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## branching.times.R (2018-01-16)
## Branching Times of a Phylogenetic Tree
## Copyright 2002-2018 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
branching.times <- function(phy)
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
phy <- reorder(phy)
n <- length(phy$tip.label)
e1 <- phy$edge[, 1]
e2 <- phy$edge[, 2]
EL <- phy$edge.length
if (is.null(EL)) {
warning("no branch length in tree")
return(numeric())
}
N <- length(e1)
xx <- numeric(phy$Nnode)
interns <- which(e2 > n)
## we loop only on the internal edges, this assumes
## that `xx' is already set with 0
for (i in interns) xx[e2[i] - n] <- xx[e1[i] - n] + EL[i]
depth <- xx[e1[N] - n] + EL[N]
xx <- depth - xx
names(xx) <-
if (is.null(phy$node.label)) (n + 1):(n + phy$Nnode)
else phy$node.label
xx
}
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