provisional version of the new reorder.phylo()

[ape.git] / man / reorder.phylo.Rd

diff --git a/man/reorder.phylo.Rd b/man/reorder.phylo.Rd
index 6a002faee528f536db02578c939b6c75408d84cf..dda3b3525c011737ef89473205f17d5a4fb247db 100644 (file)
--- a/man/reorder.phylo.Rd
+++ b/man/reorder.phylo.Rd
@@ -7,13 +7,15 @@
   the one input, but the ordering of the edges could be different.
 }
 \usage{
-\method{reorder}{phylo}(x, order = "cladewise", ...)
+\method{reorder}{phylo}(x, order = "cladewise", index.only = FALSE, ...)
 }
 \arguments{
   \item{x}{an object of class \code{"phylo"}.}
   \item{order}{a character string: either \code{"cladewise"} (the
-    default), or \code{"pruningwise"}, or any unambiguous abbreviation
-    of these.}
+    default), \code{"postorder"}, \code{"pruningwise"}, or any
+    unambiguous abbreviation of these.}
+  \item{index.only}{should the function return only the ordered indices
+    of the rows of the edge matrix?}
   \item{\dots}{further arguments passed to or from other methods.}
 }
 \details{
@@ -29,7 +31,7 @@
   multichotomies and branch lengths are preserved.
 }
 \value{
-  an object of class \code{"phylo"}.
+  an object of class \code{"phylo"}, or a numeric vector if \code{index.only = TRUE}.
 }
 \author{Emmanuel Paradis}
 \seealso{