[Adephylo-commits] r51 - in pkg: . data man

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

Author: jombart
Date: 2008-11-27 18:39:17 +0100 (Thu, 27 Nov 2008)
New Revision: 51

Added:
   pkg/data/carni70.RData
   pkg/man/carni70.Rd
Modified:
   pkg/TODO
Log:
added carni70


Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-11-27 17:28:07 UTC (rev 50)
+++ pkg/TODO	2008-11-27 17:39:17 UTC (rev 51)
@@ -46,7 +46,7 @@
 * orthogram and multivariate orthogram; use Stephane's version
 * ppca
 * migrate datasets from ade4 to adephylo:
-- carni19.Rd
+- carni19.Rd -- done
 - carni70.Rd
 - corvus.Rd
 - lizards.Rd

Added: pkg/data/carni70.RData
===================================================================
(Binary files differ)


Property changes on: pkg/data/carni70.RData
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: pkg/man/carni70.Rd
===================================================================
--- pkg/man/carni70.Rd	                        (rev 0)
+++ pkg/man/carni70.Rd	2008-11-27 17:39:17 UTC (rev 51)
@@ -0,0 +1,40 @@
+\encoding{latin1}
+\name{carni70}
+\alias{carni70}
+\docType{data}
+\title{Phylogeny and quantitative traits of carnivora}
+\description{
+This data set describes the phylogeny of 70 carnivora as reported by Diniz-Filho and Torres (2002). It also gives the geographic range size and body size corresponding to these 70 species.
+}
+\usage{data(carni70)}
+\format{
+\code{carni70} is a list containing the 2 following objects: 
+\describe{
+   \item{tre}{is a character string giving the phylogenetic tree in Newick format.
+   Branch lengths are expressed as divergence times (millions of years)} 
+   \item{tab}{is a data frame with 70 species and two traits: size (body size (kg)) ; range (geographic range size (km)).}    
+}}
+\source{
+Diniz-Filho, J. A. F., and N. M. Tôrres. (2002) Phylogenetic comparative methods and the 
+geographic range size-body size relationship in new world terrestrial carnivora. \emph{Evolutionary Ecology}, \bold{16}, 351--367.
+}
+\details{
+  This dataset replaces the former version in ade4.
+}
+\examples{
+data(carni70)
+tre <- read.tree(text=carni70$tre)
+x <- phylo4d(tre, carni70$tab)
+s.phylo4d(x)
+
+par(mar=rep(.1,4))
+s.phylo4d(x,cex.lab=.5, show.n=FALSE, ratio=.5)
+
+## transform size in log
+size <- log(carni70$tab)[,1]
+names(size) <- row.names(carni70$tab)
+tdata(x) <- cbind.data.frame(sizeLog=size, tdata(x))
+s.phylo4d(x,cex.lab=.5, show.n=FALSE, ratio=.5)
+
+}
+\keyword{datasets}