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## me.R (2023-05-15)
## Tree Estimation Based on Minimum Evolution Algorithm
## Copyright 2007 Vincent Lefort with modifications by
## Emmanuel Paradis (2008-2019)
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
fastme.bal <- function(X, nni = TRUE, spr = TRUE, tbr = FALSE)
{
if (tbr) {
warning("option 'tbr = TRUE' was ignored: see ?fastme.bal")
tbr <- FALSE
}
if (is.matrix(X)) X <- as.dist(X)
N <- as.integer(attr(X, "Size"))
if (N < 3)
stop("cannot build ME tree with less than 3 observations")
nedge <- 2L * N - 3L
ans <- .C(me_b, as.double(X), N, 1:N, as.integer(nni),
as.integer(spr), as.integer(tbr), integer(nedge),
integer(nedge), double(nedge), NAOK = TRUE)
labels <- attr(X, "Labels")
if (is.null(labels)) labels <- as.character(1:N)
labels <- labels[ans[[3]]]
obj <- list(edge = cbind(ans[[7]], ans[[8]]),
edge.length = ans[[9]],
tip.label = labels, Nnode = N - 2L)
class(obj) <- "phylo"
attr(obj, "order") <- "cladewise"
obj
}
fastme.ols <- function(X, nni = TRUE)
{
if (is.matrix(X)) X <- as.dist(X)
N <- as.integer(attr(X, "Size"))
if (N < 3)
stop("cannot build ME tree with less than 3 observations")
nedge <- 2L * N - 3L
ans <- .C(me_o, as.double(X), N, 1:N, as.integer(nni),
integer(nedge), integer(nedge), double(nedge),
NAOK = TRUE)
labels <- attr(X, "Labels")
if (is.null(labels)) labels <- as.character(1:N)
labels <- labels[ans[[3]]]
obj <- list(edge = cbind(ans[[5]], ans[[6]]),
edge.length = ans[[7]],
tip.label = labels, Nnode = N - 2L)
class(obj) <- "phylo"
attr(obj, "order") <- "cladewise"
obj
}
bionj <- 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 bionjs()")
if (any(X > 100))
stop("at least one distance was greater than 100")
N <- as.integer(attr(X, "Size"))
if (N < 3)
stop("cannot build a BIONJ tree with less than 3 observations")
ans <- .C(C_bionj, as.double(X), N, integer(2 * N - 3),
integer(2 * N - 3), double(2*N - 3), NAOK = TRUE)
labels <- attr(X, "Labels")
if (is.null(labels)) labels <- as.character(1:N)
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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