-## write.tree.R (2009-05-10)
+## write.tree.R (2009-06-16)
## Write Tree File in Parenthetic Format
write.tree <-
function (phy, file = "", append = FALSE, digits = 10, tree.names = FALSE)
{
+ output.tree.names <- FALSE
if (is.logical(tree.names)) {
output.tree.names <- tree.names
tree.names <- NULL
} else if (is.character(tree.names)) {
output.tree.names <- TRUE
- names(tree) <- tree.names
+ names(phy) <- tree.names
}
if (output.tree.names)
- names(tree) <- checkLabel(names(tree))
+ names(phy) <- checkLabel(names(phy))
if (inherits(phy, "multiPhylo")) {
write.tree(phy[[1]], file = file, append = append,
- digits = digits, tree.names = names[1])
+ digits = digits, tree.names = names(phy)[1])
if (length(phy) > 1)
for (i in 2:length(phy)) write.tree(phy[[i]], file = file,
append = TRUE, digits = digits, tree.names = names(phy)[i])