1 ## collapse.singles.R (2006-07-15)
3 ## Collapse "Single" Nodes
5 ## Copyright 2006 Ben Bolker
7 ## This file is part of the R-package `ape'.
8 ## See the file ../COPYING for licensing issues.
10 collapse.singles <- function(tree)
12 elen <- tree$edge.length
15 while (length(singles) > 0) {
16 ## changed by EP to make it slightly more efficient:
17 ## tx <- table(xmat[xmat < 0])
18 ## singles <- as.numeric(names(tx)[tx < 3])
19 tx <- tabulate(xmat[, 1])
20 singles <- which(tx == 1)
22 if (length(singles) > 0) {
24 prev.node <- which(xmat[, 2] == i)
25 next.node <- which(xmat[, 1] == i)
26 xmat[prev.node, 2] <- xmat[next.node, 2]
27 xmat <- xmat[xmat[, 1] != i, ] ## drop
28 ## changed by EP for the new coding of "phylo" (2006-10-05):
29 ## xmat[xmat < i] <- xmat[xmat < i] + 1 ## adjust indices
30 xmat[xmat > i] <- xmat[xmat > i] - 1 ## adjust indices
32 elen[prev.node] <- elen[prev.node] + elen[next.node]
33 elen <- elen[-next.node]
37 tree$edge.length <- elen