R/smaller.clade.spectrum2.R

In apTreeshape: Analyses of Phylogenetic Treeshape

smaller.clade.spectrum2 <- function(tree) 
{
    if (identical(tree, NULL)) {
        stop("invalid tree", "\n")
    }
    options(warn=-1)

    merge <- tree$merge
    number <- as.numeric(tree$names)
    number[is.na(number)] <- 1
    number <- as.numeric(number)
    spec <- matrix(0, nrow = nrow(merge), ncol = 2)
    for (node in 1:nrow(merge)) {
        if (merge[node, 1] < 0) {
            lc <- number[abs(merge[node, 1])]
        }
        else {
            lc <- spec[nrow(merge) - merge[node, 1] + 1, 1]
        }
        if (merge[node, 2] < 0) {
            rc <- number[abs(merge[node, 2])]
        }
        else {
            rc <- spec[nrow(merge) - merge[node, 2] + 1, 1]
        }
        spec[nrow(merge) - node + 1, ] <- c(rc + lc, min(rc, lc))
    }

    options(warn=0)
    return(spec)
}