[Vegan-commits] r2123 - in pkg/vegan: inst man

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

Author: jarioksa
Date: 2012-03-26 11:49:08 +0200 (Mon, 26 Mar 2012)
New Revision: 2123

Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/adonis.Rd
Log:
Merge branch 'master' into r-forge-svn-local

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-03-21 09:36:07 UTC (rev 2122)
+++ pkg/vegan/inst/ChangeLog	2012-03-26 09:49:08 UTC (rev 2123)
@@ -12,9 +12,9 @@
 	between groups) and dispersion (variability within groups) in
 	dissimilarity-based analyses.  We have warned on this for long in
 	vegan, but now we can get support from this paper. Warnings added
-	to anosim, mrpp and simper (where this worst). There could be a
-	warning in adonis as well, but there the problem is not quite as
-	bad (although Anderson warns on this in her original paper, too).
+	to anosim, mrpp, simper (where this worst) and adonis (where this
+	was already analysed by Marti Anderson when introducing the
+	method).
 	
 Version 2.1-13 (closed March 9, 2012)
 

Modified: pkg/vegan/man/adonis.Rd
===================================================================
--- pkg/vegan/man/adonis.Rd	2012-03-21 09:36:07 UTC (rev 2122)
+++ pkg/vegan/man/adonis.Rd	2012-03-26 09:49:08 UTC (rev 2123)
@@ -142,6 +142,18 @@
     side of the formula.}
   \item{terms}{The \code{\link{terms}} component of the model.}
 }
+
+\note{Anderson (2001, Fig. 4) warns that the method may confound
+  location and dispersion effects: significant differences may be caused
+  by different within-group variation (dispersion) instead of different
+  mean values of the groups (see Warton et al. 2012 for a general
+  analysis). However, it seems that \code{adonis} is less sensitive to
+  dispersion effects than some of its alternatives (\code{link{anosim}},
+  \code{\link{mrpp}}). Function \code{\link{betadisper}} is a sister
+  function to \code{adonis} to study the differences in dispersion
+  within the same geometric framework.
+}
+
 \references{
 Anderson, M.J. 2001. A new method for non-parametric multivariate
 analysis of variance. \emph{Austral Ecology}, \strong{26}: 32--46.
@@ -162,6 +174,10 @@
 community data: A comment on distance-based redundancy
 analysis. \emph{Ecology}, \strong{82}: 290--297.
 
+Warton, D.I., Wright, T.W., Wang, Y. 2012. Distance-based multivariate
+analyses confound location and dispersion effects. \emph{Methods in
+Ecology and Evolution}, 3, 89--101.
+
 Zapala, M.A. and N.J. Schork. 2006. Multivariate regression analysis of
 distance matrices for testing associations between gene expression
 patterns and related variables. \emph{Proceedings of the National Academy of