changes in reorder(, "cladewise")

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

diff --git a/R/cophenetic.phylo.R b/R/cophenetic.phylo.R
index a4f00beedb2ea32c692a77710b8b1dd0bfdbd054..a6669786814bcdb79ea941f3a2bce3937ab7b9cd 100644 (file)
--- a/R/cophenetic.phylo.R
+++ b/R/cophenetic.phylo.R
@@ -7,18 +7,18 @@
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
-dist.nodes <- function(phy)
+dist.nodes <- function(x)
 {
-    phy <- reorder(phy)
-    n <- Ntip(phy)
-    m <- phy$Nnode
+    x <- reorder(x) # required for the C code
+    n <- Ntip(x)
+    m <- x$Nnode
+    nm <- n + m
 
     d <- .C("dist_nodes", as.integer(n), as.integer(m),
-            as.integer(phy$edge[, 1] - 1L), as.integer(phy$edge[, 2] - 1L),
-            as.double(phy$edge.length), as.integer(Nedge(phy)),
+            as.integer(x$edge[, 1] - 1L), as.integer(x$edge[, 2] - 1L),
+            as.double(x$edge.length), as.integer(Nedge(x)),
             double(nm * nm), DUP = FALSE, NAOK = TRUE,
             PACKAGE = "ape")[[7]]
-    nm <- n + m
     dim(d) <- c(nm, nm)
     dimnames(d) <- list(1:nm, 1:nm)
     d