useDynLib(polysat)

export(Bruvo.distance,
       meandistance.matrix, read.GeneMapper, write.Structure,
       read.ATetra, read.Tetrasat, genambig.to.genbinary,
       genbinary.to.genambig, read.GenoDive, write.GenoDive,
       write.ATetra, write.Tetrasat, read.Structure,
       write.GeneMapper, calcFst, simpleFreq, deSilvaFreq,
       find.missing.gen,
       meandist.from.array, find.na.dist, find.na.dist.not.missing,
       Lynch.distance, write.SPAGeDi, read.SPAGeDi, write.freq.SPAGeDi,
       read.POPDIST, write.POPDIST, freq.to.genpop, genotypeProbs,
       meandistance.matrix2, assignClones, Shannon, Simpson, genotypeDiversity,
       Bruvo2.distance, reformatPloidies,alleleDiversity,read.STRand,
gendata.to.genind, Simpson.var, simAllopoly, catalanAlleles, alleleCorrelations,
       testAlGroups, mergeAlleleAssignments, recodeAllopoly, plotSSAllo,
       processDatasetAllo, plotParamHeatmap, calcPopDiff, PIC)
exportMethods(estimatePloidy, Samples, "Samples<-", Loci, "Loci<-", PopInfo,
              "PopInfo<-", PopNames, "PopNames<-", Ploidies, "Ploidies<-",
              Usatnts,
              "Usatnts<-", deleteSamples, deleteLoci, Missing, "Missing<-",
              Description, "Description<-", PopNum, "PopNum<-", Genotype,
              "Genotype<-", Genotypes, "Genotypes<-", isMissing, viewGenotypes,
              editGenotypes, Present, "Present<-", Absent, "Absent<-", summary,
              merge, pld, "pld<-", plCollapse, genIndex, show)
exportClasses(gendata, genambig, genbinary, ploidysuper, ploidymatrix, 
              ploidylocus, ploidysample, ploidyone)
import(methods)
importFrom("stats", "as.dist", "cutree", "fisher.test", "hclust", "kmeans", "heatmap", "weighted.mean")
importFrom("utils", "combn", "edit", "read.table", "stack", "write.table")
importFrom("grDevices", "dev.off", "grey.colors", "pdf", "rainbow")
importFrom("graphics", "axis", "image", "legend", "par", "plot", "text")
importFrom("Rcpp", "sourceCpp")
