[Adephylo-commits] r13 - pkg/man

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

Author: jombart
Date: 2008-11-20 20:08:31 +0100 (Thu, 20 Nov 2008)
New Revision: 13

Added:
   pkg/man/treePart.Rd
Modified:
   pkg/man/listTips.Rd
Log:
Added doc for treePart.


Modified: pkg/man/listTips.Rd
===================================================================
--- pkg/man/listTips.Rd	2008-11-20 18:59:22 UTC (rev 12)
+++ pkg/man/listTips.Rd	2008-11-20 19:08:31 UTC (rev 13)
@@ -17,7 +17,7 @@
   A list whose components are vectors of named tips for a given node.
 }
 \author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
-\seealso{\code{\link{treeNodes}} which lists the direct descendants for
+\seealso{\code{\link{listNodes}} which lists the direct descendants for
   each node. \cr
   
   \code{\link{treePart}} which defines partitions of tips

Added: pkg/man/treePart.Rd
===================================================================
--- pkg/man/treePart.Rd	                        (rev 0)
+++ pkg/man/treePart.Rd	2008-11-20 19:08:31 UTC (rev 13)
@@ -0,0 +1,36 @@
+\name{treePart}
+\alias{treePart}
+\title{Define partitions of tips according from a tree}
+\description{
+  The function \code{treePart} defines partitions of tips reflecting the
+  topology of a tree. Each node but the root is translated into a dummy
+  vector having one value for each tip: this value is '1' if the tip
+  descends from this node, and '0' otherwise.\cr
+}
+\usage{
+treePart(x)
+}
+\arguments{
+  \item{x}{A tree of  class \code{\link[pkg:ape]{phylo}},
+    \linkS4class{phylo4} or \linkS4class{phylo4d}.}
+}
+\value{
+  A data.frame of dummy vectors (in columns) having one value for each
+  tip (rows).
+}
+\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\seealso{\code{\link{listNodes}} which is called by \code{treePart}.
+}
+\examples{
+if(require(ape) & require(phylobase)){
+## make a tree
+x <- as(rtree(10),"phylo4")
+partition <- treePart(x)
+partition
+
+## plot the dummy vectors with the tree
+temp <- phylo4d(x, partition)
+s.phylo4d(temp, cent=FALSE, scale=FALSE)
+}
+}
+\keyword{manip}