adegenet: rupica – R documentation

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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.

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)

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