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## collapse.singles.R (2017-07-27)
## Collapse "Single" Nodes
## Copyright 2015 Emmanuel Paradis, 2017 Klaus Schliep
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
has.singles <- function(tree)
{
fun <- function(x) {
tab <- tabulate(x$edge[, 1])
if (any(tab == 1L)) return(TRUE)
FALSE
}
if (inherits(tree, "phylo")) return(fun(tree))
if (inherits(tree, "multiPhylo")) return(sapply(tree, fun))
}
collapse.singles <- function(tree, root.edge = FALSE)
{
n <- length(tree$tip.label)
tree <- reorder(tree) # this works now
e1 <- tree$edge[, 1]
e2 <- tree$edge[, 2]
tab <- tabulate(e1)
if (all(tab[-c(1:n)] > 1)) return(tree) # tips are zero
if (is.null(tree$edge.length)) {
root.edge <- FALSE
wbl <- FALSE
} else {
wbl <- TRUE
el <- tree$edge.length
}
if (root.edge) ROOTEDGE <- 0
## start with the root node:
ROOT <- n + 1L
while (tab[ROOT] == 1) {
i <- which(e1 == ROOT)
ROOT <- e2[i]
if (wbl) {
if (root.edge) ROOTEDGE <- ROOTEDGE + el[i]
el <- el[-i]
}
e1 <- e1[-i]
e2 <- e2[-i]
}
singles <- which(tabulate(e1) == 1)
if (length(singles) > 0) {
ii <- sort(match(singles, e1), decreasing = TRUE)
jj <- match(e1[ii], e2)
for (i in 1:length(singles)) {
e2[jj[i]] <- e2[ii[i]]
if (wbl) el[jj[i]] <- el[jj[i]] + el[ii[i]]
}
e1 <- e1[-ii]
e2 <- e2[-ii]
if (wbl) el <- el[-ii]
}
Nnode <- length(e1) - n + 1L
oldnodes <- unique(e1)
if (!is.null(tree$node.label))
tree$node.label <- tree$node.label[oldnodes - n]
newNb <- integer(max(oldnodes))
newNb[ROOT] <- n + 1L
sndcol <- e2 > n
e2[sndcol] <- newNb[e2[sndcol]] <- n + 2:Nnode
e1 <- newNb[e1]
tree$edge <- cbind(e1, e2, deparse.level = 0)
tree$Nnode <- Nnode
if (wbl) {
if (root.edge) tree$root.edge <- ROOTEDGE
tree$edge.length <- el
}
tree
}
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