-## nj.R (2009-07-10)
+## nj.R (2009-11-23)
## Neighbor-Joining Tree Estimation
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"