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