Description Format Author(s) Source References Examples
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 [email protected]
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: 301302
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30  ## 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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