various updates + adding SPR+TBR in fastme.bal()

[ape.git] / R / me.R

diff --git a/R/me.R b/R/me.R
index 93cebd378303e1b2bfee2f70a941a38e7cbfa2f4..7dca6c020cec10ad3425358756fee5bb480212f0 100644 (file)
--- a/R/me.R
+++ b/R/me.R
@@ -1,20 +1,40 @@
-## 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)
@@ -22,14 +42,10 @@
     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)
@@ -43,6 +59,6 @@ bionj <- function(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")
 }