new dist.nodes() with C code

[ape.git] / R / reorder.phylo.R

diff --git a/R/reorder.phylo.R b/R/reorder.phylo.R
index e06b26bb44e6a7e9439819d03544c52f4c4971a7..226adb946c334f048382f0f04083429de3d4078d 100644 (file)
--- a/R/reorder.phylo.R
+++ b/R/reorder.phylo.R
@@ -1,8 +1,8 @@
-## reorder.phylo.R (2010-04-02)
+## reorder.phylo.R (2012-08-01)
 
 ##   Internal Reordering of Trees
 
-## Copyright 2006-2010 Emmanuel Paradis
+## Copyright 2006-2012 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -16,16 +16,20 @@ reorder.phylo <- function(x, order = "cladewise", ...)
     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]]
+    if (order == "cladewise") {
+        neworder <-
+            .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 {
+        ##node.degree <- tabulate(x$edge[, 1])
+        neworder <-
+            .C("neworder_pruningwise", as.integer(nb.tip),
+               as.integer(nb.node), as.integer(x$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]