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## cophenetic.phylo.R (2024-12-10)
## Pairwise Distances from a Phylogenetic Tree
## Copyright 2006-2024 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
dist.nodes <- function(x, fail.if.no.length = FALSE)
{
if (is.null(x$edge.length)) {
if (fail.if.no.length) stop("the tree has no branch length")
warning("the tree has no branch length: fixing them to one.")
x <- compute.brlen(x, 1)
}
x <- reorder(x) # required for the C code
n <- Ntip(x)
m <- x$Nnode
d <- .Call(dist_nodes, n, m, x$edge, x$edge.length)
nm <- n + m
dimnames(d) <- list(1:nm, 1:nm)
d
}
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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