# Generated by roxygen2: do not edit by hand

S3method(cbind,dartR)
S3method(rbind,dartR)
export(gi2gl)
export(gl.He)
export(gl.Ho)
export(gl.add.indmetrics)
export(gl.alf)
export(gl.allele.freq)
export(gl.amova)
export(gl.check.verbosity)
export(gl.check.wd)
export(gl.colors)
export(gl.compliance.check)
export(gl.define.pop)
export(gl.diagnostics.hwe)
export(gl.dist.ind)
export(gl.dist.phylo)
export(gl.dist.pop)
export(gl.document)
export(gl.drop.ind)
export(gl.drop.loc)
export(gl.drop.pop)
export(gl.edit.recode.ind)
export(gl.edit.recode.pop)
export(gl.fbm2gen)
export(gl.fdsim)
export(gl.filter.allna)
export(gl.filter.callrate)
export(gl.filter.excess.het)
export(gl.filter.factorloadings)
export(gl.filter.hamming)
export(gl.filter.heterozygosity)
export(gl.filter.hwe)
export(gl.filter.ld)
export(gl.filter.locmetric)
export(gl.filter.maf)
export(gl.filter.monomorphs)
export(gl.filter.overshoot)
export(gl.filter.pa)
export(gl.filter.rdepth)
export(gl.filter.replicates)
export(gl.filter.reproducibility)
export(gl.filter.secondaries)
export(gl.filter.taglength)
export(gl.fixed.diff)
export(gl.fst.pop)
export(gl.gen2fbm)
export(gl.hwe.pop)
export(gl.impute)
export(gl.join)
export(gl.keep.ind)
export(gl.keep.loc)
export(gl.keep.pop)
export(gl.load)
export(gl.mahal.assign)
export(gl.make.recode.ind)
export(gl.make.recode.pop)
export(gl.map.interactive)
export(gl.merge.pop)
export(gl.pcoa)
export(gl.pcoa.plot)
export(gl.plot.heatmap)
export(gl.plot.snp.density)
export(gl.print.history)
export(gl.propShared)
export(gl.randomize.snps)
export(gl.read.PLINK)
export(gl.read.csv)
export(gl.read.dart)
export(gl.read.fasta)
export(gl.read.silicodart)
export(gl.read.vcf)
export(gl.reassign.ind)
export(gl.reassign.pop)
export(gl.recalc.metrics)
export(gl.recode.ind)
export(gl.recode.pop)
export(gl.rename.pop)
export(gl.report.allelerich)
export(gl.report.allna)
export(gl.report.bases)
export(gl.report.basics)
export(gl.report.callrate)
export(gl.report.diversity)
export(gl.report.excess.het)
export(gl.report.factorloadings)
export(gl.report.fstat)
export(gl.report.hamming)
export(gl.report.heterozygosity)
export(gl.report.hwe)
export(gl.report.ld)
export(gl.report.ld.map)
export(gl.report.locmetric)
export(gl.report.maf)
export(gl.report.monomorphs)
export(gl.report.overshoot)
export(gl.report.pa)
export(gl.report.polyploid_heterozygosity)
export(gl.report.rdepth)
export(gl.report.replicates)
export(gl.report.reproducibility)
export(gl.report.secondaries)
export(gl.report.shannon)
export(gl.report.taglength)
export(gl.sample)
export(gl.save)
export(gl.select.colors)
export(gl.select.shapes)
export(gl.set.verbosity)
export(gl.set.wd)
export(gl.sim.crosses)
export(gl.sim.genotypes)
export(gl.smearplot)
export(gl.sort)
export(gl.subsample.ind)
export(gl.subsample.loc)
export(gl.subsample.loci)
export(gl.test.heterozygosity)
export(gl.tree.fitch)
export(gl.tree.nj)
export(gl.write.csv)
export(gl2bayesAss)
export(gl2bayescan)
export(gl2bpp)
export(gl2demerelate)
export(gl2eigenstrat)
export(gl2fasta)
export(gl2faststructure)
export(gl2gapit)
export(gl2gds)
export(gl2genalex)
export(gl2genepop)
export(gl2geno)
export(gl2gi)
export(gl2hapmap)
export(gl2hiphop)
export(gl2paup.parsimony)
export(gl2paup.svdquartets)
export(gl2phylip)
export(gl2plink)
export(gl2related)
export(gl2snapper)
export(gl2structure)
export(gl2treemix)
export(gl2vcf)
export(glMean)
export(glSum)
export(theme_dartR)
export(utils.allelic.richness)
export(utils.basic.stats)
export(utils.check.datatype)
export(utils.collapse.matrix)
export(utils.flag.start)
export(utils.heatmap)
export(utils.is.fixed)
export(utils.jackknife)
export(utils.plink.run)
export(utils.plot.save)
export(utils.reset.flags)
export(utils.vcfr2genlight.polyploid)
import(adegenet)
import(adegenet, except = c(plot, glMean))
import(ape)
import(bigsnpr)
import(bigstatsr)
import(dartR.data)
import(data.table, except = c(melt,dcast))
import(foreach)
import(ggplot2)
import(patchwork)
import(reshape2)
import(stats)
import(stringr)
import(utils)
importFrom(MASS,ginv)
importFrom(SNPRelate,snpgdsClose)
importFrom(SNPRelate,snpgdsCreateGeno)
importFrom(SNPRelate,snpgdsOpen)
importFrom(SNPRelate,snpgdsSummary)
importFrom(StAMPP,stamppFst)
importFrom(StAMPP,stamppNeisD)
importFrom(ape,dist.gene)
importFrom(ape,nj)
importFrom(ape,pcoa)
importFrom(ape,plot.phylo)
importFrom(ape,root)
importFrom(ape,write.tree)
importFrom(bigstatsr,big_SVD)
importFrom(crayon,blue)
importFrom(crayon,cyan)
importFrom(crayon,green)
importFrom(crayon,red)
importFrom(crayon,yellow)
importFrom(dplyr,"%>%")
importFrom(dplyr,distinct)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate_all)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(grDevices,cm.colors)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,hcl)
importFrom(grDevices,hcl.pals)
importFrom(grDevices,palette.pals)
importFrom(grDevices,rainbow)
importFrom(grDevices,rgb)
importFrom(grDevices,rgb2hsv)
importFrom(grDevices,terrain.colors)
importFrom(grDevices,topo.colors)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,box)
importFrom(graphics,hist)
importFrom(graphics,image)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot.new)
importFrom(graphics,rect)
importFrom(graphics,strheight)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(gridExtra,grid.table)
importFrom(gridExtra,ttheme_default)
importFrom(gtools,invalid)
importFrom(methods,callNextMethod)
importFrom(methods,getPackageName)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,show)
importFrom(methods,slotNames)
importFrom(plyr,count)
importFrom(plyr,join)
importFrom(plyr,rbind.fill)
importFrom(snpStats,ld)
importFrom(snpStats,read.plink)
importFrom(snpStats,row.summary)
importFrom(snpStats,switch.alleles)
importFrom(snpStats,write.SnpMatrix)
importFrom(stats,aggregate)
importFrom(stats,as.dist)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,cov)
importFrom(stats,dist)
importFrom(stats,dpois)
importFrom(stats,hclust)
importFrom(stats,mahalanobis)
importFrom(stats,na.pass)
importFrom(stats,nobs)
importFrom(stats,optim)
importFrom(stats,optimize)
importFrom(stats,pchisq)
importFrom(stats,pgamma)
importFrom(stats,pnorm)
importFrom(stats,quantile)
importFrom(stats,rbinom)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,var)
importFrom(stats,variable.names)
importFrom(stringr,str_pad)
importFrom(tidyr,pivot_longer)
importFrom(utils,combn)
importFrom(utils,edit)
importFrom(utils,flush.console)
importFrom(utils,getTxtProgressBar)
importFrom(utils,read.csv)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importFrom(utils,write.csv)
importFrom(utils,write.table)
