-## nj.R (2006-09-15)
+## nj.R (2009-11-23)
## 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.
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")
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 = "ape")
+ obj <- list(edge = cbind(ans[[3]], ans[[4]]), edge.length = ans[[5]],
+ tip.label = labels, Nnode = N - 2L)
class(obj) <- "phylo"
reorder(obj)
}