1 ## reorder.phylo.R (2012-10-12)
3 ## Internal Reordering of Trees
5 ## Copyright 2006-2012 Emmanuel Paradis
7 ## This file is part of the R-package `ape'.
8 ## See the file ../COPYING for licensing issues.
10 reorder.phylo <- function(x, order = "cladewise", index.only = FALSE, ...)
12 ORDER <- c("cladewise", "postorder", "pruningwise")
13 io <- pmatch(order, ORDER)
14 if (is.na(io)) stop("ambiguous order")
16 nb.edge <- dim(x$edge)[1]
17 if (!is.null(attr(x, "order")))
18 if (attr(x, "order") == order)
19 if (index.only) return(1:nb.edge) else return(x)
21 if (nb.node == 1) return(x)
22 nb.tip <- length(x$tip.label)
26 .C("neworder_pruningwise", as.integer(nb.tip),
27 as.integer(nb.node), as.integer(x$edge[, 1]),
28 as.integer(x$edge[, 2]), as.integer(nb.edge),
29 integer(nb.edge), PACKAGE = "ape")[[6]]
32 .C("neworder_phylo", as.integer(nb.tip),
33 as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
34 as.integer(nb.edge), integer(nb.edge), io,
35 DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")[[5]]
37 if (index.only) return(neworder)
38 x$edge <- x$edge[neworder, ]
39 if (!is.null(x$edge.length))
40 x$edge.length <- x$edge.length[neworder]
41 attr(x, "order") <- order