[Vegan-commits] r2081 - pkg/vegan/man

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

Author: jarioksa
Date: 2012-02-10 11:34:19 +0100 (Fri, 10 Feb 2012)
New Revision: 2081

Modified:
   pkg/vegan/man/simper.Rd
Log:
expand documentation

Modified: pkg/vegan/man/simper.Rd
===================================================================
--- pkg/vegan/man/simper.Rd	2012-02-09 21:05:09 UTC (rev 2080)
+++ pkg/vegan/man/simper.Rd	2012-02-10 10:34:19 UTC (rev 2081)
@@ -16,6 +16,25 @@
 
   \item{group}{Vector assigning the groups}
 }
+
+\details{ Similarity percentage, \code{simper} (Clarke 1993) is based
+  on the decomposition of Bray-Curtis dissimilarity index (see
+  \code{\link{vegdist}}, \code{\link{designdist}}). The contribution
+  of individual species \eqn{i} to the overall Bray-Curtis dissimilarity
+  \eqn{d_{jk}}{d[jk]} is given by
+
+  \deqn{d_{ijk} = \frac{|x_{ij}-x_{ik}|}{\sum_{i=1}^S (x_{ij}+x_{ik})}}{d[ijk] = abs(x[ij]-x[ik])/sum(x[ij]+x[ik])}
+  
+  where \eqn{x} is the abundance of species \eqn{i} in sampling units
+  \eqn{j} and \eqn{k}. The overall index is the sum of the individual
+  contributions over all \eqn{S} species 
+  \eqn{d_{jk}=\sum_{i=1}^S d_{ijk}}{d[jk] = sum(i=1..S) d[ijk]}. 
+  
+  The \code{simper} functions performs pairwise comparisons of groups
+  of sampling units and finds the average percentage contributions
+  of each species to the average overall Bray-Curtis dissimilarity.
+}
+
 \value{
   A list of dataframes for every factor-combination.
   \item{contr}{average contribution to overall
@@ -33,10 +52,11 @@
 \author{
   Eduard Szöcs \email{szoe8822 at uni-landau.de}
 }
+
 \references{
-  Clarke, K.R. 1993. Non-parametric multivariate analyses
-    of changes in community structure. \emph{Austral Ecology},
-    18, 117–143.
+  Clarke, K.R. 1993. Non-parametric multivariate analyses of changes
+    in community structure. \emph{Australian Journal of Ecology}, 18,
+    117–143.
 }
 \keyword{multivariate}