some changes for ape 3.0-6

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

diff --git a/R/reorder.phylo.R b/R/reorder.phylo.R
index ee9e9e0dcf703f7da186d125f82a8f14c26b1758..e717eb26c2583c6d3cf0e371f289538c851d6ac2 100644 (file)
--- a/R/reorder.phylo.R
+++ b/R/reorder.phylo.R
@@ -1,4 +1,4 @@
-## reorder.phylo.R (2012-09-03)
+## reorder.phylo.R (2012-10-12)
 
 ##   Internal Reordering of Trees
 
@@ -13,12 +13,13 @@ reorder.phylo <- function(x, order = "cladewise", index.only = FALSE, ...)
     io <- pmatch(order, ORDER)
     if (is.na(io)) stop("ambiguous order")
     order <- ORDER[io]
+    nb.edge <- dim(x$edge)[1]
     if (!is.null(attr(x, "order")))
-        if (attr(x, "order") == order) return(x)
+        if (attr(x, "order") == order)
+            if (index.only) return(1:nb.edge) else return(x)
     nb.node <- x$Nnode
     if (nb.node == 1) return(x)
     nb.tip <- length(x$tip.label)
-    nb.edge <- dim(x$edge)[1]
     if (io == 3) {
         x <- reorder(x)
         neworder <-