X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fwrite.nexus.Rd;h=faf2ef63bf381d93929750b51e339aefb811e027;hb=48681c35f7904c17b064de9c6bf96d84581e9e52;hp=05341ff9650ff02a82704874d29f5cc2e9e382c2;hpb=c827059eeafc8cbe41c812b26979543ab287803e;p=ape.git

diff --git a/man/write.nexus.Rd b/man/write.nexus.Rd
index 05341ff..faf2ef6 100644
--- a/man/write.nexus.Rd
+++ b/man/write.nexus.Rd
@@ -2,10 +2,10 @@
 \alias{write.nexus}
 \title{Write Tree File in Nexus Format}
 \usage{
-write.nexus(..., file = "", translate = TRUE, original.data = TRUE)
+write.nexus(..., file = "", translate = TRUE, original.data = NULL)
 }
 \arguments{
-  \item{...}{either (i) a single object of class \code{"phylo"}, (ii) a
+  \item{\dots}{either (i) a single object of class \code{"phylo"}, (ii) a
     series of such objects separated by commas, or (iii) a list
     containing such objects.}
   \item{file}{a file name specified by either a variable of mode character,
@@ -14,18 +14,12 @@ write.nexus(..., file = "", translate = TRUE, original.data = TRUE)
   \item{translate}{a logical, if \code{TRUE} (the default) a translation
     of the tip labels is done which are replaced in the parenthetic
     representation with tokens.}
-  \item{original.data}{a logical, if \code{TRUE} (the default) the
-    data in the original NEXUS file are eventually written in
-    \code{"file"} (see below).}
+  \item{original.data}{deprecated; will be removed soon.}
 }
 \description{
   This function writes trees in a file with the NEXUS format.
 }
 \details{
-  If \code{original.data = TRUE}, the file as specified by the attribute
-  \code{"origin"} of the first tree is read and its data (except the
-  trees) are written in \code{file}.
-
   If several trees are given, they must have all the same tip labels.
 
   If among the objects given some are not trees of class \code{"phylo"},
@@ -40,7 +34,7 @@ write.nexus(..., file = "", translate = TRUE, original.data = TRUE)
     Biology}, \bold{46}, 590--621.
 }
 
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \seealso{
   \code{\link{read.nexus}}, \code{\link{read.tree}},
   \code{\link{write.tree}}, \code{\link{read.nexus.data}},