1 ## ladderize.R (2007-01-04)
5 ## Copyright 2007 Emmanuel Paradis
7 ## This file is part of the R-package `ape'.
8 ## See the file ../COPYING for licensing issues.
10 ladderize <- function(phy, right = TRUE)
12 foo <- function(node, END, where) {
13 start <- which(phy$edge[, 1] == node)
14 end <- c(start[-1] - 1, END)
15 size <- end - start + 1
16 desc <- phy$edge[start, 2]
17 Nclade <- length(desc)
19 o <- order(n, decreasing = right)
20 newpos <- c(0, cumsum(size[o][-Nclade])) + where
24 neworder[newpos] <<- start
26 if (desc[i] > nb.tip) foo(desc[i], end[i], newpos[i] + 1)
28 nb.tip <- length(phy$tip.label)
30 nb.edge <- dim(phy$edge)[1]
31 tmp <- reorder(phy, "pruningwise")
32 N <- .C("node_depth", as.integer(nb.tip), as.integer(nb.node),
33 as.integer(tmp$edge[, 1]), as.integer(tmp$edge[, 2]),
34 as.integer(nb.edge), double(nb.tip + nb.node),
35 DUP = FALSE, PACKAGE = "ape")[[6]]
36 neworder <- integer(nb.edge)
37 foo(nb.tip + 1, nb.edge, 1)
38 phy$edge <- phy$edge[neworder, ]
39 if (!is.null(phy$edge.length))
40 phy$edge.length <- phy$edge.length[neworder]