[Adephylo-commits] r59 - in pkg: R data man

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

Author: jombart
Date: 2008-11-28 12:54:20 +0100 (Fri, 28 Nov 2008)
New Revision: 59

Added:
   pkg/data/procella.RData
   pkg/man/procella.Rd
Modified:
   pkg/R/distances.R
Log:
Added procella. This was the last dataset to be added to adephylo.


Modified: pkg/R/distances.R
===================================================================
--- pkg/R/distances.R	2008-11-28 11:44:27 UTC (rev 58)
+++ pkg/R/distances.R	2008-11-28 11:54:20 UTC (rev 59)
@@ -113,7 +113,7 @@
     tips <- getnodes(x, tips)
     tips.names <- names(tips)
     x <- as(x, "phylo4")
-    root <- getnodes(x,rootNode(x)) # so that we have a named node
+    root <- getnodes(x, N+1) # so that we have a named node
 
     ## some checks
     if(is.character(checkval <- check_phylo4(x))) stop(checkval)

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


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

Added: pkg/man/procella.Rd
===================================================================
--- pkg/man/procella.Rd	                        (rev 0)
+++ pkg/man/procella.Rd	2008-11-28 11:54:20 UTC (rev 59)
@@ -0,0 +1,58 @@
+\name{procella}
+\alias{procella}
+\docType{data}
+\title{Phylogeny and quantitative traits of birds}
+\description{
+This data set describes the phylogeny of 19 birds as reported by Bried et al. (2002). It also gives 6 traits corresponding to these 19 species.
+}
+\usage{data(procella)}
+\format{
+\code{procella} is a list containing the 2 following objects:  
+\describe{     
+   \item{tre}{is a character string giving the phylogenetic tree in Newick format.} 
+   \item{traits}{is a data frame with 19 species and 6 traits}    
+}}
+\details{
+Variables of \code{procella$traits} are the following ones: \cr
+- site.fid: a numeric vector that describes the percentage of site fidelity\cr
+- mate.fid: a numeric vector that describes the percentage of mate fidelity\cr
+- mass: an integer vector that describes the adult body weight (g)\cr
+- ALE: a numeric vector that describes the adult life expectancy (years)\cr
+- BF: a numeric vector that describes the breeding frequencies\cr
+- col.size: an integer vector that describes the colony size (no nests monitored)
+}
+\references{
+Bried, J., Pontier, D. and Jouventin, P. (2002) Mate fidelity in monogamus birds: a re-examination of the Procellariiformes. 
+\emph{Animal Behaviour}, \bold{65}, 235--246. 
+
+See a data description at \url{http://pbil.univ-lyon1.fr/R/pps/pps037.pdf} (in French).
+}
+\details{
+  This dataset replaces the former version in ade4.
+}
+\examples{
+## load data, make tree and phylo4d object
+data(procella)
+tre <- read.tree(text=procella$tre)
+x <- phylo4d(tre, procella$traits)
+par(mar=rep(.1,4))
+s.phylo4d(x,cex.lab=.7)
+
+## test phylogenetic autocorrelation in traits
+if(require(ade4)){
+
+f1 <- function(vec){ # to replace missing data
+m <- mean(vec,na.rm=TRUE)
+vec[is.na(vec)] <- m
+return(vec)
+}
+
+traits <- data.frame(lapply(procella$traits, f1))
+prox <- proxTips(tre)
+
+myTests <- gearymoran(prox, traits)
+plot(myTests)
+}
+
+}
+\keyword{datasets}