[Adephylo-commits] r53 - in pkg: data man

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

Author: jombart
Date: 2008-11-27 18:56:16 +0100 (Thu, 27 Nov 2008)
New Revision: 53

Added:
   pkg/data/maples.RData
   pkg/man/maples.Rd
Log:
added maples.


Added: pkg/data/maples.RData
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Property changes on: pkg/data/maples.RData
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Added: pkg/man/maples.Rd
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--- pkg/man/maples.Rd	                        (rev 0)
+++ pkg/man/maples.Rd	2008-11-27 17:56:16 UTC (rev 53)
@@ -0,0 +1,50 @@
+\name{maples}
+\alias{maples}
+\docType{data}
+\title{Phylogeny and quantitative traits of flowers}
+\description{
+This data set describes the phylogeny of 17 flowers as reported by Ackerly and Donoghue (1998). It also gives 31 traits corresponding to these 17 species.
+}
+\usage{data(maples)}
+\format{
+\code{tithonia} is a list containing the 2 following objects :  
+            \item{tre}{is a character string giving the phylogenetic tree in Newick format.} 
+            \item{tab}{is a data frame with 17 species and 31 traits}    
+}
+\source{
+Data were obtained from the URL
+\url{http://www.stanford.edu/~dackerly/acerdata.html} (no longer maintained).
+}
+\references{
+Ackerly, D. D. and Donoghue, M.J. (1998) Leaf size, sappling allometry, and Corner's rules: phylogeny and correlated evolution in Maples (Acer). 
+\emph{American Naturalist}, \bold{152}, 767--791.
+}
+\details{
+  This dataset replaces the former version in ade4.
+}
+\examples{
+data(maples)
+
+## see the tree
+tre <- read.tree(text=maples$tre)
+plot(tre)
+axisPhylo()
+
+## look at two variables
+dom <- maples$tab$Dom
+bif <- maples$tab$Bif
+plot(bif,dom,pch = 20)
+abline(lm(dom~bif)) # a strong negative correlation ?
+summary(lm(dom~bif))
+cor.test(bif,dom)
+
+## look at the two variables onto the phylogeny
+temp <- phylo4d(tre, data.frame(dom,bif, row.names=tre$tip.label))
+s.phylo4d(temp) # correlation is strongly linked to phylogeny
+
+## use ape's PIC (phylogenetic independent contrasts)
+pic.bif <- pic(bif, tre)
+pic.dom <- pic(dom, tre)
+cor.test(pic.bif, pic.dom)} # correlation no longer significant
+}
+\keyword{datasets}