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## njs.R (2023-05-15)
## Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
## Copyright 2011-2013 Andrei-Alin Popescu
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
njs <- function(X, fs = 15)
{
if (fs < 1)
stop("argument 'fs' must be a non-zero positive integer")
if (is.matrix(X)) X <- as.dist(X)
X[is.na(X)] <- -1
X[X < 0] <- -1
X[is.nan(X)] <- -1
N <- 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)
ans <- .C(C_njs, as.double(X), as.integer(N), integer(2*N - 3),
integer(2*N - 3), double(2*N - 3), as.integer(fs),
NAOK = TRUE)
obj <- list(edge = cbind(ans[[3]], ans[[4]]), edge.length = ans[[5]],
tip.label = labels, Nnode = N - 2L)
class(obj) <- "phylo"
reorder(obj)
}
bionjs <- function(X, fs = 15)
{
if (fs < 1)
stop("argument 'fs' must be a non-zero positive integer")
if (is.matrix(X)) X <- as.dist(X)
X[is.na(X)] <- -1
X[X < 0] <- -1
X[is.nan(X)] <- -1
N <- attr(X, "Size")
if (N < 3) stop("cannot build a BIONJ* tree with less than 3 observations")
labels <- attr(X, "Labels")
if (is.null(labels)) labels <- as.character(1:N)
ans <- .C(C_bionjs, as.double(X), as.integer(N), integer(2*N - 3),
integer(2*N - 3), double(2*N - 3), as.integer(fs),
NAOK = TRUE)
obj <- list(edge = cbind(ans[[3]], ans[[4]]), edge.length = ans[[5]],
tip.label = labels, Nnode = N - 2L)
class(obj) <- "phylo"
reorder(obj)
}
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