o read.nexus() failed to read a file with a single tree and no
translation of tip labels.
+ o read.nexus() failed to place correctly tip labels when reading
+ a single tree with no edge lengths.
+
OTHER CHANGES
Package: ape
Version: 2.2-1
-Date: 2008-07-03
+Date: 2008-07-09
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 (2008-07-04)
+## read.nexus.R (2008-07-09)
## Read Tree File in Nexus Format
if (any(w)) { # in case all comments use at least 2 lines
s <- LEFT[w]
X[s] <- gsub("\\[[^]]*\\]", "", X[s])
- ## The previous regexp was quite tough to find: it makes
+ ## The above regexp was quite tough to find: it makes
## possible to delete series of comments on the same line:
## ...[...]xxx[...]...
## without deleting the "xxx". This regexp is in three parts:
}
if (Ntree == 1) {
trees <- trees[[1]]
- if (translation) trees$tip.label <- TRANS[, 2]
+ if (translation)
+ trees$tip.label <- TRANS[, 2][as.numeric(trees$tip.label)]
} else {
if (!is.null(tree.names)) names(trees) <- tree.names
if (translation) attr(trees, "TipLabel") <- TRANS[, 2]