[Adephylo-commits] r55 - in pkg: data man

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

Author: jombart
Date: 2008-11-27 19:12:32 +0100 (Thu, 27 Nov 2008)
New Revision: 55

Added:
   pkg/data/tithonia.RData
   pkg/man/tithonia.Rd
Log:
Added Tithonia


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


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

Added: pkg/man/tithonia.Rd
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--- pkg/man/tithonia.Rd	                        (rev 0)
+++ pkg/man/tithonia.Rd	2008-11-27 18:12:32 UTC (rev 55)
@@ -0,0 +1,61 @@
+\name{tithonia}
+\alias{tithonia}
+\docType{data}
+\title{Phylogeny and quantitative traits of flowers}
+\description{
+This data set describes the phylogeny of 11 flowers as reported by Morales (2000). It also gives morphologic and demographic traits corresponding to these 11 species.
+}
+\usage{data(tithonia)}
+\format{
+\code{tithonia} 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 11 species and 14 traits (6 morphologic traits and 8 demographic).}    
+}}
+\details{      
+Variables of \code{tithonia$tab} are the following ones : \cr
+morho1: is a numeric vector that describes the seed size (mm)\cr
+morho2: is a numeric vector that describes the flower size (mm)\cr
+morho3: is a numeric vector that describes the female leaf size (cm)\cr
+morho4: is a numeric vector that describes the head size (mm)\cr
+morho5: is a integer vector that describes the number of flowers per head \cr
+morho6: is a integer vector that describes the number of seeds per head \cr
+demo7: is a numeric vector that describes the seedling height (cm)\cr
+demo8: is a numeric vector that describes the growth rate (cm/day)\cr
+demo9: is a numeric vector that describes the germination time\cr
+demo10: is a numeric vector that describes the establishment (per cent)\cr
+demo11: is a numeric vector that describes the viability (per cent)\cr
+demo12: is a numeric vector that describes the germination (per cent)\cr
+demo13: is a integer vector that describes the resource allocation\cr
+demo14: is a numeric vector that describes the adult height (m)\cr
+}
+\source{
+Data were obtained from Morales, E. (2000) Estimating phylogenetic inertia in Tithonia (Asteraceae) : 
+a comparative approach. \emph{Evolution}, \bold{54}, 2, 475--484.
+}
+\details{
+  This dataset replaces the former version in ade4.
+}
+\examples{
+data(tithonia)
+tre <- read.tree(text=tithonia$tre)
+traits <- log(tithonia$tab + 1)
+
+## build a phylo4d object
+x <- phylo4d(tre, traits)
+par(mar=rep(.1,4))
+s.phylo4d(x)
+
+## perform a Geary/Moran test to detect phylogenetic signal in variables
+if(require(ade4)){
+
+## use branch length to define proximities
+prox1 <- proxTips(tre, method="brlength")
+gearymoran(prox, traits)
+
+## use Abouheif's proximity
+prox2 <- proxTips(tre, method="Abouheif")
+gearymoran(prox2, traits)
+}
+}
+\keyword{datasets}