## reorder.phylo.R (2010-04-02)
## Internal Reordering of Trees
## Copyright 2006-2010 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
reorder.phylo <- function(x, order = "cladewise", ...)
{
order <- match.arg(order, c("cladewise", "pruningwise"))
if (!is.null(attr(x, "order")))
if (attr(x, "order") == order) return(x)
nb.node <- x$Nnode
if (nb.node == 1) return(x)
nb.tip <- length(x$tip.label)
nb.edge <- dim(x$edge)[1]
neworder <- if (order == "cladewise")
.C("neworder_cladewise", as.integer(nb.tip),
as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
as.integer(nb.edge), integer(nb.edge),
PACKAGE = "ape")[[5]]
else
.C("neworder_pruningwise", as.integer(nb.tip),
as.integer(nb.node), as.integer(x$edge[, 1]),
as.integer(x$edge[, 2]), as.integer(nb.edge),
integer(nb.edge), PACKAGE = "ape")[[6]]
x$edge <- x$edge[neworder, ]
if (!is.null(x$edge.length))
x$edge.length <- x$edge.length[neworder]
attr(x, "order") <- order
x
}
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