| rupica {adegenet} | R Documentation |
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.
data(rupica)
rupica is a genind object with 3 supplementary components
inside the @other slot:
asc format
from the adehabitat package.showBauges()).Daniel Maillard, 'Office National de la Chasse et de la Faune Sauvage' (ONCFS), France.
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.
if(require(ade4) & 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$li,cex=1.5,add.plot=TRUE)
## Not run:
## global and local tests
Gtest <- global.rtest(rupica@tab,spca1$lw,nperm=999)
Gtest
plot(Gtest)
Ltest <- local.rtest(rupica@tab,spca1$lw,nperm=999)
Ltest
plot(Ltest)
## End(Not run)
}