[Vegan-commits] r2196 - in pkg/vegan: inst man

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

Author: jarioksa
Date: 2012-05-27 16:30:40 +0200 (Sun, 27 May 2012)
New Revision: 2196

Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/betadisper.Rd
Log:
ChangeLog, doc (\eqn{}) fix plus credit to Adrian Stier and Ben Bolker in doc about bias adjusted betadisper

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-05-27 10:34:37 UTC (rev 2195)
+++ pkg/vegan/inst/ChangeLog	2012-05-27 14:30:40 UTC (rev 2196)
@@ -4,6 +4,11 @@
 
 Version 2.1-16 (opened May 11, 2012)
 
+	* betadisper: the method is biased with small, unequal group
+	sizes. Bias corrected version can now be used with new argument
+	'bias.adjust' (defaults 'FALSE'). The problem was analysed and
+	bias correction developed by Adrian Stier and Ben Bolker.
+
 	* .checkSelect: standardise those plotting functions that have a
 	'select' argument that controls which rows of the scores are
 	plotted. All these functions now use .checkSelect() to check and

Modified: pkg/vegan/man/betadisper.Rd
===================================================================
--- pkg/vegan/man/betadisper.Rd	2012-05-27 10:34:37 UTC (rev 2195)
+++ pkg/vegan/man/betadisper.Rd	2012-05-27 14:30:40 UTC (rev 2196)
@@ -141,7 +141,7 @@
   will be biased downward. This bias matters most when comparing diversity
   among treatments with small, unequal numbers of samples.  Setting
   \code{bias.adjust=TRUE} when using \code{betadisper} imposes a 
-  \eqn{\sqrt{n/(n-1)} correction (Stier et al. 2012).
+  \eqn{\sqrt{n/(n-1)}}{sqrt(n/(n-1))} correction (Stier et al. 2012).
 }
 \value{
   The \code{anova} method returns an object of class \code{"anova"}
@@ -211,7 +211,7 @@
   density and timing of arrival affect reef fish community assembly. Ms.
   in revision, \emph{Oikos}.
 }
-\author{Gavin L. Simpson}
+\author{Gavin L. Simpson; bias correction by Adrian Stier and Ben Bolker.}
 \seealso{\code{\link{permutest.betadisper}}, \code{\link[stats]{anova.lm}},
   \code{\link{scores}}, \code{\link[graphics]{boxplot}},
   \code{\link{TukeyHSD}}. Further measure of beta diversity