chevaine {ade4} | R Documentation

## Enzymatic polymorphism in Leuciscus cephalus

### Description

This data set contains a list of two components: a spatial map and allellic profiles.

### Usage

    data(chevaine)

### Format

This data set is a list of two components:

tab
  a data frame with 27 populations and 9 allellic profiles
coo
  a list containing all the elements to build a spatial map

### Source

Exemple du logiciel GENETIX.
Belkhir k. et al. GENETIX, logiciel sous WindowsTM pour la génétique des populations. Laboratoire Génome, Populations, Interactions CNRS UMR 5000, Université de Montpellier II, Montpellier (France). http://www.univ-montp2.fr/~genetix/genetix/genetix.htm

### 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.

### 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", type = "l", 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)

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