[,dartR,ANY,ANY,ANY-method
                        indexing dartR objects correctly...
bandicoot.gl            A genlight object created via the read.dart
                        functions
cbind.dartR             adjust cbind for dartR
gi2gl                   Converts a genind object into a genlight object
gl.He                   Estimates expected Heterozygosity
gl.Ho                   Estimates observed Heterozygosity
gl.LDNe                 Estimates effective population size using the
                        Linkage Disequilibrium method based on
                        NeEstimator (V2)
gl.alf                  Calculates allele frequency of the first and
                        second allele for each loci 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.assign.grm           Population assignment using grm
gl.assign.mahalanobis   Assign an individual of unknown provenance to
                        population based on Mahalanobis Distance
gl.assign.pa            Eliminates populations as possible source
                        populations for an individual of unknown
                        provenance, using private alleles
gl.assign.pca           Assign an individual of unknown provenance to
                        population based on PCA
gl.basic.stats          Calculates basic statistics for each loci (Hs,
                        Ho, Fis etc.)
gl.blast                Aligns nucleotides sequences against those
                        present in a target database using blastn
gl.check.verbosity      Checks the current global verbosity
gl.check.wd             Checks the global working directory
gl.collapse             Collapses a distance matrix by amalgamating
                        populations with pairwise fixed difference
                        count less that a threshold
gl.colors               This is a helper function that supports the
                        creation of color palettes for all plotting
                        functions.
gl.compliance.check     Checks a genlight object to see if it complies
                        with dartR expectations and amends it to comply
                        if necessary
gl.costdistances        Calculates cost distances for a given landscape
                        (resistance matrix)
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
gl.diagnostics.sim      Comparing simulations against theoretical
                        expectations
gl.dist.ind             Calculates a distance matrix for individuals
                        defined in a genlight object
gl.dist.pop             Calculates a distance matrix for populations
                        with SNP 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
gl.edit.recode.pop      Creates or edits and applies a population
                        re-assignment table
gl.evanno               Creates an Evanno plot from a STRUCTURE run
                        object
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.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
gl.filter.hwe           Filters loci that show significant departure
                        from Hardy-Weinberg Equilibrium
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) in a genlight 'adegenet' object
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.parent.offspring
                        Filters putative parent offspring within a
                        population
gl.filter.rdepth        Filters loci based on counts of sequence tags
                        scored at a locus (read depth)
gl.filter.reproducibility
                        Filters loci in a genlight {adegenet} object
                        based on average repeatability of alleles at a
                        locus
gl.filter.secondaries   Filters loci that represent secondary SNPs in a
                        genlight object
gl.filter.sexlinked     Filters loci that are sex linked
gl.filter.taglength     Filters loci in a genlight {adegenet} object
                        based on sequence tag length
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
gl.genleastcost         Performs least-cost path analysis based on a
                        friction matrix
gl.grm                  Calculates an identity by descent matrix
gl.grm.network          Represents a genomic relationship matrix (GRM)
                        as a network
gl.hwe.pop              Performs Hardy-Weinberg tests over loci and
                        populations
gl.ibd                  Performs isolation by distance analysis
gl.impute               Imputates missing data
gl.install.vanilla.dartR
                        Installs all required packages for using all
                        functions available in dartR
gl.join                 Combines two 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.ld.distance          Plots linkage disequilibrium against distance
                        by population disequilibrium patterns
gl.ld.haplotype         Visualize patterns of linkage disequilibrium
                        and identification of haplotypes
gl.list.reports         Prints dartR reports saved in tempdir
gl.load                 Loads an object from compressed binary format
                        produced by gl.save()
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
gl.map.interactive      Creates an interactive map (based on latlon)
                        from a genlight object
gl.map.structure        Maps a STRUCTURE plot using a genlight object
gl.merge.pop            Merges two or more populations in a genlight
                        object into one population
gl.nhybrids             Creates an input file for the program
                        NewHybrids and runs it if NewHybrids is
                        installed
gl.outflank             Identifies loci under selection per population
                        using the outflank method of Whitlock and
                        Lotterhos (2015)
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.percent.freq         Generates percentage allele frequencies by
                        locus and population
gl.play.history         Replays the history and applies it to a
                        genlight object
gl.plot.faststructure   Plots fastStructure analysis results (Q-matrix)
gl.plot.heatmap         Represents a distance matrix as a heatmap
gl.plot.network         Represents a distance or dissimilarity matrix
                        as a network
gl.plot.structure       Plots STRUCTURE analysis results (Q-matrix)
gl.print.history        Prints history of a genlight object
gl.print.reports        Prints dartR reports saved in tempdir
gl.propShared           Calculates a similarity (distance) matrix for
                        individuals on the proportion of shared alleles
gl.random.snp           Randomly changes the allocation of 0's and 2's
                        in 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
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.bases         Reports summary of base pair frequencies
gl.report.callrate      Reports summary of Call Rate for loci or
                        individuals
gl.report.diversity     Calculates diversity indexes for SNPs
gl.report.fstat         Reports various statistics of genetic
                        differentiation between populations with
                        confident 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.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.parent.offspring
                        Identifies putative parent offspring within a
                        population
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.sexlinked     Identifies loci that are sex linked
gl.report.taglength     Reports summary of sequence tag length across
                        loci
gl.run.faststructure    Runs a faststructure analysis using a genlight
                        object
gl.run.structure        Runs a STRUCTURE analysis using a genlight
                        object
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
                        output 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.sfs                  Creates a site frequency spectrum based on a
                        dartR or genlight object
gl.sim.WF.run           Runs Wright-Fisher simulations
gl.sim.WF.table         Creates the reference table for running
                        gl.sim.WF.run
gl.sim.create_dispersal
                        Creates a dispersal file as input for the
                        function gl.sim.WF.run
gl.sim.emigration       Simulates emigration between populations
gl.sim.ind              Simulates individuals based on the allele
                        frequencies provided via a genlight object.
gl.sim.mutate           Simulates mutations within a genlight object
gl.sim.offspring        Simulates a specified number of offspring based
                        on alleles provided by potential father(s) and
                        mother(s)
gl.smearplot            Smear plot of SNP or presence/absence
                        (SilicoDArT) data
gl.sort                 re-sorts genlight objects
gl.spatial.autoCorr     Spatial autocorrelation following Smouse and
                        Peakall 1999
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.nj              Outputs an nj tree to summarize genetic
                        similarity among populations
gl.write.csv            Writes out data from a genlight object to csv
                        file
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
gl2dartR                Convert a genlight object to a dartR object
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 genlight object to genind object
gl2hiphop               Converts a genlight objects into hiphop format
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
gl2sfs                  Converts a genlight object into a sfs input
                        file
gl2shp                  Converts a genlight object to ESRI shapefiles
                        or kml files
gl2snapp                Converts a genlight object to nexus format
                        suitable for phylogenetic analysis by SNAPP
                        (via BEAUti)
gl2structure            Converts a genlight object to STRUCTURE
                        formatted files
gl2svdquartets          Converts a genlight object to nexus format PAUP
                        SVDquartets
gl2treemix              Converts a genlight object to a treemix input
                        file
gl2vcf                  Converts a genlight object into vcf format
interactive_reference   Shiny app for the input of the reference table
                        for the simulations
interactive_sim_run     Shiny app for the input of the simulations
                        variables
is.fixed                Tests 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
rbind.dartR             adjust rbind for dartR
testset.gl              A genlight object created via the gl.read.dart
                        function
testset.gs              A genlight object created via the
                        gl.read.silicodart function
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.
theme_dartR             dartR theme
utils.assignment        Population assignment probabilities
utils.assignment_2      Population assignment probabilities
utils.assignment_3      Population assignment probabilities
utils.assignment_4      Population assignment probabilities
utils.basic.stats       Calculates mean observed heterozygosity, mean
                        expected heterozygosity and Fis per locus, per
                        population and various population
                        differentiation measures
utils.check.datatype    Utility function to check the class of an
                        object passed to a function
utils.clumpp            Functions from package starmie for merging Q
                        matrices from Structure runs using the CLUMPP
                        algorithms.
utils.dart2genlight     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 dartR 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           Calculates expected mean expected
                        heterozygosity per population
utils.jackknife         Conducts jackknife resampling using a genlight
                        object
utils.n.var.invariant   A utility script to calculate the number of
                        variant and invariant sites by locus
utils.outflank          OutFLANK: An Fst outlier approach by Mike
                        Whitlock and Katie Lotterhos, University of
                        British Columbia.
utils.outflank.MakeDiploidFSTMat
                        Creates OutFLANK input file from individual
                        genotype info.
utils.outflank.plotter
                        Plotting functions for Fst distributions after
                        OutFLANK
utils.plot.save         An internal function to save a ggplot object to
                        disk in RDS binary format
utils.read.dart         utility function to read in DArT data
utils.recalc.avgpic     A utility script to recalculate the
                        OneRatioRef, OneRatioSnp, PICRef, PICSnp, and
                        AvgPIC by locus after some individuals or
                        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 frequency
                        of the heterozygous SNPs by locus after some
                        populations have been deleted
utils.recalc.freqhomref
                        A utility script to recalculate the frequency
                        of the homozygous reference SNP by locus after
                        some populations have been deleted
utils.recalc.freqhomsnp
                        A utility script to recalculate the frequency
                        of the homozygous alternate SNP by locus after
                        some populations have been deleted
utils.recalc.maf        A utility script to recalculate the minor
                        allele frequency by locus, typically after some
                        populations have been deleted
utils.reset.flags       A utility script to reset to FALSE (or TRUE)
                        the locus metric flags after some individuals
                        or populations have been deleted.
utils.spautocor         Spatial autocorrelation coefficient
                        calculations
utils.structure.evanno
                        Util function for evanno plots
utils.structure.genind2gtypes
                        structure util functions
utils.structure.run     Utility function to run Structure
zzz                     Setting up the package
