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/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)

Worked out examples


> library(ade4)
> ### Name: chevaine
> ### Title: Enzymatic polymorphism in Leuciscus cephalus
> ### Aliases: chevaine
> ### Keywords: datasets
> 
> ### ** 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)
> 
> 
> 
> 
> 

[Package ade4 Index]