R/plot.kselect.r

In adehabitat: Analysis of Habitat Selection by Animals

"plot.kselect" <- function(x, xax=1, yax=2, ...)
{
    ## Verifications
    if (!inherits(x, "kselect"))
        stop("Use only with 'kselect' objects")
    if (x$nf == 1) {
        warnings("One axis only : not yet implemented")
        return(invisible())
    }
    if (xax > x$nf)
        stop("Non convenient xax")
    if (yax > x$nf)
        stop("Non convenient yax")
    def.par <- par(no.readonly = TRUE)
    on.exit(par(def.par))

    ## The layout of the graphs
    nf <- layout(matrix(c(1, 2, 3, 4, 4, 5, 4, 4, 6), 3, 3),
                 respect = TRUE)
    par(mar = c(0.1, 0.1, 0.1, 0.1))

    ## 1. correlations between the PCA axes and the K-select axes
    s.corcircle(x$as, xax, yax, sub = "Axis", csub = 2, clabel = 1.25)

    ## 2. scores of the environmental variables on the
    ##    K-select axes (eigenvectors)
    s.arrow(x$l1, xax, yax, sub = "Variables", csub = 2, clabel = 1.25)

    ## 3. the eigenvalues of the analysis
    scatterutil.eigen(x$eig, wsel = c(xax, yax))

    ## 4. main graph: coordinates of the uncentered marginality vectors

    ## 4.1. We project the available points (all animals pooled) on
    ##      the axes of the K-select: matrix U (rows: points, columns: axes)
    ls<- x$ls

    ## 4.2. coordinates of the "available centroids" on the axes
    ##      of the K-select
    mav <- x$mav

    ## 4.3. coordinates of the "used centroids" on the axes
    ##      of the K-select
    mut <- x$mus

    ## 4.4. The Marginality vectors are displayed as arrows connecting the
    ##      "available" centroids to the "used" centroids

    s.label(rbind(mav, mut), xax, yax, clabel = 0, cpoint = 0,
            sub = "Marginality vectors", csub = 2) ## background
    for (i in 1:nrow(mav))
        arrows(mav[i,xax], mav[i,yax], mut[i,xax], mut[i,yax],
               lwd=2, angle=20) ## arrows
    s.label(mav, xax, yax, add.plot=TRUE, clabel=1.5) ## labels


    ## 5. coordinates of the uncentered available points on the
    ##    axes of the K-select
    s.chull(as.data.frame(ls), x$initfac,
            clabel=1.5, sub="Available Resource units", csub=2,
            optchull=1, cpoint=1)

    ## 6. coordinates of the recentred marginality vectors on the axes
    ##    on the K-select
    s.arrow(x$co, xax, yax, clabel = 1.25, cpoint = 0.5, sub = "Animals",
            csub = 2)

}