# [Picante-commits] r93 - branches/gsoc/man

Tue Jun 10 15:28:50 CEST 2008

Author: mrhelmus
Date: 2008-06-10 15:28:50 +0200 (Tue, 10 Jun 2008)
New Revision: 93

branches/gsoc/man/PSDcalc.rd
Log:
The documentation for the PSV metrics.

===================================================================
--- branches/gsoc/man/PSDcalc.rd	                        (rev 0)
+++ branches/gsoc/man/PSDcalc.rd	2008-06-10 13:28:50 UTC (rev 93)
@@ -0,0 +1,81 @@
+\name{PSDcalc}
+\alias{PSDcalc}
+\alias{PSVcalc}
+\alias{PSRcalc}
+\alias{PSEcalc}
+\alias{PSCcalc}
+\alias{spp.PSVcalc}
+\alias{PSV}
+\alias{PSR}
+\alias{PSE}
+\alias{PSD}
+\alias{PSC}
+\alias{spp.psvcalc}
+\alias{psv}
+\alias{psr}
+\alias{pse}
+\alias{psd}
+\alias{psc}
+\alias{spp.PSV}
+\title{ Phylogenetic Species Diversity Metrics }
+\description{
+  Calculate the bounded phylogenetic biodiversity metrics: phylogenetic species variability, richness, evenness and clustering for one or multiple samples.
+}
+\usage{
+\PSVcalc(samp,tree,compute.var=TRUE)
+\cr
+\PSRcalc(samp,tree,compute.var=TRUE)
+\cr
+\PSEcalc(samp,tree)
+\cr
+\PSCcalc(samp,tree,compute.var=TRUE)
+\cr
+\PSDcalc(samp,tree,compute.var=TRUE)
+\cr
+\spp.PSVcalc(samp,tree)
+}
+
+\arguments{
+  \item{samp}{ Community data matrix }
+  \item{tree}{ A phylo tree object or a phylogenetic covariance matrix }
+  \item{compute.var}{ Computes the expected variances for PSV and PSR for each community }
+}
+\details{
+ \\emph{Phylogenetic species variability (PSV)} quantifies how phylogenetic relatedness decreases the variance of a hypothetical unselected/neutral trait
+ shared by all species in a community. The expected value of PSV is statistically independent of species richness, is one when all species in a sample
+ are unrelated (i.e., a star phylogeny) and approaches zero as species become more related. PSV is directly related to mean phylogenetic distance. The
+ expected variance around PSV for any sample of a particular species richness can be approximated.
+ \To address how individual species contribute to the mean PSV of a data set, the function spp.PSVcalc gives signed proportions of the total deviation
+ from the mean PSV that occurs when all species are removed from the data set one at a time. The absolute values of these \dQuote{species effects}
+ tend to positively correlate with species prevalence.
+ \cr
+ \\emph{Phylogenetic species richness (PSR)} is the number of species in a sample multiplied by PSV. It can be considered the species richness of a sample
+ after discounting by species relatedness. The value is maximum at the species richness of the sample, and decreases towards zero as relatedness
+ increases. The expected variance around PSR for any sample of a particular species richness can be approximated.
+ \cr
+ \\emph{Phylogenetic species evenness (PSE)} is the metric PSV modified to incorporate relative species abundances. The maximum attainable value of PSE (i.e., 1)
+  occurs only if species abundances are equal and species phylogeny is a star. PSE essentially grafts each individual of a species onto the tip of the
+  phylogeny of its species with branch lengths of zero.
+  \cr
+  \\emph{Phylogenetic species clustering (PSC)} is a metric of the branch tip clustering of species across a sample's phylogeny. As PSC increases to 1, species
+   are less related to one another the tips of the phylogeny. PSC is directly related to mean nearest neighbor distance.
+}
+  \cr
+  \note{These metrics are bounded either between zero and one (PSV,PSE,PSC) or zero and species richness (PSR); but the metrics asymptotically
+  approach zero as relatedness increases. Zero can be assigned to communities with less than two species, but conclusions drawn from assigning
+  communities zero values need be carefully explored for any data set. The data sets need not be species-community data sets but may be any sample
+  data set with an associated phylogeny.
+}
+
+
+\value{
+	a dataframe of the respective phylogenetic species diversity metric values
+}
+\references{ Helmus M.R., Bland T.J., Williams C.K. & Ives A.R. (2007) Phylogenetic measures of biodiversity. American Naturalist, 169, E68-E83 }
+\author{ Matt Helmus \email{mrhelmus at gmail.com} }
+
+\keyword{univar}
+
+
+