R: Enzymatic polymorphism in Leuciscus cephalus

chevaine {ade4} | R Documentation

## 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:

tab

  a data frame with 27 populations and 9 allelic frequencies (4 locus)

coo

  a list containing all the elements to build a spatial map

eff

  a numeric containing the numbers of fish samples per station

### 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)
    }

[Package ade4 version 1.7-8 Index]