[Vegan-commits] r2428 - www

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

Author: jarioksa
Date: 2013-02-11 08:36:14 +0100 (Mon, 11 Feb 2013)
New Revision: 2428

Modified:
   www/NEWS.html
Log:
html version of tweaked NEWS

Modified: www/NEWS.html
===================================================================
--- www/NEWS.html	2013-02-11 07:35:39 UTC (rev 2427)
+++ www/NEWS.html	2013-02-11 07:36:14 UTC (rev 2428)
@@ -12,23 +12,21 @@
 
 
 
-
 <h4>BUG FIXES</h4>
 
 
-
 <ul>
-<li><p> The species scores were scaled correctly in
-<code>capscale()</code> only when Euclidean distances were used. Usually
-<code>capscale()</code> is used with non-Euclidean distances, and in
-these cases the scaling was wrong.  Most graphics will change and
-should be redone.  The change of scaling mainly influences the
-spread of species scores with respect to the site scores.
+<li><p> The species scores were scaled wrongly in
+<code>capscale()</code>. They were scaled correctly only when Euclidean
+distances were used, but usually <code>capscale()</code> is used with
+non-Euclidean distances.  Most graphics will change and should be
+redone.  The change of scaling mainly influences the spread of
+species scores with respect to the site scores.
 </p>
 </li>
 <li><p> Function <code>clamtest()</code> failed to set the minimum
 abundance threshold in some cases. In addition, the output was
-wrong when some of the possible species groups were missing. The
+wrong when some of the possible species groups were missing. Both
 problems were reported by Richard Telford (Bergen, Norway).
 </p>
 </li>
@@ -40,8 +38,8 @@
 </p>
 </li>
 <li> <p><code>multipart()</code> printed wrong information about the
-analysis type (but did analysis correctly). Reported by Valerie
-Coudrain.
+analysis type (but did the analysis correctly). Reported by
+Valerie Coudrain.
 </p>
 </li>
 <li> <p><code>oecosimu()</code> failed if its <code>nestedfun</code> returned a
@@ -69,7 +67,6 @@
 <h4>NEW FEATURES</h4>
 
 
-
 <ul>
 <li><p> The output of <code>capscale()</code> displays the value of the
 additive constant when argument <code>add = TRUE</code> was used.
@@ -145,11 +142,9 @@
 
 
 
-
 <h4>BUG FIXES</h4>
 
 
-
 <ul>
 <li> <p><code>anova(<cca_object>, ...)</code> failed with
 <code>by = "axis"</code> and <code>by = "term"</code>. The bug was reported by
@@ -167,7 +162,6 @@
 <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 find empirical
@@ -201,7 +195,6 @@
 <h4>NEW FEATURES</h4>
 
 
-
 <ul>
 <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
@@ -231,7 +224,6 @@
 <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).
@@ -254,11 +246,9 @@
 
 
 
-
 <h4>BUG FIXES</h4>
 
 
-
 <ul>
 <li> <p><code>adipart</code> assumed constant gamma diversity in
 simulations when assessing the <i>P</i>-value.  This could give
@@ -299,7 +289,6 @@
 <h4>NEW FEATURES</h4>
 
 
-
 <ul>
 <li><p> Functions for diversity partitioning (<code>adipart</code>,
 <code>hiersimu</code> and <code>multipart</code>) have now <code>formula</code>
@@ -370,11 +359,9 @@
 
 
 
-
 <h4>NEW FUNCTIONS</h4>
 
 
-
 <ul>
 <li><p> Added new nestedness functions <code>nestedbetasor</code> and
 <code>nestedbetajac</code> that implement multiple-site dissimilarity
@@ -406,7 +393,6 @@
 <h4>BUG FIXES</h4>
 
 
-
 <ul>
 <li> <p><code>betadisper()</code> failed when the <code>groups</code> was a
 factor with empty levels.
@@ -438,7 +424,6 @@
 <h4>NEW FEATURES</h4>
 
 
-
 <ul>
 <li> <p><code>metaMDS</code> argument <code>noshare = 0</code> is now
 regarded as a numeric threshold that always triggers extended
@@ -480,11 +465,9 @@
 
 
 
-
 <h4>BUG FIXES</h4>
 
 
-
 <ul>
 <li><p> Function <code>capscale</code> failed if constrained component
 had zero rank. This happened most likely in partial models when
@@ -521,7 +504,6 @@
 <h4>NEW FEATURES</h4>
 
 
-
 <ul>
 <li> <p><code>ordiarrows</code> and <code>ordisegments</code> gained argument
 <code>order.by</code> that gives a variable to sort points within
@@ -542,11 +524,9 @@
 
 
 
-
 <h4>NEW FUNCTIONS</h4>
 
 
-
 <ul>
 <li> <p><code>clamtest</code>: new function to classify species as
 generalists and specialists in two distinct habitats (CLAM test of
@@ -582,7 +562,6 @@
 <h4>BUG FIXES</h4>
 
 
-
 <ul>
 <li><p> Function <code>meandist</code> could scramble items and give
 wrong results, especially when the <code>grouping</code> was
@@ -621,7 +600,6 @@
 <h4>ANALYSES</h4>
 
 
-
 <ul>
 <li> <p><code>nesteddisc</code> is slacker and hence faster when trying
 to optimize the statistic for tied column frequencies. Tracing
@@ -637,11 +615,9 @@
 
 
 
-
 <h4>GENERAL</h4>
 
 
-
 <ul>
 <li><p> Peter Minchin joins the <span class="pkg">vegan</span> team.
 </p>
@@ -672,7 +648,6 @@
 <h4>NEW FUNCTIONS</h4>
 
 
-
 <ul>
 <li> <p><code>monoMDS</code>: a new function for non-metric
 multidimensional scaling (NMDS). This function replaces
@@ -728,7 +703,6 @@
 <h4>NEW FEATURES</h4>
 
 
-
 <ul>
 <li> <p><code>adonis</code>, <code>anosim</code>, <code>meandist</code> and
 <code>mrpp</code> warn on negative dissimilarities, and
@@ -770,7 +744,6 @@
 <h4>DEPRECATED AND DEFUNCT</h4>
 
 
-
 <ul>
 <li> <p><code>metaMDSrotate</code> was replaced with <code>MDSrotate</code>
 that can also handle the results of <code>monoMDS</code>.
@@ -789,7 +762,6 @@
 <h4>ANALYSES</h4>
 
 
-
 <ul>
 <li> <p><code>treeheight</code> uses much snappier code. The results
 should be unchanged.