o chronopl() did not work with CV = TRUE.
o chronopl() did not work with CV = TRUE.
+ o read.nexus() did not work correctly in some situations (trees on
+ multiple lines with different numbers of lines and/or with
+ comments inserted within the trees).
+
CHANGES IN APE VERSION 2.2-2
CHANGES IN APE VERSION 2.2-2
Package: ape
Version: 2.2-3
Package: ape
Version: 2.2-3
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
-## read.nexus.R (2008-09-17)
+## read.nexus.R (2008-11-24)
## Read Tree File in Nexus Format
## Read Tree File in Nexus Format
tree <- X[start:end]
rm(X)
tree <- gsub("^.*= *", "", tree)
tree <- X[start:end]
rm(X)
tree <- gsub("^.*= *", "", tree)
+ ## check whether there are empty lines from the above manips:
+ tree <- tree[tree == ""]
semico <- grep(";", tree)
Ntree <- length(semico)
## are some trees on several lines?
semico <- grep(";", tree)
Ntree <- length(semico)
## are some trees on several lines?
STRING <- character(Ntree)
s <- c(1, semico[-Ntree] + 1)
j <- mapply(":", s, semico)
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 = "")
+ if (is.list(j)) {
+ for (i in 1:Ntree)
+ STRING[i] <- paste(tree[j[[i]]], collapse = "")
+ } else {
+ for (i in 1:Ntree)
+ STRING[i] <- paste(tree[j[, i]], collapse = "")
+ }
} else STRING <- tree
}
rm(tree)
} else STRING <- tree
}
rm(tree)
Many users gave important feed-back with their encouragements,
comments, or bug reports: thanks to all of you!
Many users gave important feed-back with their encouragements,
comments, or bug reports: thanks to all of you!
-Significant bug fixes were provided by James Bullard, Éric Durand,
-Olivier François, Bret Larget, Elizabeth Purdom, Klaus Schliep,
-Li-San Wang, and Yan Wong. Contact me if I forgot someone.
+Significant bug fixes were provided by Cécile Ané, James Bullard,
+Éric Durand, Olivier François, Bret Larget, Elizabeth Purdom,
+Klaus Schliep, Li-San Wang, and Yan Wong. Contact me if I forgot
+someone.
Kurt Hornik, of the R Core Team, helped in several occasions to
fix some problems and bugs.
Kurt Hornik, of the R Core Team, helped in several occasions to
fix some problems and bugs.