chevaine {ade4} | R Documentation |
This data set contains a list of three components: spatial map, allellic profiles and sample sizes.
data(chevaine)
This data set is a list of three components:
a data frame with 27 populations and 9 allelic frequencies (4 locus)
a list containing all the elements to build a spatial map
a numeric containing the numbers of fish samples per station
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).
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) }