adegenet (version 2.1.10)

sim2pop: Simulated genotypes of two georeferenced populations

Description

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.

Format

sim2pop is a genind object with a matrix of xy coordinates as supplementary component.

Author

Thibaut Jombart

References

Balloux F (2001) Easypop (version 1.7): a computer program for oppulation genetics simulations Journal of Heredity, 92: 301-302

Examples

if (FALSE) {
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))
}