AdmixDataSim2 <- read.csv(file="AdmixDataSim2.txt", header =FALSE)
LociDataSim2 <- read.csv(file="LociDataSim2.txt", header=TRUE)
count.matrix <- prepare.data(admix.gen=AdmixDataSim2,loci.data=LociDataSim2, parental1="P1", parental2="P2", pop.id=FALSE, ind.id=FALSE, fixed=TRUE)
hi.index.sim <- est.h(introgress.data=count.matrix, loci.data=LociDataSim2,fixed=TRUE,p1.allele="P1",p2.allele="P2")
write.table(hi.index.sim, file="hindex.txt", quote=FALSE,sep=",")
mk.image(introgress.data=count.matrix,loci.data=LociDataSim2, marker.order=NULL, hi.index=hi.index.sim, ylab.image="Individuals",xlab.h="populations 2 ancestry",pdf=TRUE,out.file="image.pdf")
gen.out <- genomic.clines (introgress.data=count.matrix, hi.index=hi.index.sim, loci.data=LociDataSim2, sig.test=TRUE, method="permutation", n.reps=200)
clines.plot(cline.data=gen.out, rplots=3, cplots=3, pdf=TRUE, out.file="clines.pdf")