[Vegan-commits] r2403 - branches/2.0/inst www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Feb 3 16:50:31 CET 2013
Author: jarioksa
Date: 2013-02-03 16:50:31 +0100 (Sun, 03 Feb 2013)
New Revision: 2403
Modified:
branches/2.0/inst/NEWS.Rd
www/NEWS.html
Log:
NEWS about release 2.0-6
Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd 2013-02-03 07:28:53 UTC (rev 2402)
+++ branches/2.0/inst/NEWS.Rd 2013-02-03 15:50:31 UTC (rev 2403)
@@ -8,20 +8,41 @@
\itemize{
- \item \code{capscale} scaled species scores wrongly when other
- dissimilarties than Euclidean distances were used.
+ \item The species scores were scaled correctly in
+ \code{capscale()} only when Euclidean distances were used. Most
+ graphics will change and should be redone. The function also
+ now displays the value of the additive constant when argument
+ \code{add = TRUE} was used.
- \item \code{clamtest}
+ \item Function \code{clamtest()} failed to set the minimum
+ abundance threshold in some cases. The output was wrong when
+ some of the possible species groups were missing. The problems
+ were reported by Richard Telford (Bergen, Norway).
- \item \code{envfit} handles unused factor levels.
+ \item Plotting an object fitted by \code{envfit()} would fail if
+ \code{p.max} was used and there were unused levels for one or
+ more factors. The unused levels could result from deletion of
+ observations with missing values or simply the result of
+ supplying a subset of a larger data set to \code{envfit()}.
- \item \code{multipart} printed wrong information about the
- analysis type (but did analysis correctly).
+ \item \code{multipart()} printed wrong information about the
+ analysis type (but did analysis correctly). Reported by Valerie
+ Coudrain.
- \item \code{procrustes}
+ \item \code{oecosimu()} failed if its \code{nestedfun} returned
+ a data frame. A more fundamental fix will be in \pkg{vegan}
+ 2.2-0.
- \item \code{treedive} and \code{treedist} name matching.
+ \item The plot of two-dimensional \code{procrustes()} solutions
+ often draw original axes in a wrong angle. The problem was
+ reported by Elizabeth Ottesen (MIT).
+ \item Function \code{treedive()} for functional diversity did
+ not correctly match the species names in the community data and
+ classification tree when the tree containted species that did
+ not occur in the data. Related function \code{treedist()} for
+ phylogenetic distances did not try to match the names at all.
+
}
} % bug fixes
@@ -30,19 +51,48 @@
\itemize{
- \item \code{dispindmorisita} gains \eqn{P}-value.
+ \item \code{dispindmorisita()} output gained a new column for
+ Chi-squared based probabilities that the null hypothesis (random
+ distribution) is true.
- \item \code{metaMDS} and \code{monoMDS} have new default
- convergence criteria.
+ \item \code{metaMDS()} and \code{monoMDS()} have new default
+ convergence criteria. Most importantly, scale factor of the
+ gradient (\code{sfgrmin}) is stricter. The former limit was too
+ slack with large data sets and iterations stopped early without
+ getting close to the solution. In addition, \code{scores()}
+ ignore now requests to dimensions beyond those calculated
+ instead of failing, and \code{scores()} for \code{metaMDS()}
+ results do not drop dimensions.
- \item \code{ordiR2step} gained new argument \code{R2scope} and
- handles partial redundancy analysis (pRDA).
+ \item \code{msoplot()} gained \code{legend} argument for
+ positioning the legend.
- \item \code{orditorp} gained argument \code{select}
+ \item Nestedness function \code{nestednodf()} gained a \code{plot}
+ method.
- \item \code{protest} prints both \eqn{m_{12}^2}{squared m12} and
- \eqn{R^2}{R2}.
+ \item \code{ordiR2step()} gained new argument \code{R2scope}
+ (defaults \code{TRUE}) which can be used to turn off the
+ criterion of stopping when the adjusted \eqn{R^2}{R2} of the
+ current model exceeds that of the scope. This option allows
+ model building when the \code{scope} would be overdetermined
+ (number of predictors higher than number of observations).
+ \code{ordiR2step()} now handles partial redundancy analysis
+ (pRDA).
+
+ \item \code{orditorp()} gained argument \code{select} to select
+ the rows or columns of the results to display.
+
+ \item \code{protest()} prints the standardized residual sum of
+ squared \eqn{m_{12}^2}{squared m12} in addition to the squared
+ Procrustes correlation \eqn{R^2}{R2}. Both were calculated, but
+ only the latter was displayed.
+
+ \item \code{wcmdscale()} gained methods for \code{print},
+ \code{plot} etc. of the results. These methods are only used if
+ the full \code{wcmdscale} result is returned with, e.g.,
+ argument \code{eig = TRUE}.
+
}
} % new features
Modified: www/NEWS.html
===================================================================
--- www/NEWS.html 2013-02-03 07:28:53 UTC (rev 2402)
+++ www/NEWS.html 2013-02-03 15:50:31 UTC (rev 2403)
@@ -8,6 +8,121 @@
<h2>vegan News</h2>
+<h3>Changes in version 2.0-6</h3>
+
+
+
+
+<h4>BUG FIXES</h4>
+
+
+
+<ul>
+<li><p> The species scores were scaled correctly in
+<code>capscale()</code> only when Euclidean distances were used. Most
+graphics will change and should be redone. The function also
+now displays the value of the additive constant when argument
+<code>add = TRUE</code> was used.
+</p>
+</li>
+<li><p> Function <code>clamtest()</code> failed to set the minimum
+abundance threshold in some cases. The output was wrong when
+some of the possible species groups were missing. The problems
+were reported by Richard Telford (Bergen, Norway).
+</p>
+</li>
+<li><p> Plotting an object fitted by <code>envfit()</code> would fail if
+<code>p.max</code> was used and there were unused levels for one or
+more factors. The unused levels could result from deletion of
+observations with missing values or simply the result of
+supplying a subset of a larger data set to <code>envfit()</code>.
+</p>
+</li>
+<li> <p><code>multipart()</code> printed wrong information about the
+analysis type (but did analysis correctly). Reported by Valerie
+Coudrain.
+</p>
+</li>
+<li> <p><code>oecosimu()</code> failed if its <code>nestedfun</code> returned
+a data frame. A more fundamental fix will be in <span class="pkg">vegan</span>
+2.2-0.
+</p>
+</li>
+<li><p> The plot of two-dimensional <code>procrustes()</code> solutions
+often draw original axes in a wrong angle. The problem was
+reported by Elizabeth Ottesen (MIT).
+</p>
+</li>
+<li><p> Function <code>treedive()</code> for functional diversity did
+not correctly match the species names in the community data and
+classification tree when the tree containted species that did
+not occur in the data. Related function <code>treedist()</code> for
+phylogenetic distances did not try to match the names at all.
+</p>
+</li></ul>
+
+
+
+
+<h4>NEW FEATURES</h4>
+
+
+
+<ul>
+<li> <p><code>dispindmorisita()</code> output gained a new column for
+Chi-squared based probabilities that the null hypothesis (random
+distribution) is true.
+</p>
+</li>
+<li> <p><code>metaMDS()</code> and <code>monoMDS()</code> have new default
+convergence criteria. Most importantly, scale factor of the
+gradient (<code>sfgrmin</code>) is stricter. The former limit was too
+slack with large data sets and iterations stopped early without
+getting close to the solution. In addition, <code>scores()</code>
+ignore now requests to dimensions beyond those calculated
+instead of failing, and <code>scores()</code> for <code>metaMDS()</code>
+results do not drop dimensions.
+</p>
+</li>
+<li> <p><code>msoplot()</code> gained <code>legend</code> argument for
+positioning the legend.
+</p>
+</li>
+<li><p> Nestedness function <code>nestednodf()</code> gained a <code>plot</code>
+method.
+</p>
+</li>
+<li> <p><code>ordiR2step()</code> gained new argument <code>R2scope</code>
+(defaults <code>TRUE</code>) which can be used to turn off the
+criterion of stopping when the adjusted <i>R2</i> of the
+current model exceeds that of the scope. This option allows
+model building when the <code>scope</code> would be overdetermined
+(number of predictors higher than number of observations).
+</p>
+<p><code>ordiR2step()</code> now handles partial redundancy analysis
+(pRDA).
+</p>
+</li>
+<li> <p><code>orditorp()</code> gained argument <code>select</code> to select
+the rows or columns of the results to display.
+</p>
+</li>
+<li> <p><code>protest()</code> prints the standardized residual sum of
+squared <i>squared m12</i> in addition to the squared
+Procrustes correlation <i>R2</i>. Both were calculated, but
+only the latter was displayed.
+</p>
+</li>
+<li> <p><code>wcmdscale()</code> gained methods for <code>print</code>,
+<code>plot</code> etc. of the results. These methods are only used if
+the full <code>wcmdscale</code> result is returned with, e.g.,
+argument <code>eig = TRUE</code>.
+</p>
+</li></ul>
+
+
+
+
<h3>Changes in version 2.0-5</h3>
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