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## ladderize.R (2023-02-09)
## Ladderize a Tree
## Copyright 2007-2023 Emmanuel Paradis, 2022 Klaus Schliep
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
ladderize <- function(phy, right = TRUE)
{
desc_fun <- function(x) {
parent <- x[, 1]
children <- x[, 2]
res <- vector("list", max(x))
for (i in seq_along(parent))
res[[parent[i]]] <- c(res[[parent[i]]], children[i])
res
}
if (!is.null(phy$edge.length)) {
el <- numeric(max(phy$edge))
el[phy$edge[, 2]] <- phy$edge.length
}
nb.tip <- length(phy$tip.label)
nb.node <- phy$Nnode
nb.edge <- dim(phy$edge)[1]
phy <- reorder(phy, "postorder")
N <- .C(node_depth, as.integer(nb.tip),
as.integer(phy$edge[, 1]), as.integer(phy$edge[, 2]),
as.integer(nb.edge), double(nb.tip + nb.node), 1L)[[5]]
ii <- order(x <- phy$edge[, 1], y <- N[phy$edge[, 2]], decreasing = right)
desc <- desc_fun(phy$edge[ii, ])
tmp <- integer(nb.node)
new_anc <- integer(nb.node)
new_anc[1] <- tmp[1] <- nb.tip + 1L
k <- nb.node
pos <- 1L
while (pos > 0L && k > 0) {
current <- tmp[pos]
new_anc[k] <- current
k <- k - 1L
dc <- desc[[current]]
ind <- dc > nb.tip
if (any(ind)) {
l <- sum(ind)
tmp[pos -1L + seq_len(l)] <- dc[ind]
pos <- pos + l - 1L
} else {
pos <- pos - 1L
}
}
edge <- cbind(rep(new_anc, lengths(desc[new_anc])), unlist(desc[new_anc]))
phy$edge <- edge
if (!is.null(phy$edge.length)) phy$edge.length <- el[edge[, 2L]]
attr(phy, "order") <- "postorder"
reorder(phy)
}
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