[Adephylo-commits] r36 - pkg/man

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

Author: jombart
Date: 2008-11-26 15:00:06 +0100 (Wed, 26 Nov 2008)
New Revision: 36

Modified:
   pkg/man/distRoot.Rd
Log:
Wrote the doc for distRoot.


Modified: pkg/man/distRoot.Rd
===================================================================
--- pkg/man/distRoot.Rd	2008-11-26 13:48:26 UTC (rev 35)
+++ pkg/man/distRoot.Rd	2008-11-26 14:00:06 UTC (rev 36)
@@ -2,11 +2,11 @@
 \alias{distRoot}
 \title{Compute the distance of tips to the root}
 \description{
-  The function \code{distRoot} computes the distance of each tip to the
+  The function \code{distRoot} computes the distance of a set of tips to the
   root. Several distances can be used, defaulting to the sum of branch lengths.
 }
 \usage{
-distRoot(x, method=c("brlength","nAncestors","Abouheif"))
+distRoot(x, tips, method=c("brlength","nNodes","Abouheif","sumDD"))
 }
 \arguments{
   \item{x}{a tree of  class \code{\link[pkg:ape]{phylo}},
@@ -15,27 +15,49 @@
     ambiguity) specifying the method used to compute distances ;
     possible values are:\cr
     - \code{brlength}: branch length \cr
-    - \code{nAncestors}: number of Ancestors \cr
-    - \code{Abouheif}: Abouheif's distance \cr
+    - \code{nNodes}: number of nodes on the path between the nodes \cr
+    - \code{Abouheif}: Abouheif's distance (see details) \cr
+    - \code{sumDD}: sum of direct descendants of all nodes on the path
+    (see details) \cr
   }
 }
 \value{
   A numeric vector containing one distance value for each tip.
 }
+\details{
+  \code{Abouheif} distance refers to the phylogenetic distance
+  underlying the test of Abouheif (see references). Let P be the set of
+  all the nodes in the path going from \code{node1} to \code{node2}. Let
+  DDP be the number of direct descendants from each node in P. Then, the
+  so-called 'Abouheif' distance is the product of all terms in DDP.\cr
+
+   \code{sumDD} refers to a phylogenetic distance quite similar to that
+  of Abouheif. We consider the same sets P and DDP. But instead of
+  computing the product of all terms in DDP, this distance computes the
+  sum of all terms in DDP.
+}
 \author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
-\seealso{\code{\link{distTips}} which computes several phylogenetic
-  distances between tips.
+\references{
+  Pavoine, S.; Ollier, S.; Pontier, D. & Chessel, D. (2008) Testing for
+  phylogenetic signal in life history variable: Abouheif's test
+  revisited. \emph{Theoretical Population Biology}: \bold{73}, 79-91.
 }
+\seealso{\code{\link{distTips}} which computes the same phylogenetic
+  distances, but between tips.
+}
 \examples{
 if(require(ape) & require(phylobase)){
 ## make a tree
-x <- as(rtree(10),"phylo4")
-D <- distRoot(x)
-D
+x <- as(rtree(50),"phylo4")
+## compute 4 different distances
+met <- c("brlength","nNodes","Abouheif","sumDD")
+D <- lapply(met, function(e) distRoot(x, method=e) )
+names(D) <- met
+D <- as.data.frame(D)
 
 ## plot these distances along with the tree
 temp <- phylo4d(x, D)
-s.phylo4d(temp, cent=FALSE, scale=FALSE)
+s.phylo4d(temp, show.node=FALSE, cex.lab=.6)
 }
 }
 \keyword{manip}