R: Microsatellites genotypes of 335 chamois (Rupicapra...
rupica
R Documentation
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.
Format
rupica is a genind object with 3 supplementary components
inside the @other slot:
xy
a matrix containing the
spatial coordinates of the genotypes.
mnt
a raster map of elevation,
with the asc format from the adehabitat package.
showBauges
a function to display the map of elevation with an
appropriate legend (use showBauges()).
Source
Daniel Maillard, 'Office National de la Chasse et de la Faune
Sauvage' (ONCFS), 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
data(rupica)
rupica
## Not run:
if(require(adehabitat)){
## 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)
}
## End(Not run)