[Adephylo-commits] r57 - in pkg: data man

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

Author: jombart
Date: 2008-11-28 12:27:57 +0100 (Fri, 28 Nov 2008)
New Revision: 57

Added:
   pkg/data/palm.RData
   pkg/man/palm.Rd
Log:
Added palm dataset.


Added: pkg/data/palm.RData
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Property changes on: pkg/data/palm.RData
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Added: pkg/man/palm.Rd
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--- pkg/man/palm.Rd	                        (rev 0)
+++ pkg/man/palm.Rd	2008-11-28 11:27:57 UTC (rev 57)
@@ -0,0 +1,52 @@
+\encoding{latin1}
+\name{palm}
+\alias{palm}
+\docType{data}
+\title{Phylogenetic and quantitative traits of amazonian palm trees}
+\description{
+This data set describes the phylogeny of 66 amazonian palm trees. It also gives 7 traits corresponding to these 66 species.
+}
+\usage{data(palm)}
+\format{
+\code{palm} is a list containing the 2 following objects: 
+\describe{ 
+   \item{tre}{is a character string giving the phylogenetic tree in Newick format.} 
+   \item{traits}{is a data frame with 66 species (rows) and 7 traits (columns).}
+} }
+\details{
+Variables of \code{palm$traits} are the following ones: \cr
+- rord: specific richness with five ordered levels\cr
+- h: height in meter (squared transform)\cr
+- dqual: diameter at breast height in centimeter with five levels \code{sout : subterranean}, \code{ d1(0, 5 cm)}, \code{ d2(5, 15 cm)}, \code{ d3(15, 30 cm)} and \code{ d4(30, 100 cm)}\cr
+- vfruit: fruit volume in \eqn{mm^{3}}{mm^3} (logged transform)\cr
+- vgrain: seed volume in \eqn{mm^{3}}{mm^3} (logged transform)\cr
+- aire: spatial distribution area (\eqn{km^{2}}{km^2})\cr
+- alti: maximum altitude in meter (logged transform)\cr       
+}
+\source{
+This data set was obtained by Clémentine Gimaret-Carpentier\cr
+ \email{gimaret at biomserv.univ-lyon1.fr}.
+}
+\details{
+  This dataset replaces the former version in ade4.
+}
+\examples{
+## load data, make a tree and a phylo4d object
+data(palm)
+tre <- read.tree(text=palm$tre)
+rord <- as.integer(palm$traits$rord) # just use this for plotting purpose
+traits <- data.frame(rord, palm$traits[,-1])
+x <- phylo4d(tre, traits)
+
+## plot data
+par(mar=rep(.1,4))
+s.phylo4d(x, cex.lab=.6)
+
+## test phylogenetic autocorrelation
+if(require(ade4)){
+prox <- proxTips(x, method="sumDD")
+phylAutoTests <- gearymoran(prox, traits[,-3], nrep=499)
+plot(phylAutoTests)
+}
+}
+\keyword{datasets}