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## nj.R (2021-05-10)
## Neighbor-Joining Tree Estimation
## Copyright 2004-2021 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 (anyNA(X))
stop("missing values are not allowed in the distance matrix\nConsider using njs()")
if (any(is.infinite(X)))
stop("infinite values are not allowed in the distance matrix")
N <- as.integer(attr(X, "Size"))
if (N < 3) stop("cannot build an NJ tree with less than 3 observations")
labels <- attr(X, "Labels")
if (is.null(labels)) labels <- as.character(1:N)
DIST <- numeric(length(X))
DIST[] <- X[]
obj <- .Call(C_nj, DIST, N)
names(obj) <- c("edge", "edge.length")
dim(obj[[1]]) <- c(2L * N - 3L, 2L)
obj$tip.label <- labels
obj$Nnode <- N - 2L
class(obj) <- "phylo"
reorder(obj)
}
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