adegenet (version 1.4-2)

rupica: Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains (France)

Description

This data set contains the genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains, in France. No prior clustering about individuals is known. Each genotype is georeferenced. These data also contain a raster map of elevation of the sampling area.

Usage

data(rupica)

encoding

UTF-8

source

Daniel Maillard, 'Office National de la Chasse et de la Faune Sauvage' (ONCFS), France.

References

Cassar S (2008) Organisation spatiale de la variabilité génétique et phénotypique à l'échelle du paysage: le cas du chamois et du chevreuil, en milieu de montagne. PhD Thesis. University Claude Bernard - Lyon 1, France. Cassar S, Jombart T, Loison A, Pontier D, Dufour A-B, Jullien J-M, Chevrier T, Maillard D. Spatial genetic structure of Alpine chamois (Rupicapra rupicapra): a consequence of landscape features and social factors? submitted to Molecular Ecology.

Examples

if(require(adehabitat) && require(spdep)){

data(rupica)
rupica

## see the sampling area
showBauges <- rupica$other$showBauges
showBauges()
points(rupica$other$xy,col="red")

## perform a sPCA
spca1 <- spca(rupica,type=5,d1=0,d2=2300,plot=FALSE,scannf=FALSE,nfposi=2,nfnega=0)
barplot(spca1$eig,col=rep(c("black","grey"),c(2,100)),main="sPCA eigenvalues")
screeplot(spca1,main="sPCA eigenvalues: decomposition")

## data visualization
showBauges(,labcex=1)
s.value(spca1$xy,spca1$ls[,1],add.p=TRUE,csize=.5)
add.scatter.eig(spca1$eig,1,1,1,posi="topleft",sub="Eigenvalues")

showBauges(,labcex=1)
s.value(spca1$xy,spca1$ls[,2],add.p=TRUE,csize=.5)
add.scatter.eig(spca1$eig,2,2,2,posi="topleft",sub="Eigenvalues")

rupica$other$showBauges()
colorplot(spca1$xy,spca1$li,cex=1.5,add.plot=TRUE)

## global and local tests
Gtest <- global.rtest(rupica@tab,spca1$lw,nperm=999)
Gtest
plot(Gtest)
Ltest <- local.rtest(rupica@tab,spca1$lw,nperm=999)
Ltest
plot(Ltest)
}