adegenet: sim2pop – R documentation

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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(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)

adegenet

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release