[Adephylo-commits] r88 - in pkg: R man

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

Author: jombart
Date: 2008-12-12 19:24:42 +0100 (Fri, 12 Dec 2008)
New Revision: 88

Modified:
   pkg/R/partition.R
   pkg/man/treePart.Rd
Log:
treePart doc; now treePart outputs data.frames.


Modified: pkg/R/partition.R
===================================================================
--- pkg/R/partition.R	2008-12-12 18:13:58 UTC (rev 87)
+++ pkg/R/partition.R	2008-12-12 18:24:42 UTC (rev 88)
@@ -67,7 +67,7 @@
     res <- res[,-1]
 
     if(result=="basis"){
-        return(as.matrix(res)) # res is a matrix of dummy vectors
+        return(res) # res is a data.frame of dummy vectors
     }
 
 
@@ -138,7 +138,7 @@
     rownames(res) <- x at tip.label
     colnames(res) <- paste("V",1:ncol(res))
 
-    return(res)
+    return(as.data.frame(res))
 
 } # end treePart
 

Modified: pkg/man/treePart.Rd
===================================================================
--- pkg/man/treePart.Rd	2008-12-12 18:13:58 UTC (rev 87)
+++ pkg/man/treePart.Rd	2008-12-12 18:24:42 UTC (rev 88)
@@ -3,24 +3,39 @@
 \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
+  topology of a tree. There are two possible outputs (handled by the
+  argument \code{result}):\cr
+  - \code{basis} mode: 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
+  - \code{orthobasis}: in this mode, an orthonormal basis is derived
+  from the basis previously mentionned. This orthobasis was proposed in
+  the orthogram (Ollier \emph{et al.} 2006).
 }
 \usage{
-treePart(x)
+treePart(x, result=c("basis", "orthobasis"))
 }
 \arguments{
-  \item{x}{A tree of  class \code{\link[pkg:ape]{phylo}},
+  \item{x}{a tree of  class \code{\link[pkg:ape]{phylo}},
     \linkS4class{phylo4} or \linkS4class{phylo4d}.}
+  \item{result}{a character string specifying the type of result: either
+  a basis of dummy vectors (\code{basis}), or an orthobasis derived from these dummy vectors (\code{orthobasis}).}
 }
 \value{
-  A data.frame of dummy vectors (in columns) having one value for each
+  A matrix 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{listDD}} which is called by \code{treePart}.
+\seealso{
+  - \code{\link{listDD}} which is called by \code{treePart}.\cr
+  - \code{\link{orthogram}}, which uses by default the orthobasis
+  produced by \code{treePart}.\cr
 }
+\details{
+  Orthobasis produced by this function are identical to those stored in
+  the \$Bscores component of deprecated \link[pkg:ade4]{phylog} objects,
+  from the ade4 package.
+}
 \examples{
 if(require(ape) & require(phylobase)){
 ## make a tree