[Picante-commits] r168 - in branches/phylosor: R man

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

Author: hmorlon
Date: 2008-11-06 19:29:44 +0100 (Thu, 06 Nov 2008)
New Revision: 168

Added:
   branches/phylosor/R/phylosor.R
   branches/phylosor/man/phylosor.Rd
Log:
Adding phylosor beta diversity metric code and documentation

Added: branches/phylosor/R/phylosor.R
===================================================================
--- branches/phylosor/R/phylosor.R	                        (rev 0)
+++ branches/phylosor/R/phylosor.R	2008-11-06 18:29:44 UTC (rev 168)
@@ -0,0 +1,52 @@
+phylosor=function(samp,tree)
+{
+	s=nrow(samp)
+	sample_names=rownames(samp)
+	pairs=s*(s-1)/2
+	
+	plot1.list=c()
+	plot2.list=c()
+	sor.list=c()
+	phylosor.list=c()
+
+	
+	count=0
+	for (l in 1:(s-1))
+	{
+		spl=sum(samp[l,])
+		pdl=.pdshort(samp[l,],tree)
+		for (k in (l+1):s)
+		{
+			count=count+1
+			spk=sum(samp[k,])
+			pdk=.pdshort(samp[k,],tree)
+			sharedlk=sum(samp[l,]*samp[k,])
+			pdsharedlk=.pdshort(samp[l,],tree)+.pdshort(samp[k,],tree)-.pdshort((samp[l,]+samp[k,]),tree)
+			avglk=0.5*(spl+spk)
+			pdavglk=0.5*(pdl+pdk)
+			sorlk=sharedlk/avglk
+			phylosorlk=pdsharedlk/pdavglk
+			plot1.list=c(plot1.list,sample_names[l])
+			plot2.list=c(plot2.list,sample_names[k])
+			sor.list=c(sor.list,sorlk)
+			phylosor.list=c(phylosor.list,phylosorlk)
+			}
+			}
+			data.frame(plot1=plot1.list,plot2=plot2.list,sor=sor.list,phylosor=phylosor.list)}
+
+		
+	
+.pdshort=function(comm,tree)
+{
+
+	nbspecies=length(comm)
+	species = names(comm)
+	index = species[comm == 0]
+        if (length(index) >= (nbspecies - 1)) 
+        {PD <- NA}
+        else {
+            sub.tree <- drop.tip(tree, index)
+            PD <- sum(sub.tree$edge.length)}
+            return(PD)}
+
+	

Added: branches/phylosor/man/phylosor.Rd
===================================================================
--- branches/phylosor/man/phylosor.Rd	                        (rev 0)
+++ branches/phylosor/man/phylosor.Rd	2008-11-06 18:29:44 UTC (rev 168)
@@ -0,0 +1,25 @@
+\name{phylosor}
+\alias{phylosor}
+
+\title{Compute phylogenetic index of beta-diversity Phylosor}
+\description{Compute phylogenetic index of similarity Phylosor
+  
+}
+\usage{
+phylosor(samp, tree)    
+}
+
+\arguments{
+  \item{samp}{ Community data matrix }
+  \item{tree}{ Phylo object}
+}
+\value{
+  dataframe with four colums: plot number 1; plot number 2; sorensen index; phylosor index
+}
+\references{Bryant, J.B., Lamanna, C., Morlon, H., Kerkhoff, A.J., Enquist, B.J., Green, J.L. 2008. Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences 105 Supplement 1: 1505-11511
+}
+\author{ Helene Morlon <morlon.helene at gmail.com> }
+\examples{
+data(phylocom)
+phylosor(phylocom$sample, phylocom$phylo)}
+\keyword{univar}