provisional version of the new reorder.phylo()

[ape.git] / man / write.tree.Rd

diff --git a/man/write.tree.Rd b/man/write.tree.Rd
index d184456f7b0b011fb7192db967b270f2bbccfb0b..7a512449ff3ee64f126b6d527e35a2f1374c04ec 100644 (file)
--- a/man/write.tree.Rd
+++ b/man/write.tree.Rd
@@ -3,10 +3,10 @@
 \title{Write Tree File in Parenthetic Format}
 \usage{
 write.tree(phy, file = "", append = FALSE,
-           digits = 10)
+           digits = 10, tree.names = FALSE)
 }
 \arguments{
-  \item{phy}{an object of class \code{"phylo"}.}
+  \item{phy}{an object of class \code{"phylo"} or \code{"multiPhylo"}.}
   \item{file}{a file name specified by either a variable of mode character,
     or a double-quoted string; if \code{file = ""} (the default) then the
     tree is written on the standard output connection (i.e. the console).}
@@ -15,6 +15,10 @@ write.tree(phy, file = "", append = FALSE,
     the file (if it exists) is overwritten (\code{FALSE} the default).}
   \item{digits}{a numeric giving the number of digits used for printing
     branch lengths.}
+  \item{tree.names}{either a logical or a vector of mode character. If
+    \code{TRUE} then any tree names will be written prior to the tree on
+    each line. If character, specifies the name of \code{"phylo"}
+    objects which can be written to the file.}
 }
 \description{
   This function writes in a file a tree in parenthetic format using the
@@ -22,11 +26,17 @@ write.tree(phy, file = "", append = FALSE,
 }
 \value{
   a vector of mode character if \code{file = ""}, none (invisible
-  `NULL') otherwise.
+  \code{NULL}) otherwise.
 }
 \details{
   The node labels and the root edge length, if available, are written in
   the file.
+
+  If \code{tree.names == TRUE} then a variant of the Newick format is
+  written for which the name of a tree precedes the Newick format tree
+  (parentheses are eventually deleted beforehand). The tree names are
+  taken from the \code{names} attribute if present (they are ignored if
+  \code{tree.names} is a character vector).
 }
 \references{
   Felsenstein, J. The Newick tree format.
@@ -36,10 +46,12 @@ write.tree(phy, file = "", append = FALSE,
   \url{http://evolution.genetics.washington.edu/phylip/newick_doc.html}
 }
 
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis, Daniel Lawson
+  \email{dan.lawson@bristol.ac.uk}, and Klaus Schliep
+  \email{kschliep@snv.jussieu.fr}}
 \seealso{
   \code{\link{read.tree}}, \code{\link{read.nexus}},
   \code{\link{write.nexus}}
 }
 \keyword{manip}
-\keyword{IO}
+\keyword{IO}
\ No newline at end of file