R/aldous.test.R

In bcm-uga/apTreeshape: Analyses of Phylogenetic Treeshape

#comment
"aldous.test" <-
function (tree, xmin = 20, ...)
{
    if (identical(tree, NULL)) {
        stop("invalid tree", "\n")
    }
    if (xmin < 0.1) {
        xmin = 0.1
    }
    clade = smaller.clade.spectrum(tree)
    if (xmin > clade[1, 1]) {
        stop("'xmin' greater than the size of the tree")
    }
    ##clade = clade[clade[, 1] > xmin, ]
    xlab = "Size of parent clade (log scale)"
    ylab = "Size of smaller daughter clade (log scale)"
    plot(clade, pch = 20, xlab = xlab, log = "xy", ylab = ylab,
        xlim = c(xmin, max(clade[1, ]) + 10), ...)
    if (xmin >= 10) {
        x = xmin + 5
        text(x = x, y = 3/2 + 0.1, label = "PDA model", col = 4)
        text(x = x, y = x/4 - 1, label = "Yule model", col = 4)
    }
    else {
        x = 20
        text(x = x, y = 3/2 + 0.1, label = "PDA model", col = 4)
        text(x = x, y = x/4 + 2, label = "Yule model", col = 4)
    }
    mod = rq(clade[, 2] ~ clade[, 1])
    x = sort(clade[, 1])
    coef = coefficients(mod)
    abline(coef,untf=TRUE, col = 3)
    abline(0, 1/4, untf = TRUE)
    abline(3/2, 0, untf = TRUE)
    abline(v = 30, lty = 3)
}