-## me.R (2011-05-12)
+## me.R (2012-09-14)
## Tree Estimation Based on Minimum Evolution Algorithm
## Copyright 2007 Vincent Lefort with modifications by
-## Emmanuel Paradis (2008-2011)
+## Emmanuel Paradis (2008-2012)
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
{
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_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")
+ 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),
+ DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")
+ 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"))
- 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")
+ nedge <- 2L * N - 3L
+ ans <- .C("me_o", as.double(X), N, 1:N, as.integer(nni),
+ integer(nedge), integer(nedge), double(nedge),
+ DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")
+ 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"))
- 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")
+
+ ans <- .C("bionj", as.double(X), N, integer(2 * N - 3),
+ integer(2 * N - 3), double(2*N - 3),
+ DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")
+ 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)
}