a dartR genlight object
gl.keep.loc             Removes all but the specified loci from a
                        genlight object
gl.keep.pop             Removes all but the specified populations from
                        a dartR genlight object
gl.load                 Loads an object from compressed binary format
                        produced by gl.save()
gl.mahal.assign         Assigns individuals to populations with an
                        associated probability
gl.make.recode.ind      Creates a proforma recode_ind file for
                        reassigning individual (=specimen) names
gl.make.recode.pop      Creates a proforma recode_pop_table file for
                        reassigning population names @family data
                        manipulation
gl.map.interactive      Creates an interactive map (based on latlon)
                        from a genlight object
gl.merge.pop            Merges two or more populations in a dartR
                        genlight object into one population
gl.pcoa                 Ordination applied to genotypes in a genlight
                        object (PCA), in an fd object, or to a distance
                        matrix (PCoA)
gl.pcoa.plot            Bivariate or trivariate plot of the results of
                        an ordination generated using gl.pcoa()
gl.plot.heatmap         Represents a distance matrix as a heatmap
gl.print.history        Prints history of a genlight object
gl.prop.shared          Calculates a similarity (distance) matrix for
                        individuals on the proportion of shared alleles
                        @family distance
gl.randomize.snps       Randomly changes the allocation of 0's and 2's
                        in a genlight object
gl.read.PLINK           Reads PLINK data file into a genlight object
gl.read.csv             Reads SNP data from a csv file into a genlight
                        object
gl.read.dart            Imports DArT data into dartR and converts it
                        into a dartR genlight object
gl.read.fasta           Reads FASTA files and converts them to genlight
                        object
gl.read.silicodart      Imports presence/absence data from SilicoDArT
                        to genlight {agegenet} format (ploidy=1)
gl.read.vcf             Converts a vcf file into a genlight object
gl.reassign.pop         Assigns an individual metric as pop in a
                        genlight {adegenet} object
gl.recalc.metrics       Recalculates locus metrics when individuals or
                        populations are deleted from a genlight
                        {adegenet} object @family environment
gl.recode.ind           Recodes individual (=specimen = sample) labels
                        in a genlight object
gl.recode.pop           Recodes population assignments in a genlight
                        object
gl.rename.pop           Renames a population in a genlight object
gl.report.allelerich    Report allelic richness per population from a
                        genlight object
gl.report.allna         Reports loci that are all NA across individuals
                        and/or populations with all NA across loci
gl.report.bases         Reports summary of base pair frequencies
gl.report.basics        Basic statistics for a genlight object
gl.report.callrate      Reports summary of Call Rate for loci or
                        individuals
gl.report.diversity     Calculates diversity indexes for SNPs
gl.report.excess.het    Report loci with excess of heterozygosity
gl.report.factorloadings
                        Reports factor loadings for a PCA or PCoA
gl.report.fstat         Reports various statistics of genetic
                        differentiation between populations with
                        confidence intervals
gl.report.hamming       Calculates the pairwise Hamming distance
                        between DArT trimmed DNA sequences
gl.report.heterozygosity
                        Reports observed, expected and unbiased
                        heterozygosities and FIS (inbreeding
                        coefficient) by population or by individual
                        from SNP data
gl.report.hwe           Reports departure from Hardy-Weinberg
                        proportions
gl.report.ld            Calculates pairwise population based Linkage
                        Disequilibrium across all loci using the
                        specified number of cores @family matched
                        report
gl.report.ld.map        Calculates pairwise linkage disequilibrium by
                        population
gl.report.locmetric     Reports summary of the slot $other$loc.metrics
gl.report.maf           Reports minor allele frequency (MAF) for each
                        locus in a SNP dataset
gl.report.monomorphs    Reports monomorphic loci
gl.report.overshoot     Reports loci for which the SNP has been trimmed
                        from the sequence tag along with the adaptor
gl.report.pa            Reports private alleles (and fixed alleles) per
                        pair of populations
gl.report.polyploid_heterozygosity
                        Reports observed, expected and unbiased
                        heterozygosities and FIS (inbreeding
                        coefficient) by population or by individual
                        from SNP data
gl.report.rdepth        Reports summary of Read Depth for each locus
gl.report.replicates    Identify replicated individuals
gl.report.reproducibility
                        Reports summary of RepAvg (repeatability
                        averaged over both alleles for each locus) or
                        reproducibility (repeatability of the scores
                        for fragment presence/absence)
gl.report.secondaries   Reports loci containing secondary SNPs in
                        sequence tags and calculates number of
                        invariant sites
gl.report.shannon       Report SNP diversity from a genlight object,
                        with reference to Ma, Z., Li, L., & Zhang, Y.
                        P. (2020). Defining individual-level genetic
                        diversity and similarity profiles. Scientific
                        reports, 10(1), 5805.
gl.report.taglength     Reports summary of sequence tag length across
                        loci
gl.sample               Samples individuals from populations
gl.save                 Saves an object in compressed binary format for
                        later rapid retrieval
gl.select.colors        Selects colors from one of several palettes and
                        outputs as a vector
gl.select.shapes        Selects shapes from the base R shape palette
                        and outputs as a vector
gl.set.verbosity        Sets the default verbosity level
gl.set.wd               Sets the default working directory
gl.sim.cross            Generates random crosses between fathers and
                        mothers
gl.sim.genotypes        Generate random genotypes
gl.smearplot            Smear plot
gl.sort                 Sorts genlight objects
gl.subsample.ind        Subsample individuals from a genlight object
gl.subsample.loc        Subsample loci from a genlight object
gl.subsample.loci       Subsamples n loci from a genlight object and
                        return it as a genlight object
gl.test.heterozygosity
                        Tests the difference in heterozygosity between
                        populations taken pairwise
gl.tree.fitch           Generates a distance phylogeny
gl.tree.nj              Outputs a tree to summarize genetic similarity
                        among populations (e.g. phenogram)
gl.write.csv            Writes out data from a genlight object to csv
                        file
gl2bayesAss             Converts a genlight object into bayesAss (BA3)
                        input format
gl2bayescan             Converts a genlight object into a format
                        suitable for input to Bayescan
gl2bpp                  Converts a genlight object into a format
                        suitable for input to the BPP program
gl2demerelate           Creates a dataframe suitable for input to
                        package {Demerelate} from a genlight {adegenet}
                        object
gl2eigenstrat           Converts a genlight object into eigenstrat
                        format
gl2fasta                Concatenates DArT trimmed sequences and outputs
                        a FASTA file
gl2faststructure        Converts a genlight object into faststructure
                        format (to run faststructure elsewhere)
gl2gds                  Converts a genlight object into gds format
gl2genalex              Converts a genlight object into a format
                        suitable for input to genalex
gl2genepop              Converts a genlight object into genepop format
                        (and file)
gl2geno                 Converts a genlight object to geno format from
                        package LEA
gl2gi                   Converts a genind object into a genlight object
gl2hiphop               Converts a genlight objects into hiphop format
gl2paup.parsimony       Converts a genlight object to nexus format for
                        parsimony phylogeny analysis in PAUP and,
                        optionally produces accompanying files for
                        parallel processing.
gl2paup.svdquartets     Converts a genlight object to nexus format PAUP
                        SVDquartets
gl2phylip               Creates a Phylip input distance matrix from a
                        genlight (SNP) {adegenet} object
gl2plink                Converts a genlight object into PLINK format
gl2related              Converts a genlight object to format suitable
                        to be run with Coancestry
gl2sa                   Converts genlight objects to the format used in
                        the SNPassoc package
gl2snapper              Converts a genlight object to nexus format
                        suitable for phylogenetic analysis by Snapper
                        (via BEAUti) @family linker
gl2structure            Converts a genlight object to STRUCTURE
                        formatted files
gl2treemix              Converts a genlight object to a treemix input
                        file
gl2vcf                  Converts a genlight object into vcf format
rbind.dartR             adjust rbind for dartR
theme_dartR             Default theme for dartR plots
utils.basic.stats       Calculates mean observed heterozygosity, mean
                        expected heterozygosity and FIS per locus, per
                        population and various population
                        differentiation measures @family utilities
utils.check.datatype    Utility function to check the class of an
                        object passed to a function
utils.collapse.matrix   Collapses a distance matrix calculated for
                        individuals to a distance matrix for
                        populations defined in a dartR genlight object
utils.dart2genlight     An internal function to converts DarT to
                        genlight.
utils.dist.binary       Calculates a distance matrix for individuals
                        defined in a dartR genlight object using binary
                        P/A data (SilicoDArT)
utils.dist.ind.snp      Calculates a distance matrix for individuals
                        defined in a genlight object using SNP data
                        (DArTseq)
utils.flag.start        A utility script to flag the start of a script
utils.hamming           Calculates the Hamming distance between two
                        DArT trimmed DNA sequences
utils.het.pop           An internal function that calculates expected
                        mean heterozygosity per population
utils.impute            An internal script [Custodian to provide a
                        title]
utils.is.fixed          An internal function to tests if two
                        populations are fixed at a given locus
utils.jackknife         An internal function to conducts jackknife
                        resampling using a genlight object
utils.n.var.invariant   An internal utility function to calculate the
                        number of variant and invariant sites by locus
utils.plink.run         Runs PLINK from within R
utils.plot.save         An internal function to save a ggplot object to
                        disk in RDS binary format
utils.read.dart         Utility to import DarT data to R
utils.read.fasta        An internal script to read a fastA file into a
                        genlight object
utils.read.ped          An internal script [Custodian to provide a
                        title]
utils.recalc.avgpic     A utility function to recalculate intermediate
                        locus metrics
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 frequency
                        of the heterozygous SNPs by locus after some
                        populations have been deleted
utils.recalc.freqhomref
                        #' An internal utility function to recalculate
                        the frequency of the homozygous reference SNP
                        by locus after some populations have been
                        deleted
utils.recalc.freqhomsnp
                        A utility function to recalculate the frequency
                        of the homozygous alternate SNP by locus after
                        some populations have been deleted
utils.recalc.maf        A utility function to recalculate the minor
                        allele frequency by locus, typically after some
                        populations have been deleted
utils.reset.flags       #' An internal utility function to reset to
                        FALSE (or TRUE) the locus metric flags after
                        some individuals or populations have been
                        deleted.
utils.transpose         An internal utility function to transpose a
                        genlight object.
utils.vcfr2genlight.polyploid
                        Utility function to convert polyploid vcfR
                        object as genlight
zzz                     Setting up the package Setting theme, colors
                        and verbosity
