ade4 (version 1.7-5)

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)

Format

This data set is a list of three components:

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/pdf/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")
}

if(!adegraphicsLoaded()) {
  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)
}