ade4 (version 1.4-3)

chevaine: Enzymatic polymorphism in Leuciscus cephalus

Description

This data set contains a list of three components: spatial map, allellic profiles and sample sizes.

Usage

data(chevaine)

References

Guinand B., Bouvet Y. and Brohon B. (1996) Spatial aspects of genetic differentiation of the European chub in the Rhone River basin. Journal of Fish Biology, 49, 714--726.

See a data description at http://pbil.univ-lyon1.fr/R/pps/pps054.pdf (in French).

Examples

data(chevaine)
'fun.chevaine' <- function(label=TRUE) {
    opar <- par(mar = par("mar"))
        on.exit(par(opar))
        par(mar = c(0.1, 0.1, 0.1, 0.1))
    s.label(chevaine$coo$poi, xlim = c(-20,400), clab = 0, cpoi = 0)
    invisible(lapply(chevaine$coo$lac, polygon, col = "blue", lwd = 2)) 
    invisible(lapply(chevaine$coo$riv, points, col = "blue", type = "l", lwd = 2))
    if (label){
        s.label(chevaine$coo$poi, clab = 0.75, add.p = TRUE)
        s.label(chevaine$coo$sta, add.p = TRUE, clab = 0.5)
    }
    arrows(200,100,300,100, code = 3, angle = 15, length = 0.2)
    text(250,125,"50 Km")
}

fun.chevaine()

che.genet <- freq2genet(chevaine$tab)
che.pca <- dudi.pca(che.genet$tab, center = che.genet$center, scannf = FALSE, nf = 3)

par(mfrow = c(1,2))
fun.chevaine(FALSE)
s.value(chevaine$coo$sta, che.pca$li[,1], csi = 2, add.p = TRUE)
fun.chevaine(FALSE)
s.value(chevaine$coo$sta, che.pca$li[,2], csi = 2, add.p = TRUE)

w = prep.fuzzy.var (che.genet$tab, che.genet$loc.blocks)
che.fca <- dudi.fca(w, scannf = FALSE, nf = 3)

fun.chevaine(FALSE)
s.value(chevaine$coo$sta, che.fca$li[,1], csi = 1.5, add.p = TRUE)
fun.chevaine(FALSE)
s.value(chevaine$coo$sta, che.fca$li[,2], csi = 1.5, add.p = TRUE)