[Vegan-commits] r2473 - branches/2.0/inst www

Thu Mar 7 15:14:15 CET 2013

Author: jarioksa
Date: 2013-03-07 15:14:15 +0100 (Thu, 07 Mar 2013)
New Revision: 2473

Modified:
   branches/2.0/inst/NEWS.Rd
   www/NEWS.html
Log:
NEWS about things merged to 2.0-7

Modified: branches/2.0/inst/NEWS.Rd
===================================================================

--- branches/2.0/inst/NEWS.Rd	2013-03-07 08:56:26 UTC (rev 2472)
+++ branches/2.0/inst/NEWS.Rd	2013-03-07 14:14:15 UTC (rev 2473)
@@ -2,6 +2,50 @@
 \title{vegan News}
 \encoding{UTF-8}
 
+\section{Changes in version 2.0.7}{
+
+  \subsection{NEW FUNCTIONS}{
+    \itemize{
+
+      \item \code{tabasco()} is a new function for graphical display
+      of community data matrix.  Technically it is only an interface
+      to \R \code{heatmap}, but its user interface and intended use is
+      closer to \pkg{vegan} \code{vegemite}. The function can reorder
+      the community data matrix similarly as \code{vegemite}, for
+      instance, by ordination results. Unlike \code{heatmap}, it only
+      displays dendrograms if supplied by the user, and it defaults to
+      re-order the dendrograms by correspondence analysis.  Species
+      are usually ordered to match site ordering.
+
+    }
+  } % new functions
+
+  \subsection{BUG FIXES}{
+    \itemize{
+
+      \item Function \code{fitspecaccum(..., model = "asymp")} fitted
+      logistic model instead of asymptotic model (or the same as 
+      \code{model = "logis"}).
+
+      \item \code{nestedtemp()} failed with very sparse data (fill
+      \eqn{< 0.38}\%).
+
+    }
+  } % bug fixes 
+
+  \subsection{NEW FEATURES}{
+    \itemize{
+
+      \item The \code{plot} function for constrained ordination
+      results (\code{cca}, \code{rda}, \code{capscale}) gained
+      argument \code{axis.bp} (defaults \code{TRUE}) which can be used
+      to suppress plotting axis scale for biplot arrays.
+
+    }
+  } % new features
+
+} % vegan 2.0-7
+
 \section{Changes in version 2.0-6}{
 
   \subsection{BUG FIXES}{

Modified: www/NEWS.html
===================================================================
--- www/NEWS.html	2013-03-07 08:56:26 UTC (rev 2472)
+++ www/NEWS.html	2013-03-07 14:14:15 UTC (rev 2473)
@@ -8,13 +8,73 @@
 
 <h2>vegan News</h2>
 
+<h3>Changes in version 2.0.7</h3>
+
+
+
+
+<h4>NEW FUNCTIONS</h4>
+
+
+
+<ul>
+<li> <p><code>tabasco()</code> is a new function for graphical display
+of community data matrix.  Technically it is only an interface
+to <font face="Courier New,Courier" color="#666666"><b>R</b></font> <code>heatmap</code>, but its user interface and intended use is
+closer to <span class="pkg">vegan</span> <code>vegemite</code>. The function can reorder
+the community data matrix similarly as <code>vegemite</code>, for
+instance, by ordination results. Unlike <code>heatmap</code>, it only
+displays dendrograms if supplied by the user, and it defaults to
+re-order the dendrograms by correspondence analysis.  Species
+are usually ordered to match site ordering.
+</p>
+</li></ul>
+
+ 
+
+
+<h4>BUG FIXES</h4>
+
+
+
+<ul>
+<li><p> Function <code>fitspecaccum(..., model = "asymp")</code> fitted
+logistic model instead of asymptotic model (or the same
+<code>model = "logis"</code>).
+</p>
+</li>
+<li> <p><code>nestedtemp()</code> failed with very sparse data (fill
+<i>< 0.38</i>%).
+</p>
+</li></ul>
+
+ 
+
+
+<h4>NEW FEATURES</h4>
+
+
+
+<ul>
+<li><p> The <code>plot</code> function for constrained ordination
+results (<code>cca</code>, <code>rda</code>, <code>capscale</code>) gained
+argument <code>axis.bp</code> (defaults <code>TRUE</code>) which can be used
+to suppress plotting axis scale for biplot arrays.
+</p>
+</li></ul>
+
+ 
+
+
 <h3>Changes in version 2.0-6</h3>
 
 
 
+
 <h4>BUG FIXES</h4>
 
 
+
 <ul>
 <li><p> The species scores were scaled wrongly in
 <code>capscale()</code>. They were scaled correctly only when Euclidean
@@ -67,6 +127,7 @@
 <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.
@@ -142,9 +203,11 @@
 
 
 
+
 <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
@@ -162,6 +225,7 @@
 <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
@@ -195,6 +259,7 @@
 <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
@@ -224,6 +289,7 @@
 <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).
@@ -246,9 +312,11 @@
 
 
 
+
 <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
@@ -289,6 +357,7 @@
 <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>
@@ -359,9 +428,11 @@
 
 
 
+
 <h4>NEW FUNCTIONS</h4>
 
 
+
 <ul>
 <li><p> Added new nestedness functions <code>nestedbetasor</code> and
 <code>nestedbetajac</code> that implement multiple-site dissimilarity
@@ -393,6 +464,7 @@
 <h4>BUG FIXES</h4>
 
 
+
 <ul>
 <li> <p><code>betadisper()</code> failed when the <code>groups</code> was a
 factor with empty levels.
@@ -424,6 +496,7 @@
 <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
@@ -465,9 +538,11 @@
 
 
 
+
 <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
@@ -504,6 +579,7 @@
 <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
@@ -524,9 +600,11 @@
 
 
 
+
 <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
@@ -562,6 +640,7 @@
 <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
@@ -600,6 +679,7 @@
 <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
@@ -615,9 +695,11 @@
 
 
 
+
 <h4>GENERAL</h4>
 
 
+
 <ul>
 <li><p> Peter Minchin joins the <span class="pkg">vegan</span> team.
 </p>
@@ -648,6 +730,7 @@
 <h4>NEW FUNCTIONS</h4>
 
 
+
 <ul>
 <li> <p><code>monoMDS</code>: a new function for non-metric
 multidimensional scaling (NMDS). This function replaces
@@ -703,6 +786,7 @@
 <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
@@ -744,6 +828,7 @@
 <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>.
@@ -762,6 +847,7 @@
 <h4>ANALYSES</h4>
 
 
+
 <ul>
 <li> <p><code>treeheight</code> uses much snappier code. The results
 should be unchanged.

