[Adephylo-commits] r52 - in pkg: . data man

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

Author: jombart
Date: 2008-11-27 18:44:34 +0100 (Thu, 27 Nov 2008)
New Revision: 52

Added:
   pkg/data/lizards.RData
   pkg/man/lizards.Rd
Modified:
   pkg/TODO
Log:
added lizards


Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-11-27 17:39:17 UTC (rev 51)
+++ pkg/TODO	2008-11-27 17:44:34 UTC (rev 52)
@@ -47,9 +47,8 @@
 * ppca
 * migrate datasets from ade4 to adephylo:
 - carni19.Rd -- done
-- carni70.Rd
-- corvus.Rd
-- lizards.Rd
+- carni70.Rd -- done
+- lizards.Rd -- done
 - maples.Rd
 - mjrochet.Rd
 - palm.Rd

Added: pkg/data/lizards.RData
===================================================================
(Binary files differ)


Property changes on: pkg/data/lizards.RData
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: pkg/man/lizards.Rd
===================================================================
--- pkg/man/lizards.Rd	                        (rev 0)
+++ pkg/man/lizards.Rd	2008-11-27 17:44:34 UTC (rev 52)
@@ -0,0 +1,53 @@
+\name{lizards}
+\alias{lizards}
+\docType{data}
+\title{Phylogeny and quantitative traits of lizards}
+\description{
+This data set describes the phylogeny of 18 lizards as reported by Bauwens and D\'iaz-Uriarte (1997). 
+It also gives life-history traits corresponding to these 18 species.
+}
+\usage{data(lizards)}
+\format{
+\code{lizards} is a list containing the 3 following objects : 
+\describe{    
+   \item{traits}{is a data frame with 18 species and 8 traits.}  
+   \item{hprA}{is a character string giving the phylogenetic tree (hypothesized phylogenetic relationships based on immunological distances) in Newick format.} 
+   \item{hprB}{is a character string giving the phylogenetic tree (hypothesized phylogenetic relationships based on morphological characteristics) in Newick format.}
+}}
+\details{
+Variables of \code{lizards$traits} are the following ones : 
+mean.L (mean length (mm)), matur.L (length at maturity (mm)), 
+max.L (maximum length (mm)), hatch.L (hatchling length (mm)),
+hatch.m (hatchling mass (g)), clutch.S (Clutch size),
+age.mat (age at maturity (number of months of activity)),
+clutch.F (clutch frequency).
+}
+\references{
+Bauwens, D., and D\'iaz-Uriarte, R. (1997) Covariation of life-history traits in lacertid lizards: a comparative study. 
+\emph{American Naturalist}, \bold{149}, 91--111. 
+
+See a data description at \url{http://pbil.univ-lyon1.fr/R/pps/pps063.pdf} (in French).
+}
+\details{
+  This dataset replaces the former version in ade4.
+}
+\examples{
+data(lizards)
+traits <- data.frame(log(lizards$traits))
+
+## see data
+data(lizards)
+liz.tr <- read.tree(tex=lizards$hprA) # make a tree
+liz <- phylo4d(liz.tr, traits) # make a phylo4d object
+s.phylo4d(liz)
+
+## compute and plot principal components
+liz.pca1 <- dudi.pca(traits, scannf=FALSE, nf=2) # PCA of traits
+myPC <- phylo4d(liz.tr, liz.pca1$li) # store PC in a phylo4d object
+varlab <- paste("Principal \ncomponent", 1:2) # make labels for PCs
+s.phylo4d(myPC, ratio=.8, var.lab=varlab) # plot the PCs
+add.scatter.eig(liz.pca1$eig,2,1,2,posi="topleft", inset=c(0,.15))
+title("Phylogeny and the principal components")
+
+}
+\keyword{datasets}