o prop.part() failed with a single tree with the default option
'check.labels = TRUE'.
+ o summary.DNAbin() failed to display correctly the summary of
+ sequence lengths with lists of sequences of 10,000 bases or more
+ (because summary.default uses 4 significant digits by default).
+
+ o read.nexus() failed to read a file with a single tree with line
+ breaks in the Newick string.
+
OTHER CHANGES
o The data sets bird.orders and bird.families are now stored as
- Newick strings; e.g., the command data(bird.orders) calls
+ Newick strings; i.e., the command data(bird.orders) calls
read.tree().
Package: ape
Version: 2.2-2
-Date: 2008-07-22
+Date: 2008-09-17
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 (2008-06-08)
+## DNA.R (2008-08-07)
## Manipulations and Comparisons of DNA Sequences
cat("Label:", nms, "\n\n")
} else {
cat(n, "DNA sequences in binary format stored in a list.\n\n")
- cat("Summary of sequence lengths:\n")
- print(summary(unlist(lapply(object, length))))
+ tmp <- unlist(lapply(object, length))
+ mini <- min(tmp)
+ maxi <- max(tmp)
+ if (mini == maxi)
+ cat("All sequences of same length:", maxi, "\n")
+ else {
+ cat("Mean sequence length:", round(mean(tmp), 3), "\n")
+ cat(" Shortest sequence:", mini, "\n")
+ cat(" Longest sequence:", maxi, "\n")
+ }
TAIL <- "\n\n"
if (printlen < n) {
nms <- nms[1:printlen]
-## read.nexus.R (2008-07-11)
+## read.nexus.R (2008-09-17)
## Read Tree File in Nexus Format
semico <- grep(";", tree)
Ntree <- length(semico)
## are some trees on several lines?
- if (any(diff(semico) != 1)) {
- STRING <- character(Ntree)
- s <- c(1, semico[-Ntree] + 1)
- j <- mapply(":", s, semico)
- for (i in 1:Ntree)
- STRING[i] <- paste(tree[j[, i]], collapse = "")
- } else STRING <- tree
+ if (Ntree == 1 && length(tree) > 1) STRING <- paste(tree, collapse = "") else {
+ if (any(diff(semico) != 1)) {
+ STRING <- character(Ntree)
+ s <- c(1, semico[-Ntree] + 1)
+ j <- mapply(":", s, semico)
+ for (i in 1:Ntree)
+ STRING[i] <- paste(tree[j[, i]], collapse = "")
+ } else STRING <- tree
+ }
rm(tree)
STRING <- gsub(" ", "", STRING)
colon <- grep(":", STRING)
\arguments{
\item{...}{either a series of objects of class \code{"phylo"}
separated by commas, or a list containing such objects.}
- \item{x}{a list, a matrix, or a data frame containing the (aligned)
- DNA sequences.}
+ \item{x}{a list or a matrix containing the (aligned) DNA sequences.}
\item{model}{the model to be fitted to each tree (as an object of
\code{"DNAmodel"}).}
\item{B}{the number of bootstrap replicates.}
}
\details{
The present implementation follows the original formulation of
- Shimodaira and Hasegawa (1999). A difference is that the bootstrap
+ Shimodaira and Hasegawa (1999) with the difference that the bootstrap
resampling is done on the original sequence data rather than the RELL
- method as sugested by Shimodaira and Hasegawa.
+ method suggested by Shimodaira and Hasegawa.
}
\value{
a numeric vector with the P-value associated with each tree given in