o read.nexus() failed to read a file with a single tree with line
breaks in the Newick string.
+ o del.gaps() returned a list of empty sequences when there were no
+ gaps.
+
OTHER CHANGES
Package: ape
Version: 2.2-2
-Date: 2008-09-17
+Date: 2008-10-02
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
-## DNA.R (2008-08-07)
+## DNA.R (2008-10-02)
## Manipulations and Comparisons of DNA Sequences
{
deleteGaps <- function(x) {
i <- which(x == 4)
- x[-i]
+ if (length(i)) x[-i] else x
}
if (class(x) != "DNAbin") x <- as.DNAbin(x)
}
\examples{
data(woodmouse)
-y <- seg.sites(woodmouse)
-s <- length(y)
-n <- length(woodmouse)
+s <- length(seg.sites(woodmouse))
+n <- nrow(woodmouse)
theta.s(s, n)
theta.s(s, n, variance = TRUE)
}