stabler and faster C code for ME and BIONJ

[ape.git] / R / me.R

diff --git a/R/me.R b/R/me.R
index 25cd4ab9e46f23544432f03f50e6a4f76505674b..93cebd378303e1b2bfee2f70a941a38e7cbfa2f4 100644 (file)
--- a/R/me.R
+++ b/R/me.R
@@ -1,41 +1,48 @@
-## me.R (2007-07-12)
+## me.R (2008-01-12)
 
-##      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)
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
-fastme.bal <- function(X, nni = TRUE)
+.fastme <- function(X, nni, lib)
 {
     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(lib, 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 - 2),
+              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]])
-}
+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)
-    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 - 2),
+              class = "phylo")
 }