-## as.phylo.R (2007-03-05)
+## as.phylo.R (2010-04-06)
## Conversion Among Tree Objects
-## Copyright 2005-2007 Emmanuel Paradis
+## Copyright 2005-2010 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
as.phylo.hclust <- function(x, ...)
{
N <- dim(x$merge)[1]
- edge <- matrix(NA, 2*N, 2)
+ edge <- matrix(0L, 2*N, 2)
edge.length <- numeric(2*N)
## `node' gives the number of the node for the i-th row of x$merge
- node <- numeric(N)
- node[N] <- N + 2
- cur.nod <- N + 3
- j <- 1
+ node <- integer(N)
+ node[N] <- N + 2L
+ cur.nod <- N + 3L
+ j <- 1L
for (i in N:1) {
edge[j:(j + 1), 1] <- node[i]
for (l in 1:2) {
- k <- j + l - 1
- if (x$merge[i, l] > 0) {
- edge[k, 2] <- node[x$merge[i, l]] <- cur.nod
- cur.nod <- cur.nod + 1
- edge.length[k] <- x$height[i] - x$height[x$merge[i, l]]
+ k <- j + l - 1L
+ y <- x$merge[i, l]
+ if (y > 0) {
+ edge[k, 2] <- node[y] <- cur.nod
+ cur.nod <- cur.nod + 1L
+ edge.length[k] <- x$height[i] - x$height[y]
} else {
- edge[k, 2] <- -x$merge[i, l]
+ edge[k, 2] <- -y
edge.length[k] <- x$height[i]
}
}
- j <- j + 2
+ j <- j + 2L
}
if (is.null(x$labels))
- x$labels <- as.character(1:(N + 1))
- obj <- list(edge = edge, edge.length = edge.length,
+ x$labels <- as.character(1:(N + 1))
+ obj <- list(edge = edge, edge.length = edge.length / 2,
tip.label = x$labels, Nnode = N)
class(obj) <- "phylo"
reorder(obj)