[Picante-commits] r189 - pkg/man

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

Author: skembel
Date: 2009-07-02 23:25:11 +0200 (Thu, 02 Jul 2009)
New Revision: 189

Added:
   pkg/man/ses.pd.Rd
Log:
...and its documentation

Added: pkg/man/ses.pd.Rd
===================================================================
--- pkg/man/ses.pd.Rd	                        (rev 0)
+++ pkg/man/ses.pd.Rd	2009-07-02 21:25:11 UTC (rev 189)
@@ -0,0 +1,55 @@
+\name{ses.pd}
+\alias{ses.pd}
+
+\title{ Standardized effect size of PD }
+\description{
+  Standardized effect size of phylogenetic diversity (Faith's PD) in communities.
+}
+\usage{
+ses.pd(samp, tree, null.model = c("taxa.labels", "sample.pool",
+            "phylogeny.pool", "independentswap", "trialswap"),
+            runs = 999, iterations = 1000, ...)
+}
+
+\arguments{
+  \item{ samp }{ Community data matrix }
+  \item{ tree }{ Phylogeny (phylo object) }
+  \item{ null.model }{ Null model to use (see Details section for description) }
+  \item{ runs }{ Number of randomizations }
+  \item{ iterations }{ Number of iterations to use for each randomization (for independent swap and trial null models) }
+  \item{ ... }{ Additional arguments to \code{\link{pd}} function }
+}
+
+\value{
+  A data frame of results for each community
+  \item{ntaxa}{Number of taxa in community}
+  \item{pd.obs}{Observed PD in community}
+  \item{pd.rand.mean}{Mean PD in null communities}
+  \item{pd.rand.sd}{Standard deviation of PD in null communities}
+  \item{pd.obs.rank}{Rank of observed PD vs. null communities}
+  \item{pd.obs.z}{Standardized effect size of PD vs. null communities (= (pd.obs - pd.rand.mean) / pd.rand.sd)}
+  \item{pd.obs.p}{P-value (quantile) of observed PD vs. null communities (= mpd.obs.rank / runs + 1)}
+  \item{runs}{Number of randomizations}  
+}
+\details{
+Currently implemented null models (arguments to null.model):
+\describe{
+    \item{taxa.labels}{ Shuffle taxa labels across tips of phylogeny (across all taxa included in phylogeny)}
+    \item{sample.pool}{ Randomize community data matrix by drawing species from pool of species occurring in at least one community (sample pool) with equal probability}  
+    \item{phylogeny.pool}{ Randomize community data matrix by drawing species from pool of species occurring in the phylogeny (phylogeny pool) with equal probability}  
+    \item{frequency}{ Randomize community data matrix abundances within species (maintains species occurence frequency)}
+    \item{richness}{ Randomize community data matrix abundances within samples (maintains sample species richness)}
+    \item{independentswap}{ Randomize community data matrix with the independent swap algorithm (Gotelli 2000) maintaining species occurrence frequency and sample species richness }
+    \item{trialswap}{ Randomize community data matrix with the trial-swap algorithm (Miklos & Podani 2004) maintaining species occurrence frequency and sample species richness }
+    }
+}
+
+\references{ Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. \url{http://www.phylodiversity.net/phylocom/}.
+
+Proches, S., Wilson, J.R.U. and Cowling, R.M. 2006. How much evolutionary history in a 10 x 10m plot? Proceedings of Royal Society of London B, Biological Sciences 273:1143-1148.}
+\author{ Steven Kembel <skembel at uoregon.edu> }
+\seealso{ \code{\link{pd}}, \code{\link{randomizeSample}}  }
+\examples{
+data(phylocom)
+ses.pd(phylocom$sample, phylocom$phylo, null.model="taxa.labels", runs=99)}
+\keyword{univar}