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assignPOP_v1.R
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assignPOP_v1.R
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################ establish refpops
library(assignPOP)
library(klaR)
library(mime)
library(genepopedit)
work_dir <- "/Users/macbook2017/Desktop/dapc/"
setwd(work_dir)
all.gen = "px_ddRAD_2018_432_6230_mac3_thin500.gen"
all.renamed.gen="all.renamed.gen"
species = "px_2018"
genepop_ID(genepop=all.gen, path=paste0(work_dir, all.renamed.gen))
PopNames.all <- genepop_detective(all.renamed.gen, variable="Pops")
PopCounts.all <- genepop_detective(all.renamed.gen, variable="PopNum")
PopCounts.all
pop.sublist <- c("GXNN", "YNDH")
pop.sublistname <- paste(pop.sublist, collapse ="_", sep=".")
subset_genepop(genepop= all.renamed.gen, keep = TRUE,
spop = pop.sublist,
path = paste0(work_dir, paste(pop.sublistname, ".gen", sep="")))
used.PopNames <- genepop_detective(paste(pop.sublistname, ".gen", sep=""), variable="Pops")
all_ref <- read.Genepop(paste(pop.sublistname, ".gen", sep=""), pop.names=used.PopNames)
#all_inc <- read.Genepop( "nokin_allq9_inc.txt")
#all_ref_rd <- reduce.allele(all_ref, p = 0.95)
assign_trial = assign.MC(all_ref, train.inds=c(0.92), train.loci=c(0.8),
loci.sample="fst", iterations=100, dir = paste(species, pop.sublistname, ".mc_svm/", sep=""), model="svm" )
accuMC <- accuracy.MC(dir = paste(species, pop.sublistname, ".mc_svm/", sep=""))
pdf(file=paste(species, pop.sublistname, ".assignpop.mc.plot.pdf", sep=""))
accuracy.plot(accuMC, pop = c("all", used.PopNames))
dev.off()
#file.remove("all.renamed.gen")