-## collapse.singles.R (2006-07-15)
+## collapse.singles.R (2008-06-19)
## 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$tip.label)
+ ## end
singles <- NA
while (length(singles) > 0) {
## changed by EP to make it slightly more efficient:
xmat[xmat > i] <- xmat[xmat > i] - 1 ## adjust indices
## END
elen[prev.node] <- elen[prev.node] + elen[next.node]
+ ## added by Elizabeth Purdom (2008-06-19):
+ if (!is.null(node.lab)) node.lab <- node.lab[-c(i - ntip)]
+ nnode <- nnode - 1
+ ## end
elen <- elen[-next.node]
}
}
tree$edge <- xmat
tree$edge.length <- elen
+ ## added by Elizabeth Purdom (2008-06-19):
+ tree$node.label <- node.lab
+ tree$Nnode <- nnode
+ ## end
tree
}