[Vegan-commits] r2551 - in pkg/vegan: R man

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

Author: jarioksa
Date: 2013-07-10 13:48:41 +0200 (Wed, 10 Jul 2013)
New Revision: 2551

Added:
   pkg/vegan/man/disp_weight.Rd
Modified:
   pkg/vegan/R/disp_weight.R
Log:
added documentation

Modified: pkg/vegan/R/disp_weight.R
===================================================================
--- pkg/vegan/R/disp_weight.R	2013-07-10 11:48:39 UTC (rev 2550)
+++ pkg/vegan/R/disp_weight.R	2013-07-10 11:48:41 UTC (rev 2551)
@@ -1,5 +1,5 @@
 `disp_weight` <-
-    function(comm, group, nperm)
+    function(comm, group, nperm = 1000)
 {
     # number of replicates per group
     nrep <- tabulate(group) 

Added: pkg/vegan/man/disp_weight.Rd
===================================================================
--- pkg/vegan/man/disp_weight.Rd	                        (rev 0)
+++ pkg/vegan/man/disp_weight.Rd	2013-07-10 11:48:41 UTC (rev 2551)
@@ -0,0 +1,56 @@
+\encoding{UTF-8}
+\name{disp_weight}
+\alias{disp_weight}
+\title{Dispersion-based weighting of species counts}
+
+\description{Transform abundance data using dispersion-based weighting of species counts}
+
+\usage{disp_weight(comm, group, nperm = 1000)}
+
+\arguments{
+  \item{comm}{Community data matrix.}
+  \item{group}{Factor describing the group structure.}
+  \item{nperm}{Number of permutations}
+}
+
+\details{
+Dispersion weighting can be used when there are \emph{a priori} defined groups 
+(eg. lacation of samples). 
+
+The dispersion index (D) is calculated as ratio between 
+variance and mean and averaged across groups. D can then be used as divisor to 
+downweight species abundances.
+
+However species should be only downweighted, when there is evidence for 
+over-dispersion (D > 1). This is tested using a permutational Chi-squared test. 
+If this test shows statistically significant over-dispersion then the species is 
+downweighted by 1/D, else the divisor is 1.
+}
+
+\value{
+A data.frame with three columns:
+    \item{D}{Average Dispersion index}
+    \item{p}{p-value of permutation test that D = 1}
+    \item{weights}{weights to apply to community data}
+}
+
+\references{
+Clarke, K. R., M. G. Chapman, P. J. Somerfield, and H. R. Needham. 2006. Dispersion-based Weighting of Species Counts in Assemblage Analyses. \emph{Marine Ecology Progress Series}, 320, 11–27.
+}
+\author{
+  Eduard Szöcs \email{szoe8822 at uni-landau.de}
+}
+
+
+\examples{
+data(dune)
+data(dune.env)
+# calculate weights
+dpw <- disp_weight(dune, dune.env$Management, nperm = 100)
+# calculate transformed data
+sweep(dune, MARGIN = 2, dpw$weights, `*`)
+}
+
+
+\keyword{multivariate}
+