## collapse.singles.R (2013-01-16)

##    Collapse "Single" Nodes

## Copyright 2006 Ben Bolker, 2013 Klaus Schliep

## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.

collapse.singles <- function(tree)
{
    tree <- reorder(tree) # added by Klaus
    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$tip.label)
    ## end
    ## Added by Klaus (2013-01-16):
    tx <- tabulate(xmat[, 1])
    singles <- which(tx == 1)
    if (length(singles) > 0) {
        prev.nodes <- match(singles, xmat[,2])
        next.nodes <- match(singles, xmat[,1])
        for(j in length(singles):1) {
            i <- singles[j]
            xmat[prev.nodes[j], 2] <- xmat[next.nodes[j], 2]
            elen[prev.nodes[j]] <- elen[prev.nodes[j]] + elen[next.nodes[j]]
        }
        xmat <- xmat[-next.nodes,]
        elen <- elen[-next.nodes]
        if (!is.null(node.lab)) node.lab <- node.lab[-c(singles - ntip)]
        nnode = nnode - as.integer(length(singles))
        tmp = integer(max(xmat))
        tmp[sort(unique(as.vector(xmat)))] = as.integer(c(1:(ntip+nnode)))
        xmat[] = tmp[xmat]
    }
    # End
    tree$edge <- xmat
    tree$edge.length <- elen
    ## added by Elizabeth Purdom (2008-06-19):
    tree$node.label <- node.lab
    tree$Nnode <- nnode
    ## end
    tree
}