[Phylobase-commits] r396 - pkg/man

[noreply at r-forge.r-project.org]

Author: pdc
Date: 2008-12-22 05:46:27 +0100 (Mon, 22 Dec 2008)
New Revision: 396

Modified:
   pkg/man/reorder-methods.Rd
Log:
documentation for reorder -- no examples yet


Modified: pkg/man/reorder-methods.Rd
===================================================================
--- pkg/man/reorder-methods.Rd	2008-12-22 04:34:45 UTC (rev 395)
+++ pkg/man/reorder-methods.Rd	2008-12-22 04:46:27 UTC (rev 396)
@@ -7,48 +7,48 @@
 \alias{orderIndex}
 \title{reordering trees within phylobase objects}
 \description{
- ~~ Methods for function \code{reorder} in Package `stats' ~~
+ Methods for reordering trees into various traversal orders
 }
 \section{Methods}{
   \describe{
-    \item{phylo = "phylo"}{reorders a \code{phylo} object}
-    \item{phylo = "phylo4"}{reorders a \linkS4class{phylo4} object}
-    \item{phylo = "phylo4d"}{reorders a \linkS4class{phylo4d} object}
+    \item{x = "phylo"}{reorders a \code{phylo} object}
+    \item{x = "phylo4"}{reorders a \linkS4class{phylo4} object}
+    \item{x = "phylo4d"}{reorders a \linkS4class{phylo4d} object}
   }
 }
 
 \usage{
-orderIndex(phy, order = c('preorder','postorder'))
 \S4method{reorder}{phylo}(x, ...)
 \S4method{reorder}{phylo4}(x, ...)
 \S4method{reorder}{phylo4d}(x, ...)
+orderIndex(phy, order = c('preorder','postorder'))
 }
 
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{phy}{a \code{phylo4} or \code{phylo4d} object}
   \item{x}{a \code{phylo4} or \code{phylo4d} object}
-  \item{order}{'preorder' or 'postorder' for preferred order}
-  \item{\dots}{ ~~Describe \code{\dots} here~~ }
+  \item{order}{The desired traversal order currently only 'preorder' and 'postorder' are allowed}
+  \item{\dots}{ A required order agrument (see above) is the only additional argument accepted. }
 }
 \details{
-  ~~ If necessary, more details than the description above ~~
+The \code{reorder} method takes \code{phylo4} or \code{phylo4d} tree and orders the edge matrix (e.g. \code{edges(phy)}) in the requested traversal order.  Currently only two orderings are permitted and both require rooted trees.  In "postorder" a nodes descendants come before that node, thus the root, being ancestral to all nodes, comes last.  "Preorder" is the converse, a node is visited before it's descendants, thus the root comes first.
+
+A method is also defined that takes an \code{ape phylo} object.  This also takes an order argument, however, 'pruningwise' and 'cladewise' are the only acceptable parameters.  This is because this method actually uses the \code{ape reorder()} command to complete the ordering.  
 }
 \value{
-  ~Describe the value returned
-  If it is a LIST, use
-  \item{comp1 }{Description of 'comp1'}
-  \item{comp2 }{Description of 'comp2'}
-  ...
+A \code{phylo4} or \code{phylo4d} object with the edge, label, lenght and data slots ordered as \code{order}.
 }
-\references{ ~put references to the literature/web site here ~ }
 \author{Peter Cowan}
 \note{
-  preorder corresponds to 'cladewise' in the ape package,
-  postorder corresponds (almost but close enough?) to 'pruningwise'
-  see ...
+  The "preorder" parameter corresponds to "cladewise" in the \code{ape} package, and "postorder" corresponds (almost but close enough?) to "pruningwise".  
+  
+  See \url{http://ape.mpl.ird.fr/misc/FormatTreeR_28July2008.pdf}
 }
-\seealso{ ~~objects to See Also as \code{\link{help}}, ~~~ }
+\seealso{\code{\link[ape]{reorder.phylo}} in the \code{ape} package. 
+ \code{\link{ancestors}} \code{\link{ancestor}} \code{\link{siblings}}
+ \code{\link{children}} \code{\link{descendants}}
+}
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.
 \keyword{methods}