[Vegan-commits] r2812 - branches/2.0/inst www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Dec 8 16:19:46 CET 2013
Author: jarioksa
Date: 2013-12-08 16:19:45 +0100 (Sun, 08 Dec 2013)
New Revision: 2812
Modified:
branches/2.0/inst/NEWS.Rd
www/NEWS.html
Log:
NEWS about 2.0-10
Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd 2013-12-08 07:44:18 UTC (rev 2811)
+++ branches/2.0/inst/NEWS.Rd 2013-12-08 15:19:45 UTC (rev 2812)
@@ -2,6 +2,80 @@
\title{vegan News}
\encoding{UTF-8}
+\section{Changes in version 2.0-10}{
+
+ \subsection{GENERAL}{
+ \itemize{
+
+ \item This version is adapted to the changes in \pkg{permute}
+ package version 0.8-0 and no more triggers NOTEs in package
+ checks. This release may be the last of the 2.0 series, and the
+ next \pkg{vegan} release is scheduled to be a major release with
+ newly designed \code{oecosimu} and community pattern simulation,
+ support for parallel processing, and full support of the
+ \pkg{permute} package. If you are interested in these
+ developments, you may try the development versions of
+ \pkg{vegan} in
+ \href{http://r-forge.r-project.org/projects/vegan/}{R-Forge} or
+ \href{https://github.com/jarioksa/vegan}{GitHub} and report the
+ problems and user experience to us. } } % end general
+
+ \subsection{BUG FIXES}{
+
+ \itemize{
+
+ \item \code{envfit} function assumed that all external variables
+ were either numeric or factors, and failed if they were, say,
+ character strings. Now only numeric variables are taken as
+ continuous vectors, and all other variables (character strings,
+ logical) are coerced to factors if possible. The function also
+ should work with degenerate data, like only one level of a
+ factor or a constant value of a continuous environmental
+ variable.
+
+ \item \code{nestednodf} with quantitative data was not
+ consistent with binary models, and the fill was wrongly
+ calculated with quantitative data.
+
+ \item \code{oecosimu} now correctly adapts displayed quantiles
+ of simulated values to the \code{alternative} test direction.
+
+ \item \code{renyiaccum} plotting failed if only one level of
+ diversity \code{scale} was used.
+
+ }
+ } % bug fixes
+
+ \subsection{NEW FEATURES}{
+ \itemize{
+
+ \item The Kempton and Taylor algorithm was found unreliable in
+ \code{fisherfit} and \code{fisher.alpha}, and now the estimation
+ of Fisher \eqn{\alpha}{alpha} is only based on the number of
+ species and the number of individuals. The estimation of
+ standard errors and profile confidence intervals also had to be
+ scrapped.
+
+ \item \code{renyiaccum}, \code{specaccum} and
+ \code{tsallisaccum} functions gained \code{subset} argument.
+
+ \item \code{renyiaccum} can now add a \code{collector} curve to
+ to the analysis. The collector curve is the diversity
+ accumulation in the order of the sampling units. With an
+ interesting ordering or sampling units this allows comparing
+ actual species accumulations with the expected randomized
+ accumulation.
+
+ \item \code{specaccum} can now perform weighted accumulation
+ using the sampling effort as weights.
+
+ }
+
+ } % new features
+
+
+} % end 2.0-10
+
\section{Changes in version 2.0-9}{
\itemize{
Modified: www/NEWS.html
===================================================================
--- www/NEWS.html 2013-12-08 07:44:18 UTC (rev 2811)
+++ www/NEWS.html 2013-12-08 15:19:45 UTC (rev 2812)
@@ -8,6 +8,94 @@
<h2>vegan News</h2>
+<h3>Changes in version 2.0-10</h3>
+
+
+
+<h4>GENERAL</h4>
+
+
+<ul>
+<li><p> This version is adapted to the changes in <span class="pkg">permute</span>
+package version 0.8-0 and no more triggers NOTEs in package
+checks. This release may be the last of the 2.0 series, and the
+next <span class="pkg">vegan</span> release is scheduled to be a major release with
+newly designed <code>oecosimu</code> and community pattern simulation,
+support for parallel processing, and full support of the
+<span class="pkg">permute</span> package. If you are interested in these
+developments, you may try the development versions of
+<span class="pkg">vegan</span> in
+<a href="http://r-forge.r-project.org/projects/vegan/">R-Forge</a> or
+<a href="https://github.com/jarioksa/vegan">GitHub</a> and report the
+problems and user experience to us. </p>
+</li></ul>
+
+
+
+<h4>BUG FIXES</h4>
+
+
+<ul>
+<li> <p><code>envfit</code> function assumed that all external variables
+were either numeric or factors, and failed if they were, say,
+character strings. Now only numeric variables are taken as
+continuous vectors, and all other variables (character strings,
+logical) are coerced to factors if possible. The function also
+should work with degenerate data, like only one level of a
+factor or a constant value of a continuous environmental
+variable.
+</p>
+</li>
+<li> <p><code>nestednodf</code> with quantitative data was not
+consistent with binary models, and the fill was wrongly
+calculated with quantitative data.
+</p>
+</li>
+<li> <p><code>oecosimu</code> now correctly adapts displayed quantiles
+of simulated values to the <code>alternative</code> test direction.
+</p>
+</li>
+<li> <p><code>renyiaccum</code> plotting failed if only one level of
+diversity <code>scale</code> was used.
+</p>
+</li></ul>
+
+
+
+
+<h4>NEW FEATURES</h4>
+
+
+
+<ul>
+<li><p> The Kempton and Taylor algorithm was found unreliable in
+<code>fisherfit</code> and <code>fisher.alpha</code>, and now the estimation
+of Fisher <i>alpha</i> is only based on the number of
+species and the number of individuals. The estimation of
+standard errors and profile confidence intervals also had to be
+scrapped.
+</p>
+</li>
+<li> <p><code>renyiaccum</code>, <code>specaccum</code> and
+<code>tsallisaccum</code> functions gained <code>subset</code> argument.
+</p>
+</li>
+<li> <p><code>renyiaccum</code> can now add a <code>collector</code> curve to
+to the analysis. The collector curve is the diversity
+accumulation in the order of the sampling units. With an
+interesting ordering or sampling units this allows comparing
+actual species accumulations with the expected randomized
+accumulation.
+</p>
+</li>
+<li> <p><code>specaccum</code> can now perform weighted accumulation
+using the sampling effort as weights.
+</p>
+</li></ul>
+
+
+
+
<h3>Changes in version 2.0-9</h3>
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