[Vegan-commits] r2547 - branches/2.0/inst www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jul 9 15:54:12 CEST 2013
Author: jarioksa
Date: 2013-07-09 15:54:12 +0200 (Tue, 09 Jul 2013)
New Revision: 2547
Modified:
branches/2.0/inst/NEWS.Rd
www/NEWS.html
Log:
NEWS about 2.0-8
Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd 2013-07-09 13:32:28 UTC (rev 2546)
+++ branches/2.0/inst/NEWS.Rd 2013-07-09 13:54:12 UTC (rev 2547)
@@ -2,8 +2,40 @@
\title{vegan News}
\encoding{UTF-8}
-\section{Changes in version 2.0.7}{
+\section{Changes in version 2.0-8}{
+ \subsection{GENERAL}{
+ \itemize{
+
+ \item This is a maintenance release that fixes some issues
+ raised by changed in \R{} toolset for processing vignettes. In
+ the same we also fix some typographic issues in the vignettes.
+
+ }
+ } % general
+
+ \subsection{NEW FEATURES}{
+ \itemize{
+
+ \item \code{ordisurf} gained new arguments for more flexible
+ definition of fitted models to better utilize the
+ \pkg{mgcv}\code{::gam} function. The linewidth of contours can
+ now be set with the argument \code{lwd}.
+
+ \item Labels to arrows are more cleanly positioned in
+ \code{plot} functions for the results of \code{envfit},
+ \code{cca}, \code{rda} and \code{capscale}.
+
+ \item The wording for setting test direction is now clearer in
+ \code{oecosimu}.
+
+ }
+ } % new features
+
+}
+
+\section{Changes in version 2.0-7}{
+
\subsection{NEW FUNCTIONS}{
\itemize{
Modified: www/NEWS.html
===================================================================
--- www/NEWS.html 2013-07-09 13:32:28 UTC (rev 2546)
+++ www/NEWS.html 2013-07-09 13:54:12 UTC (rev 2547)
@@ -8,16 +8,54 @@
<h2>vegan News</h2>
-<h3>Changes in version 2.0.7</h3>
+<h3>Changes in version 2.0-8</h3>
+<h4>GENERAL</h4>
-<h4>NEW FUNCTIONS</h4>
+<ul>
+<li><p> This is a maintenance release that fixes some issues
+raised by changed in <font face="Courier New,Courier" color="#666666"><b>R</b></font> toolset for processing vignettes. In
+the same we also fix some typographic issues in the vignettes.
+</p>
+</li></ul>
+
+
+<h4>NEW FEATURES</h4>
+
+
<ul>
+<li> <p><code>ordisurf</code> gained new arguments for more flexible
+definition of fitted models to better utilize the
+<span class="pkg">mgcv</span><code>::gam</code> function. The linewidth of contours can
+now be set with the argument <code>lwd</code>.
+</p>
+</li>
+<li><p> Labels to arrows are more cleanly positioned in
+<code>plot</code> functions for the results of <code>envfit</code>,
+<code>cca</code>, <code>rda</code> and <code>capscale</code>.
+</p>
+</li>
+<li><p> The wording for setting test direction is now clearer in
+<code>oecosimu</code>.
+</p>
+</li></ul>
+
+
+
+
+<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 an interface to <font face="Courier New,Courier" color="#666666"><b>R</b></font>
<code>heatmap</code>, but its use is closer to <span class="pkg">vegan</span> function
@@ -36,7 +74,6 @@
<h4>BUG FIXES</h4>
-
<ul>
<li><p> Function <code>fitspecaccum(..., model = "asymp")</code> fitted
logistic model instead of asymptotic model (or the same as
@@ -54,7 +91,6 @@
<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
@@ -74,7 +110,6 @@
<h4>DEPRECATED</h4>
-
<ul>
<li><p> The result objects of <code>cca</code>, <code>rda</code> and
<code>capscale</code> will no longer have scores <code>u.eig</code>,
@@ -93,11 +128,9 @@
-
<h4>BUG FIXES</h4>
-
<ul>
<li><p> The species scores were scaled wrongly in
<code>capscale()</code>. They were scaled correctly only when Euclidean
@@ -150,7 +183,6 @@
<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.
@@ -226,11 +258,9 @@
-
<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
@@ -248,7 +278,6 @@
<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
@@ -282,7 +311,6 @@
<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
@@ -312,7 +340,6 @@
<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).
@@ -335,11 +362,9 @@
-
<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
@@ -380,7 +405,6 @@
<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>
@@ -451,11 +475,9 @@
-
<h4>NEW FUNCTIONS</h4>
-
<ul>
<li><p> Added new nestedness functions <code>nestedbetasor</code> and
<code>nestedbetajac</code> that implement multiple-site dissimilarity
@@ -487,7 +509,6 @@
<h4>BUG FIXES</h4>
-
<ul>
<li> <p><code>betadisper()</code> failed when the <code>groups</code> was a
factor with empty levels.
@@ -519,7 +540,6 @@
<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
@@ -561,11 +581,9 @@
-
<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
@@ -602,7 +620,6 @@
<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
@@ -623,11 +640,9 @@
-
<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
@@ -663,7 +678,6 @@
<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
@@ -702,7 +716,6 @@
<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
@@ -718,11 +731,9 @@
-
<h4>GENERAL</h4>
-
<ul>
<li><p> Peter Minchin joins the <span class="pkg">vegan</span> team.
</p>
@@ -753,7 +764,6 @@
<h4>NEW FUNCTIONS</h4>
-
<ul>
<li> <p><code>monoMDS</code>: a new function for non-metric
multidimensional scaling (NMDS). This function replaces
@@ -809,7 +819,6 @@
<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
@@ -851,7 +860,6 @@
<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>.
@@ -870,7 +878,6 @@
<h4>ANALYSES</h4>
-
<ul>
<li> <p><code>treeheight</code> uses much snappier code. The results
should be unchanged.
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