[Adephylo-commits] r54 - in pkg: . data man

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

Author: jombart
Date: 2008-11-27 19:00:52 +0100 (Thu, 27 Nov 2008)
New Revision: 54

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


Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-11-27 17:56:16 UTC (rev 53)
+++ pkg/TODO	2008-11-27 18:00:52 UTC (rev 54)
@@ -49,7 +49,7 @@
 - carni19.Rd -- done
 - carni70.Rd -- done
 - lizards.Rd -- done
-- maples.Rd
+- maples.Rd -- done
 - mjrochet.Rd
 - palm.Rd
 - procella.Rd

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


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

Added: pkg/man/mjrochet.Rd
===================================================================
--- pkg/man/mjrochet.Rd	                        (rev 0)
+++ pkg/man/mjrochet.Rd	2008-11-27 18:00:52 UTC (rev 54)
@@ -0,0 +1,54 @@
+\encoding{latin1}
+\name{mjrochet}
+\alias{mjrochet}
+\docType{data}
+\title{Phylogeny and quantitative traits of teleos fishes}
+\description{
+This data set describes the phylogeny of 49 teleos fishes as reported by Rochet et al. (2000). It also gives life-history traits corresponding to these 49 species.
+}
+\usage{data(mjrochet)}
+\format{
+\code{mjrochet} is a list containing the 2 following objects : 
+\describe{ 
+   \item{tre}{is a character string giving the phylogenetic tree in Newick format.}
+   \item{tab}{is a data frame with 49 rows and 7 traits.}  
+}}
+\details{
+ Variables of \code{mjrochet$tab} are the following ones : tm (age at maturity (years)), 
+ lm (length at maturity (cm)), l05 (length at 5 per cent survival (cm)),
+ t05 (time to 5 per cent survival (years)), fb (slope of the log-log fecundity-length relationship),
+ fm (fecundity the year of maturity), egg (volume of eggs (\eqn{mm^{3}}{mm^3})).
+}
+\source{
+Data taken from: \cr
+    Summary of data - Clupeiformes : \url{http://www.ifremer.fr/maerha/clupe.html} \cr
+    Summary of data - Argentiniformes : \url{http://www.ifremer.fr/maerha/argentin.html} \cr
+    Summary of data - Salmoniformes : \url{http://www.ifremer.fr/maerha/salmon.html} \cr
+    Summary of data - Gadiformes : \url{http://www.ifremer.fr/maerha/gadi.html} \cr
+    Summary of data - Lophiiformes : \url{http://www.ifremer.fr/maerha/loph.html} \cr
+    Summary of data - Atheriniformes : \url{http://www.ifremer.fr/maerha/ather.html} \cr
+    Summary of data - Perciformes : \url{http://www.ifremer.fr/maerha/perci.html} \cr
+    Summary of data - Pleuronectiformes : \url{http://www.ifremer.fr/maerha/pleuro.html} \cr
+    Summary of data - Scorpaeniformes : \url{http://www.ifremer.fr/maerha/scorpa.html} \cr
+    Phylogenetic tree : \url{http://www.ifremer.fr/maerha/life_history.html}
+}
+\references{
+Rochet, M. J., Cornillon, P-A., Sabatier, R. and Pontier, D. (2000) 
+Comparative analysis of phylogenic and fishing effects in life history patterns of teleos fishes.
+\emph{Oïkos}, \bold{91}, 255--270.
+}
+\details{
+  This dataset replaces the former version in ade4.
+}
+\examples{
+data(mjrochet)
+tre <- read.tree(text=mjrochet$tre) # make a tree
+traits <- log((mjrochet$tab))
+
+## build a phylo4d
+mjr <- phylo4d(tre, traits)
+
+## see data
+s.phylo4d(mjr,cex.lab=.5,show.node=FALSE,symb="square")
+}
+\keyword{datasets}