R/heights.phylo.R

In melmasri/HPprediction: Host-parasite prediction based on phylogeny

heights.phylo <-
function(x){
    phy=x
	phy <- reorder(phy, "postorder")
	n <- length(phy$tip.label)
	n.node <- phy$Nnode
	xx <- numeric(n + n.node)
	for (i in nrow(phy$edge):1) xx[phy$edge[i, 2]] <- xx[phy$edge[i, 1]] + phy$edge.length[i]
	root = ifelse(is.null(phy$root.edge), 0, phy$root.edge)
	labs = c(phy$tip.label, phy$node.label)
	depth = max(xx)
	tt = depth - xx
	idx = 1:length(tt)
	dd = phy$edge.length[idx]
	mm = match(1:length(tt), c(phy$edge[, 2], Ntip(phy) + 1))
	dd = c(phy$edge.length, root)[mm]
	ss = tt + dd
	res = cbind(ss, tt)
	rownames(res) = idx
	colnames(res) = c("start", "end")
	res = data.frame(res)
	res
}