-## collapse.singles.R (2006-07-15)
+## collapse.singles.R (2010-07-23)
## Collapse "Single" Nodes
{
elen <- tree$edge.length
xmat <- tree$edge
+ ## added by Elizabeth Purdom (2008-06-19):
+ node.lab <- tree$node.label
+ nnode <- tree$Nnode
+ ntip <- length(tree$tip.label)
+ ## end
singles <- NA
while (length(singles) > 0) {
## changed by EP to make it slightly more efficient:
prev.node <- which(xmat[, 2] == i)
next.node <- which(xmat[, 1] == i)
xmat[prev.node, 2] <- xmat[next.node, 2]
- xmat <- xmat[xmat[, 1] != i, ] ## drop
+ xmat <- xmat[xmat[, 1] != i, ] # drop
## changed by EP for the new coding of "phylo" (2006-10-05):
## xmat[xmat < i] <- xmat[xmat < i] + 1 ## adjust indices
- xmat[xmat > i] <- xmat[xmat > i] - 1 ## adjust indices
+ xmat[xmat > i] <- xmat[xmat > i] - 1L ## adjust indices # changed '1' by '1L' (2010-07-23)
## END
elen[prev.node] <- elen[prev.node] + elen[next.node]
+ ## added by Elizabeth Purdom (2008-06-19):
+ if (!is.null(node.lab)) node.lab <- node.lab[-c(i - ntip)]
+ nnode <- nnode - 1L
+ ## end
elen <- elen[-next.node]
}
}
tree$edge <- xmat
tree$edge.length <- elen
+ ## added by Elizabeth Purdom (2008-06-19):
+ tree$node.label <- node.lab
+ tree$Nnode <- nnode
+ ## end
tree
}