X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Freorder.phylo.Rd;h=c81beee8a42147fad49ce2b08f0a6703cd49e493;hb=dff741171e7afe3f9aaa2d9cb19c2f91995e8623;hp=6a002faee528f536db02578c939b6c75408d84cf;hpb=21eb56120c84786502f24ff9c27b39d5badfe1f7;p=ape.git

diff --git a/man/reorder.phylo.Rd b/man/reorder.phylo.Rd
index 6a002fa..c81beee 100644
--- a/man/reorder.phylo.Rd
+++ b/man/reorder.phylo.Rd
@@ -7,29 +7,43 @@
   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{
   Because in a tree coded as an object of class \code{"phylo"} each
   branch is represented by a row in the element `edge', there is an
   arbitrary choice for the ordering of these rows. \code{reorder} allows
-  to reorder these rows according to two rules: in the
+  to reorder these rows according to three rules: in the
   \code{"cladewise"} order each clade is formed by a series of
-  contiguous rows; this is the order returned by
-  \code{\link{read.tree}}. In the \code{"pruningwise"} order, rows are
-  arranged so that ``pruning'' the tree (or post-order tree traversal)
-  can be done by descending along the rows of `edge'. The possible
-  multichotomies and branch lengths are preserved.
+  contiguous rows. In the \code{"postorder"} order, the rows are
+  arranged so that computations following pruning-like algorithm the
+  tree (or postorder tree traversal) can be done by descending along
+  these rows (conversely, a preorder tree traversal can be performed by
+  moving from the last to the first row). The \code{"pruningwise"} order
+  is an alternative ``pruning'' order which is actually a bottom-up
+  traversal order (Valiente 2002). (This third choice might be removed
+  in the future as it merely duplicates the second one which is more
+  efficient.) The possible multichotomies and branch lengths are preserved.
+
+  Note that for a given order, there are several possible orderings of
+  the rows of `edge'.
 }
 \value{
-  an object of class \code{"phylo"}.
+  an object of class \code{"phylo"} (with the attribute \code{"order"}
+  set accordingly), or a numeric vector if \code{index.only = TRUE}.
+}
+\references{
+  Valiente, G. (2002) \emph{Algorithms on Trees and Graphs.} New York:
+  Springer.
 }
 \author{Emmanuel Paradis}
 \seealso{
@@ -38,9 +52,8 @@
 }
 \examples{
 data(bird.families)
-tr <- reorder(bird.families, "p")
+tr <- reorder(bird.families, "postorder")
 all.equal(bird.families, tr) # uses all.equal.phylo actually
 all.equal.list(bird.families, tr) # bypasses the generic
 }
-
 \keyword{manip}