sim2pop | 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.
sim2pop
is a genind object with a matrix of xy coordinates as
supplementary component.
Thibaut Jombart t.jombart@imperial.ac.uk
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)
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