fixing nj() with many 0 distances

[ape.git] / R / nj.R

diff --git a/R/nj.R b/R/nj.R
index c99bce3306aed82dbe0ba85ab54f3d5a28174040..6f60d8ec8b7d9bd53c16d983f2850e40289d80bf 100644 (file)
--- a/R/nj.R
+++ b/R/nj.R
@@ -1,8 +1,8 @@
-## nj.R (2006-09-15)
+## nj.R (2009-07-10)
 
 ##   Neighbor-Joining Tree Estimation
 
-## Copyright 2004-2006 Emmanuel Paradis
+## Copyright 2004-2009 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -13,13 +13,11 @@ nj <- function(X)
     N <- attr(X, "Size")
     labels <- attr(X, "Labels")
     if (is.null(labels)) labels <- as.character(1:N)
-    edge1 <- edge2 <- integer(2*N - 3)
-    edge.length <- numeric(2*N - 3)
-    ans <- .C("nj", as.double(X), as.integer(N), as.integer(edge1),
-              as.integer(edge2), as.double(edge.length), PACKAGE = "ape")
-    obj <- list(edge = cbind(ans[[3]], ans[[4]]),
-                edge.length = ans[[5]], tip.label = labels)
-    obj$Nnode <- N - 2
+    ans <- .C("nj", as.double(X), as.integer(N), integer(2*N - 3),
+              integer(2*N - 3), double(2*N - 3),
+              DUP = FALSE, NAOK = TRUE, PACKAGE = "apex")
+    obj <- list(edge = cbind(ans[[3]], ans[[4]]), edge.length = ans[[5]],
+                tip.label = labels, Nnode = N - 2L)
     class(obj) <- "phylo"
     reorder(obj)
 }