[Vegan-commits] r2303 - branches/2.0/inst www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Sep 27 19:07:21 CEST 2012
Author: jarioksa
Date: 2012-09-27 19:07:20 +0200 (Thu, 27 Sep 2012)
New Revision: 2303
Modified:
branches/2.0/inst/NEWS.Rd
www/NEWS.html
Log:
update NEWS
Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd 2012-09-27 16:41:12 UTC (rev 2302)
+++ branches/2.0/inst/NEWS.Rd 2012-09-27 17:07:20 UTC (rev 2303)
@@ -4,6 +4,21 @@
\section{Changes in version 2.0-5}{
+ \subsection{BUG FIXES}{
+
+ \itemize{
+
+ \item \code{anova(<cca_object>, ...)} failed with \code{by =
+ "axis"} and \code{by = "term"}. The bug was reported by Dr Sven
+ Neulinger (Christian Albrecht University, Kiel, Germany).
+
+ \item \code{radlattice} did not honourour argument \code{BIC =
+ TRUE}, but always displayed AIC.
+
+ }
+
+ } % bug fixes
+
\subsection{NEW FUNCTIONS}{
\itemize{
@@ -22,8 +37,14 @@
Function \code{oecosimu} already had \code{density} and
\code{densityplot}, but they are now similar to other \pkg{vegan}
methods, and also work with \code{adipart}, \code{hiersimu} and
- \code{multipart}.
+ \code{multipart}.
+ \item \code{radfit} functions got a \code{predict} method that
+ also accepts arguments \code{newdata} and \code{total} for new
+ ranks and site totals for prediction. The functions can also
+ interpolate to non-integer \dQuote{ranks}, and in some models
+ also extrapolate.
+
}
} % new functions
@@ -41,6 +62,13 @@
care: Permutation tests can be biased if the missing values were
originally in matching or fixed positions.
+ \item \code{radfit} results can be consistently accessed with
+ the same methods whether they were a single model for a single
+ site, all models for a single site or all models for all sites
+ in the data. All functions now have methods \code{AIC},
+ \code{coef}, \code{deviance}, \code{logLik}, \code{fitted},
+ \code{predict} and \code{residuals}.
+
}
} % new features
Modified: www/NEWS.html
===================================================================
--- www/NEWS.html 2012-09-27 16:41:12 UTC (rev 2302)
+++ www/NEWS.html 2012-09-27 17:07:20 UTC (rev 2303)
@@ -13,6 +13,24 @@
+<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 Dr Sven
+Neulinger (Christian Albrecht University, Kiel, Germany).
+</p>
+</li>
+<li> <p><code>radlattice</code> did not honourour argument <code>BIC =
+ TRUE</code>, but always displayed AIC.
+</p>
+</li></ul>
+
+
+
+
<h4>NEW FUNCTIONS</h4>
@@ -33,9 +51,16 @@
<p>Function <code>oecosimu</code> already had <code>density</code> and
<code>densityplot</code>, but they are now similar to other <span class="pkg">vegan</span>
methods, and also work with <code>adipart</code>, <code>hiersimu</code> and
-<code>multipart</code>.
+<code>multipart</code>.
</p>
-</ul>
+</li>
+<li> <p><code>radfit</code> functions got a <code>predict</code> method that
+also accepts arguments <code>newdata</code> and <code>total</code> for new
+ranks and site totals for prediction. The functions can also
+interpolate to non-integer “ranks”, and in some models
+also extrapolate.
+</p>
+</li></ul>
@@ -57,7 +82,15 @@
care: Permutation tests can be biased if the missing values were
originally in matching or fixed positions.
</p>
-</ul>
+</li>
+<li> <p><code>radfit</code> results can be consistently accessed with
+the same methods whether they were a single model for a single
+site, all models for a single site or all models for all sites
+in the data. All functions now have methods <code>AIC</code>,
+<code>coef</code>, <code>deviance</code>, <code>logLik</code>, <code>fitted</code>,
+<code>predict</code> and <code>residuals</code>.
+</p>
+</li></ul>
@@ -76,7 +109,7 @@
<font face="Courier New,Courier" color="#666666"><b>R</b></font>. Internal changes in <font face="Courier New,Courier" color="#666666"><b>R</b></font> caused an error in
<code>betadisper</code>.
</p>
-</ul>
+</li></ul>
@@ -122,7 +155,7 @@
<code>capscale</code> results which do not need row weights.
Reported by Glenn De'ath.
</p>
-</ul>
+</li></ul>
@@ -192,7 +225,7 @@
<code>select</code> only some of the items for plotting. The
argument can be used only with one set of points.
</p>
-</ul>
+</li></ul>
@@ -229,7 +262,7 @@
<a href="https://github.com/jarioksa/vegan">GitHub</a>
by Eduard Szöcs (Uni Landau, Germany).
</p>
-</ul>
+</li></ul>
@@ -261,7 +294,7 @@
was reported as an error in <code>ordiplot</code> in
<a href="https://stat.ethz.ch/pipermail/r-sig-ecology/2012-February/002768.html">R-sig-ecology</a> mailing list.
</p>
-</ul>
+</li></ul>
@@ -302,7 +335,7 @@
intensity. Thanks to consultation to Yong Cao (Univ Illinois,
USA).
</p>
-</ul>
+</li></ul>
@@ -344,7 +377,7 @@
speed-up in the internal f.test() function is fully
realised. Reported by Nicholas Lewin-Koh.
</p>
-</ul>
+</li></ul>
@@ -364,7 +397,7 @@
are class centroids of each point, but for constrained ordination
with no <code>groups</code> they are the LC scores.
</p>
-</ul>
+</li></ul>
@@ -405,7 +438,7 @@
[<a href="http://www.esajournals.org/doi/abs/10.1890/ES10-00117.1">doi:10.1890/ES10-00117.1</a>],
and was developed with the consultation of Brian Inouye.
</p>
-</ul>
+</li></ul>
@@ -444,7 +477,7 @@
results but you probably wish to upgrade <span class="pkg">vegan</span> to avoid
annoying warnings.
</p>
-</ul>
+</li></ul>
@@ -459,7 +492,7 @@
showed that in most cases an improved ordering was found rather
early in tries, and the results are equally good in most cases.
</p>
-</ul>
+</li></ul>
@@ -495,7 +528,7 @@
<span class="pkg">permute</span>, but currently only <code>betadisper</code> uses the new
feature.
</p>
-</ul>
+</li></ul>
@@ -551,7 +584,7 @@
were implemented because they were found good for species-area
models by Dengler (<EM>J. Biogeogr.</EM> 36, 728-744; 2009).
</p>
-</ul>
+</li></ul>
@@ -593,7 +626,7 @@
the length of the <code>pool</code> matches the number of
observations.
</p>
-</ul>
+</li></ul>
@@ -612,7 +645,7 @@
was not intended for normal use, but packages depending on that
code in <span class="pkg">vegan</span> should instead depend on <span class="pkg">permute</span>.
</p>
-</ul>
+</li></ul>
@@ -625,7 +658,7 @@
<li> <p><code>treeheight</code> uses much snappier code. The results
should be unchanged.
</p>
-</ul>
+</li></ul>
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