updated phymltest() for PhyML 3.0 + changed rbind.DNAbin()

[ape.git] / R / mlphylo.R

diff --git a/R/mlphylo.R b/R/mlphylo.R
index 35dd73780562a6e4406db563b4778f84eeaad7f7..5f4b6ecd56cee8758c28c0b06ace72cc07a8ccbd 100644 (file)
--- a/R/mlphylo.R
+++ b/R/mlphylo.R
@@ -1,4 +1,4 @@
-## mlphylo.R (2008-01-03)
+## mlphylo.R (2008-07-15)
 
 ##   Estimating Phylogenies by Maximum Likelihood
 
@@ -45,7 +45,6 @@ mlphylo <-
       stop("some branch lengths are greater than one.")
     phy <- reorder(phy, "pruningwise")
     if (!quiet) cat("Preparing the sequences...\n")
-    BF <- if (model$model %in% 1:2) rep(0.25, 4) else base.freq(x)
     if (is.list(x)) x <- as.matrix(x)
     if (is.null(rownames(x)))
         stop("DNA sequences have no names") # safe...
@@ -54,6 +53,7 @@ mlphylo <-
 of the tree do not match") # safe here also
     x <- x[phy$tip.label, ]
     Y <- prepareDNA(x, model)
+    BF <- if (Y$model %in% 1:2) rep(0.25, 4) else base.freq(x)
     S <- length(Y$weight)
     npart <- dim(Y$partition)[2] # the number of overall partitions
     ## in case of negative branch lengths:
@@ -148,7 +148,7 @@ prepareDNA <- function(X, DNAmodel)
     }
 
     class(SEQ) <- "DNAbin"
-    ANC <- array(1, c(nrow(SEQ) - 2, ncol(SEQ), 4))
+    ANC <- array(0, c(nrow(SEQ) - 2, ncol(SEQ), 4))
 
     ## 'partition' gives the start and end of each partition:
     partition <- matrix(1, 2, npart)