[Vegan-commits] r2278 - www

Mon Sep 10 14:05:42 CEST 2012

Author: jarioksa
Date: 2012-09-10 14:05:42 +0200 (Mon, 10 Sep 2012)
New Revision: 2278

Modified:
   www/NEWS.html
Log:
update

Modified: www/NEWS.html
===================================================================

--- www/NEWS.html	2012-09-10 12:04:53 UTC (rev 2277)
+++ www/NEWS.html	2012-09-10 12:05:42 UTC (rev 2278)
@@ -8,6 +8,79 @@
 
 <h2>vegan News</h2>
 
+<h3>Changes in version 2.0-5</h3>
+
+
+
+
+<h4>NEW FUNCTIONS</h4>
+
+
+
+<ul>
+<li><p> Most <span class="pkg">vegan</span> functions with permutation tests have now a
+<code>density</code> method that can be used to fit empirical
+probability distributions of permutations. There is a new
+<code>plot</code> method for these function that displays both the
+density and the observed statistic. The <code>density</code> function is
+available for <code>adonis</code>, <code>anosim</code>, <code>mantel</code>,
+<code>mantel.partial</code>, <code>mrpp</code>, <code>permutest.cca</code> and
+<code>procrustes</code>.
+</p>
+<p>Function <code>adonis</code> can return several statistics, and it has
+now a <code>densityplot</code> method (based on <span class="pkg">lattice</span>).
+</p>
+<p>Function <code>oecosimu</code> already had <code>density</code> and
+<code>densityplot</code>, but they are now similar to other <span class="pkg">vegan</span>
+methods, and also work with <code>adipart</code>, <code>hiersimu</code> and
+<code>multipart</code>. 
+</p>
+</ul>
+
+ 
+
+
+<h4>NEW FEATURES</h4>
+
+
+
+<ul>
+<li><p> Function for additive and multiplicative diversity
+partioning (<code>adipart</code>, <code>hiersimu</code> and <code>multipart</code>)
+have more flexible formula interface. Skipping the formula will
+now give a simple partitioning into alpha, beta and gamma
+diversity in <code>adipart</code> and <code>multipart</code>.
+</p>
+</li>
+<li><p> Labels can now be set in the <code>plot</code> of <code>envfit</code>
+results. The labels must be given in the same order that the
+function uses internally, and new support function <code>labels</code>
+can be used to display the default labels in their correct order.  
+</p>
+</ul>
+
+ 
+
+
+<h4>INSTALLATION AND BUILDING</h4>
+
+
+
+<ul>
+<li><p> Building of <span class="pkg">vegan</span> vignettes failed with the latest
+version of LaTeX (TeXLive 2012).
+</p>
+</li>
+<li><p> Changes in <font face="Courier New,Courier" color="#666666"><b>R</b></font> testing procedures gave warnings for
+<code>betadisper</code> and <code>cIndexKM</code> in development version of
+<font face="Courier New,Courier" color="#666666"><b>R</b></font>.  Internal changes in <font face="Courier New,Courier" color="#666666"><b>R</b></font> caused an error in
+<code>betadisper</code>.
+</p>
+</ul>
+
+ 
+
+
 <h3>Changes in version 2.0-4</h3>
 
 
@@ -49,7 +122,7 @@
 <code>capscale</code> results which do not need row weights.
 Reported by Glenn De'ath.
 </p>
-</li></ul>
+</ul>
 
 
 
@@ -119,7 +192,7 @@
 <code>select</code> only some of the items for plotting. The
 argument can be used only with one set of points.
 </p>
-</li></ul>
+</ul>
 
  
 
@@ -156,7 +229,7 @@
 <a href="https://github.com/jarioksa/vegan">GitHub</a>
 by Eduard Szöcs (Uni Landau, Germany).
 </p>
-</li></ul>
+</ul>
 
  
 
@@ -188,7 +261,7 @@
 was reported as an error in <code>ordiplot</code> in
 <a href="https://stat.ethz.ch/pipermail/r-sig-ecology/2012-February/002768.html">R-sig-ecology</a> mailing list.
 </p>
-</li></ul>
+</ul>
 
  
 
@@ -229,7 +302,7 @@
 intensity. Thanks to consultation to Yong Cao (Univ Illinois,
 USA).
 </p>
-</li></ul>
+</ul>
 
  
 
@@ -271,7 +344,7 @@
 speed-up in the internal f.test() function is fully
 realised. Reported by Nicholas Lewin-Koh.
 </p>
-</li></ul>
+</ul>
 
   
 
@@ -291,7 +364,7 @@
 are class centroids of each point, but for constrained ordination
 with no <code>groups</code> they are the LC scores.
 </p>
-</li></ul>
+</ul>
 		 
   
 
@@ -332,7 +405,7 @@
 [<a href="http://www.esajournals.org/doi/abs/10.1890/ES10-00117.1">doi:10.1890/ES10-00117.1</a>],
 and was developed with the consultation of Brian Inouye.
 </p>
-</li></ul>
+</ul>
 
  
 
@@ -371,7 +444,7 @@
 results but you probably wish to upgrade <span class="pkg">vegan</span> to avoid
 annoying warnings.
 </p>
-</li></ul>
+</ul>
 	
  
 
@@ -386,7 +459,7 @@
 showed that in most cases an improved ordering was found rather
 early in tries, and the results are equally good in most cases.
 </p>
-</li></ul>
+</ul>
 
  
 
@@ -422,7 +495,7 @@
 <span class="pkg">permute</span>, but currently only <code>betadisper</code> uses the new
 feature. 
 </p>
-</li></ul>
+</ul>
 
  
 
@@ -478,7 +551,7 @@
 were implemented because they were found good for species-area
 models by Dengler (<EM>J. Biogeogr.</EM> 36, 728-744; 2009).
 </p>
-</li></ul>
+</ul>
 
  
 
@@ -520,7 +593,7 @@
 the length of the <code>pool</code> matches the number of
 observations.
 </p>
-</li></ul>
+</ul>
 
  
 
@@ -539,7 +612,7 @@
 was not intended for normal use, but packages depending on that
 code in <span class="pkg">vegan</span> should instead depend on <span class="pkg">permute</span>.
 </p>
-</li></ul>
+</ul>
   
  
 
@@ -552,7 +625,7 @@
 <li> <p><code>treeheight</code> uses much snappier code. The results
 should be unchanged.
 </p>
-</li></ul>
+</ul>
 
  
 

