sim2pop {adegenet} | R Documentation |
This simple data set was obtained by sampling two populations evolving
in a island model, simulated using Easypop (2.0.1). See source
for simulation details. Sample sizes were respectively 100 and 30
genotypes. The genotypes were given spatial coordinates so that both
populations were spatially differentiated.
data(sim2pop)
sim2pop
is a genind object with a matrix of xy coordinates as
supplementary component.
Thibaut Jombart jombart@biomserv.univ-lyon1.fr
Easypop version 2.0.1 was run with the following parameters: - two diploid populations, one sex, random mating - 1000 individuals per population - proportion of migration: 0.002 - 20 loci - mutation rate: 0.0001 (KAM model) - maximum of 50 allelic states - 1000 generations (last one taken)
Balloux F (2001) Easypop (version 1.7): a computer program for oppulation genetics simulations Journal of Heredity, 92: 301-302
## Not run: data(sim2pop) if(require(hierfstat)){ ## try and find the Fst temp <- genind2hierfstat(sim2pop) varcomp.glob(temp[,1],temp[,-1]) # Fst = 0.038 } ## run monmonier algorithm # build connection network gab <- chooseCN(sim2pop@other$xy,ask=FALSE,type=2) # filter random noise pca1 <- dudi.pca(sim2pop@tab,scale=FALSE, scannf=FALSE, nf=1) # run the algorithm mon1 <- monmonier(sim2pop@other$xy,dist(pca1$l1[,1]),gab,scanthres=FALSE) # graphical display temp <- sim2pop@pop levels(temp) <- c(17,19) temp <- as.numeric(as.character(temp)) plot(mon1) points(sim2pop@other$xy,pch=temp,cex=2) legend("topright",leg=c("Pop A", "Pop B"),pch=c(17,19)) ## End(Not run)