NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(cbind,dartR)
S3method(rbind,dartR)
export(gi2gl)
export(gl.He)
export(gl.Ho)
export(gl.LDNe)
export(gl.alf)
export(gl.amova)
export(gl.assign.grm)
export(gl.assign.mahalanobis)
export(gl.assign.pa)
export(gl.assign.pca)
export(gl.basic.stats)
export(gl.blast)
export(gl.check.verbosity)
export(gl.collapse)
export(gl.compliance.check)
export(gl.costdistances)
export(gl.define.pop)
export(gl.diagnostics.hwe)
export(gl.diagnostics.sim)
export(gl.dist.ind)
export(gl.dist.pop)
export(gl.drop.ind)
export(gl.drop.loc)
export(gl.drop.pop)
export(gl.edit.recode.ind)
export(gl.edit.recode.pop)
export(gl.evanno)
export(gl.fdsim)
export(gl.filter.allna)
export(gl.filter.callrate)
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.parent.offspring)
export(gl.filter.rdepth)
export(gl.filter.reproducibility)
export(gl.filter.secondaries)
export(gl.filter.sexlinked)
export(gl.filter.taglength)
export(gl.fixed.diff)
export(gl.fst.pop)
export(gl.genleastcost)
export(gl.grm)
export(gl.grm.network)
export(gl.hwe.pop)
export(gl.ibd)
export(gl.impute)
export(gl.install.vanilla.dartR)
export(gl.join)
export(gl.keep.ind)
export(gl.keep.loc)
export(gl.keep.pop)
export(gl.ld.distance)
export(gl.ld.haplotype)
export(gl.list.reports)
export(gl.load)
export(gl.make.recode.ind)
export(gl.make.recode.pop)
export(gl.map.interactive)
export(gl.map.structure)
export(gl.merge.pop)
export(gl.nhybrids)
export(gl.outflank)
export(gl.pcoa)
export(gl.pcoa.plot)
export(gl.percent.freq)
export(gl.play.history)
export(gl.plot.heatmap)
export(gl.plot.network)
export(gl.plot.structure)
export(gl.print.history)
export(gl.print.reports)
export(gl.propShared)
export(gl.random.snp)
export(gl.read.csv)
export(gl.read.dart)
export(gl.read.fasta)
export(gl.read.silicodart)
export(gl.read.vcf)
export(gl.reassign.pop)
export(gl.recalc.metrics)
export(gl.recode.ind)
export(gl.recode.pop)
export(gl.rename.pop)
export(gl.report.bases)
export(gl.report.callrate)
export(gl.report.diversity)
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.parent.offspring)
export(gl.report.rdepth)
export(gl.report.reproducibility)
export(gl.report.secondaries)
export(gl.report.sexlinked)
export(gl.report.taglength)
export(gl.run.structure)
export(gl.sample)
export(gl.save)
export(gl.select.colors)
export(gl.select.shapes)
export(gl.set.verbosity)
export(gl.sfs)
export(gl.sim.WF.run)
export(gl.sim.WF.table)
export(gl.sim.create_dispersal)
export(gl.sim.emigration)
export(gl.sim.ind)
export(gl.sim.mutate)
export(gl.sim.offspring)
export(gl.smearplot)
export(gl.sort)
export(gl.spatial.autoCorr)
export(gl.subsample.loci)
export(gl.test.heterozygosity)
export(gl.tree.nj)
export(gl.write.csv)
export(gl2bayescan)
export(gl2bpp)
export(gl2demerelate)
export(gl2eigenstrat)
export(gl2fasta)
export(gl2faststructure)
export(gl2gds)
export(gl2genalex)
export(gl2genepop)
export(gl2geno)
export(gl2gi)
export(gl2hiphop)
export(gl2phylip)
export(gl2plink)
export(gl2related)
export(gl2sa)
export(gl2sfs)
export(gl2shp)
export(gl2snapp)
export(gl2structure)
export(gl2svdquartets)
export(gl2treemix)
export(gl2vcf)
export(is.fixed)
export(utils.assignment)
export(utils.assignment_2)
export(utils.assignment_3)
export(utils.assignment_4)
export(utils.basic.stats)
export(utils.check.datatype)
export(utils.dist.binary)
export(utils.dist.ind.snp)
export(utils.hamming)
export(utils.het.pop)
export(utils.jackknife)
export(utils.n.var.invariant)
export(utils.outflank)
export(utils.outflank.MakeDiploidFSTMat)
export(utils.outflank.plotter)
export(utils.spautocor)
export(utils.structure.evanno)
export(utils.structure.genind2gtypes)
export(utils.structure.run)
import(adegenet, except = plot)
import(crayon, except = c(chr, '%+%'))
import(dartR.data)
import(data.table, except = c(melt,dcast))
import(fields, except = flame)
import(foreach)
import(ggplot2)
import(patchwork)
import(reshape2)
import(shiny)
import(stats)
import(stringr)
import(utils)
importFrom(MASS,kde2d)
importFrom(MASS,write.matrix)
importFrom(PopGenReport,gd.kosman)
importFrom(PopGenReport,gd.smouse)
importFrom(PopGenReport,lgrMMRR)
importFrom(PopGenReport,wassermann)
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(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,everything)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_all)
importFrom(dplyr,mutate_at)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,starts_with)
importFrom(dplyr,ungroup)
importFrom(dplyr,vars)
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,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,legend)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,points)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(gridExtra,grid.table)
importFrom(gridExtra,ttheme_default)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,show)
importFrom(plyr,count)
importFrom(plyr,join)
importFrom(plyr,rbind.fill)
importFrom(raster,plot)
importFrom(sp,"coordinates<-")
importFrom(sp,"proj4string<-")
importFrom(sp,CRS)
importFrom(sp,Line)
importFrom(sp,Lines)
importFrom(sp,SpatialLines)
importFrom(sp,SpatialLinesLengths)
importFrom(sp,SpatialPointsDataFrame)
importFrom(stats,IQR)
importFrom(stats,as.dist)
importFrom(stats,coef)
importFrom(stats,complete.cases)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,dpois)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,nobs)
importFrom(stats,optim)
importFrom(stats,optimize)
importFrom(stats,pchisq)
importFrom(stats,pgamma)
importFrom(stats,pnorm)
importFrom(stats,qnorm)
importFrom(stats,quantile)
importFrom(stats,rbinom)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,step)
importFrom(stats,variable.names)
importFrom(stringr,str_pad)
importFrom(stringr,str_trim)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(utils,available.packages)
importFrom(utils,combn)
importFrom(utils,edit)
importFrom(utils,flush.console)
importFrom(utils,getTxtProgressBar)
importFrom(utils,install.packages)
importFrom(utils,installed.packages)
importFrom(utils,read.csv)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importFrom(utils,write.csv)
importFrom(utils,write.table)
importFrom(vegan,mantel)