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## speciesTree.R (2013-08-12)
## Species Trees
## Copyright 2010-2013 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
speciesTree <- function(x, FUN = min)
### FUN = min => MAXTREE (Liu et al. 2010)
### FUN = sum => shallowest divergence (Maddison & Knowles 2006)
{
test.ultra <- which(!unlist(lapply(x, is.ultrametric)))
if (length(test.ultra))
stop(paste("the following trees were not ultrametric:\n",
paste(test.ultra, collapse = " ")))
Ntree <- length(x)
D <- lapply(x, cophenetic.phylo)
nms <- rownames(D[[1]])
n <- length(nms)
M <- matrix(0, n*(n - 1)/2, Ntree)
for (i in 1:Ntree) M[, i] <- as.dist(D[[i]][nms, nms])
Y <- apply(M, 1, FUN)
attributes(Y) <- list(Size = n, Labels = nms, Diag = FALSE,
Upper = FALSE, class = "dist")
as.phylo(hclust(Y, "single"))
}
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