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## cophenetic.phylo.R (2021-06-14)
## Pairwise Distances from a Phylogenetic Tree
## Copyright 2006-2021 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
dist.nodes <- function(x)
{
x <- reorder(x) # required for the C code
n <- Ntip(x)
m <- x$Nnode
nm <- n + m
if (nm > floor(sqrt(2^31 - 1))) stop("tree too big")
d <- .C(dist_nodes, as.integer(n), as.integer(m),
as.integer(x$edge[, 1] - 1L), as.integer(x$edge[, 2] - 1L),
as.double(x$edge.length), as.integer(Nedge(x)),
double(nm * nm), NAOK = TRUE)[[7]]
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
}
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