[Vegan-commits] r2407 - branches/2.0/inst www

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

Author: jarioksa
Date: 2013-02-04 19:05:25 +0100 (Mon, 04 Feb 2013)
New Revision: 2407

Modified:
   branches/2.0/inst/NEWS.Rd
   www/NEWS.html
Log:
NEWS about merge of faster protest + tweaks

Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd	2013-02-04 17:45:14 UTC (rev 2406)
+++ branches/2.0/inst/NEWS.Rd	2013-02-04 18:05:25 UTC (rev 2407)
@@ -39,7 +39,7 @@
 
       \item Function \code{treedive()} for functional diversity did
       not correctly match the species names in the community data and
-      classification tree when the tree containted species that did
+      classification tree when the tree contained species that did
       not occur in the data.  Related function \code{treedist()} for
       phylogenetic distances did not try to match the names at all.
 
@@ -83,11 +83,15 @@
       \item \code{orditorp()} gained argument \code{select} to select
       the rows or columns of the results to display.
 
-      \item \code{protest()} prints the standardized residual sum of
-      squared \eqn{m_{12}^2}{squared m12} in addition to the squared
+      \item \code{protest()} prints the standardized residual
+      statistic \eqn{m_{12}^2}{squared m12} in addition to the squared
       Procrustes correlation \eqn{R^2}{R2}.  Both were calculated, but
       only the latter was displayed.
 
+      Permutation tests are much faster in \code{protest()}. Instead
+      of calling repeatedly \code{procrustes()}, the goodness of fit
+      statistic is evaluated within then function.
+
       \item \code{wcmdscale()} gained methods for \code{print},
       \code{plot} etc. of the results. These methods are only used if
       the full \code{wcmdscale} result is returned with, e.g.,

Modified: www/NEWS.html
===================================================================
--- www/NEWS.html	2013-02-04 17:45:14 UTC (rev 2406)
+++ www/NEWS.html	2013-02-04 18:05:25 UTC (rev 2407)
@@ -55,7 +55,7 @@
 </li>
 <li><p> Function <code>treedive()</code> for functional diversity did
 not correctly match the species names in the community data and
-classification tree when the tree containted species that did
+classification tree when the tree contained species that did
 not occur in the data.  Related function <code>treedist()</code> for
 phylogenetic distances did not try to match the names at all.
 </p>
@@ -107,11 +107,15 @@
 the rows or columns of the results to display.
 </p>
 </li>
-<li> <p><code>protest()</code> prints the standardized residual sum of
-squared <i>squared m12</i> in addition to the squared
+<li> <p><code>protest()</code> prints the standardized residual
+statistic <i>squared m12</i> in addition to the squared
 Procrustes correlation <i>R2</i>.  Both were calculated, but
 only the latter was displayed.
 </p>
+<p>Permutation tests are much faster in <code>protest()</code>. Instead
+of calling repeatedly <code>procrustes()</code>, the goodness of fit
+statistic is evaluated within then function.
+</p>
 </li>
 <li> <p><code>wcmdscale()</code> gained methods for <code>print</code>,
 <code>plot</code> etc. of the results. These methods are only used if