Package: ape
Version: 2.2-1
-Date: 2008-07-09
+Date: 2008-07-11
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
-## sh.test.R (2006-07-06)
+## sh.test.R (2008-07-11)
## Shimodaira-Hasegawa Test
-## Copyright 2006 Emmanuel Paradis
+## Copyright 2006-2008 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
## Step 1:
foo <- function(PHY)
- attr(mlphylo(model, x, PHY, search.tree = FALSE, quiet = TRUE), "loglik")
+ attr(mlphylo(x, PHY, model, search.tree = FALSE, quiet = TRUE), "loglik")
Talpha <- sapply(phy, foo)
Talpha <- max(Talpha) - Talpha
for (i in 1:B) {
boot.samp <- x[, sample(ncol(x), replace = TRUE)]
for (j in 1:ntree)
- M[j, i] <- attr(mlphylo(model, boot.samp, phy[[j]],
+ M[j, i] <- attr(mlphylo(boot.samp, phy[[j]], model,
search.tree = FALSE, quiet = TRUE),
"loglik")
}