## cophenetic.phylo.R (2012-08-14)

##   Pairwise Distances from a Phylogenetic Tree

## Copyright 2006-2012 Emmanuel Paradis

## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.

dist.nodes <- function(phy)
{
    phy <- reorder(phy)
    n <- Ntip(phy)
    m <- phy$Nnode

    d <- .C("dist_nodes", as.integer(n), as.integer(m),
            as.integer(phy$edge[, 1] - 1L), as.integer(phy$edge[, 2] - 1L),
            as.double(phy$edge.length), as.integer(Nedge(phy)),
            double(nm * nm), DUP = FALSE, NAOK = TRUE,
            PACKAGE = "ape")[[7]]
    nm <- n + m
    dim(d) <- c(nm, nm)
    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
}