-## me.R (2008-01-12)
+## me.R (2009-01-07)
## Tree Estimation Based on Minimum Evolution Algorithm
## Copyright 2007 Vincent Lefort with modifications by
-## Emmanuel Paradis (2008)
+## Emmanuel Paradis (2008-2009)
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
-.fastme <- function(X, nni, lib)
+fastme.bal <- function(X, nni = TRUE, spr = TRUE, tbr = TRUE)
{
if (is.matrix(X)) X <- as.dist(X)
N <- as.integer(attr(X, "Size"))
labels <- sprintf("%6s", 1:N)
edge1 <- edge2 <- integer(2*N - 3)
- ans <- .C(lib, as.double(X), N, labels, as.integer(nni),
+
+ ans <- .C("me_b", as.double(X), N, labels, as.integer(nni),
+ as.integer(spr), as.integer(tbr), edge1, edge2,
+ double(2*N - 3), character(N), PACKAGE = "ape")
+
+ labels <- substr(ans[[10]], 1, 6)
+ LABS <- attr(X, "Labels")
+ labels <- if (!is.null(LABS)) LABS[as.numeric(labels)]
+ else gsub("^ ", "", labels)
+ structure(list(edge = cbind(ans[[7]], ans[[8]]), edge.length = ans[[9]],
+ tip.label = labels, Nnode = N - 2L),
+ class = "phylo")
+}
+
+fastme.ols <- function(X, nni = TRUE)
+{
+ if (is.matrix(X)) X <- as.dist(X)
+ N <- as.integer(attr(X, "Size"))
+ labels <- sprintf("%6s", 1:N)
+ edge1 <- edge2 <- integer(2*N - 3)
+ ans <- .C("me_o", as.double(X), N, labels, as.integer(nni),
edge1, edge2, double(2*N - 3), character(N),
PACKAGE = "ape")
labels <- substr(ans[[8]], 1, 6)
labels <- if (!is.null(LABS)) LABS[as.numeric(labels)]
else gsub("^ ", "", labels)
structure(list(edge = cbind(ans[[5]], ans[[6]]), edge.length = ans[[7]],
- tip.label = labels, Nnode = N - 2),
+ tip.label = labels, Nnode = N - 2L),
class = "phylo")
}
-fastme.bal <- function(X, nni = TRUE) .fastme(X, nni, "me_b")
-
-fastme.ols <- function(X, nni = TRUE) .fastme(X, nni, "me_o")
-
bionj <- function(X)
{
if (is.matrix(X)) X <- as.dist(X)
labels <- if (!is.null(LABS)) LABS[as.numeric(labels)]
else gsub("^ ", "", labels)
structure(list(edge = cbind(ans[[4]], ans[[5]]), edge.length = ans[[6]],
- tip.label = labels, Nnode = N - 2),
+ tip.label = labels, Nnode = N - 2L),
class = "phylo")
}