## cophenetic.phylo.R (2010-11-15)
## Pairwise Distances from a Phylogenetic Tree
## Copyright 2006-2010 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
dist.nodes <- function(x)
{
if (is.null(x$edge.length))
stop("your tree has no branch lengths")
trim <- FALSE
if (!is.binary.tree(x) || !is.rooted(x)) {
trim <- TRUE
x <- makeNodeLabel(x)
x <- multi2di(x, random = FALSE)
}
n <- length(x$tip.label)
n.node <- x$Nnode
N <- n + n.node
x <- reorder(x, order = "pruningwise")
res <- matrix(NA, N, N)
res[cbind(1:N, 1:N)] <- 0 # implicit mode conversion
## I like the simplicity of this one:
res[x$edge] <- res[x$edge[, 2:1]] <- x$edge.length
## compute the distances ...
for (i in seq(from = 1, by = 2, length.out = n.node)) {
j <- i + 1
anc <- x$edge[i, 1]
des1 <- x$edge[i, 2]
des2 <- x$edge[j, 2]
## If `des1' is a node, we look for the nodes and tips for
## which the distance up to `des1' has already been
## computed, including `des1' itself. For all these, we can
## compute the distance up to `anc' and all node(s) and
## tip(s) in `des2'.
if (des1 > n) des1 <- which(!is.na(res[des1, ]))
## id. for `des2'
if (des2 > n) des2 <- which(!is.na(res[des2, ]))
## The following expression is vectorized only on `des2' and
## not on `des1' because they may be of different lengths.
for (y in des1)
res[y, des2] <- res[des2, y] <- res[anc, y] + res[anc, des2]
## compute the distances between the tip(s) and node(s)
## in `des2' and the ancestor of `anc'; id. for `des2'
## (only if it is not the root)
if (anc != n + 1) {
ind <- which(x$edge[, 2] == anc)
nod <- x$edge[ind, 1] # the ancestor of `anc'
l <- x$edge.length[ind]
res[des2, nod] <- res[nod, des2] <- res[anc, des2] + l
res[des1, nod] <- res[nod, des1] <- res[anc, des1] + l
}
}
if (trim) {
i <- which(x$node.label == "") + n
res <- res[-i, -i]
N <- dim(res)[1]
}
dimnames(res)[1:2] <- list(1:N)
res
}
cophenetic.phylo <- function(x)
{
n <- length(x$tip.label)
ans <- dist.nodes(x)[1:n, 1:n]
dimnames(ans)[1:2] <- list(x$tip.label)
ans
}
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