final commit for ape 3.0-8

[ape.git] / R / nj.R

diff --git a/R/nj.R b/R/nj.R
index 6f60d8ec8b7d9bd53c16d983f2850e40289d80bf..b12bd42a1c8bc00519d6c92348158ad2dcfb6783 100644 (file)
--- a/R/nj.R
+++ b/R/nj.R
@@ -1,4 +1,4 @@
-## nj.R (2009-07-10)
+## nj.R (2009-11-23)
 
 ##   Neighbor-Joining Tree Estimation
 
@@ -10,12 +10,14 @@
 nj <- function(X)
 {
     if (is.matrix(X)) X <- as.dist(X)
+    if (any(is.na(X)))
+        stop("missing values are not allowed in the distance matrix\nConsider using njs()")
     N <- attr(X, "Size")
     labels <- attr(X, "Labels")
     if (is.null(labels)) labels <- as.character(1:N)
     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")
+              DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")
     obj <- list(edge = cbind(ans[[3]], ans[[4]]), edge.length = ans[[5]],
                 tip.label = labels, Nnode = N - 2L)
     class(obj) <- "phylo"