R: Toy hybrid dataset

hybridtoy {adegenet} | R Documentation

## Toy hybrid dataset

### Description

Toy hybrid dataset

### Format

a genind object

### Author(s)

Data simulated by Marie-Pauline Beugin. Example by Thibaut Jombart.

### Examples

    data(hybridtoy)
    x <- hybridtoy
    pca1 <- dudi.pca(tab(x), scannf=FALSE, scale=FALSE)
    s.class(pca1$li, pop(x))

    if(require(ggplot2)) {
    p <- ggplot(pca1$li, aes(x=Axis1)) +
        geom_density(aes(fill=pop(x)), alpha=.4, adjust=1) +
        geom_point(aes(y=0, color=pop(x)), pch="|", size=10, alpha=.5)
    p
    }

    ## kmeans
    km <- find.clusters(x, n.pca=10, n.clust=2)
    table(pop(x), km$grp)

    ## dapc
    dapc1 <- dapc(x, pop=km$grp, n.pca=10, n.da=1)
    scatter(dapc1)
    scatter(dapc1, grp=pop(x))
    compoplot(dapc1, col.pal=spectral, n.col=2)

    ## ML-EM with hybrids
    res <- snapclust(x, k=2, hybrids=TRUE, detailed=TRUE)
    compoplot(res, n.col=3)
    table(res$group, pop(x))

[Package adegenet version 2.1.4 Index]