R: Microsatellites genotypes of 335 chamois (Rupicapra...

rupica {adegenet} | 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.

### References

Cassar S (2008) Organisation spatiale de la variabilité génétique et phénotypique a 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

    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)

[Package adegenet version 2.1.4 Index]