R: Simulated genotypes of two georeferenced populations

sim2pop {adegenet} | R Documentation

## 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(s)

Thibaut Jombart t.jombart@imperial.ac.uk

### Source

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)

### References

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

### Examples

    ## 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)

[Package adegenet version 2.1.4 Index]