[Vegan-commits] r2226 - pkg/vegan/inst

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2012-07-07 16:16:47 +0200 (Sat, 07 Jul 2012)
New Revision: 2226

Modified:
   pkg/vegan/inst/NEWS.Rd
Log:
update to NEWS of the release 2.0-4

Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd	2012-06-19 13:57:52 UTC (rev 2225)
+++ pkg/vegan/inst/NEWS.Rd	2012-07-07 14:16:47 UTC (rev 2226)
@@ -2,6 +2,102 @@
 \title{vegan News}
 \encoding{UTF-8}
 
+\section{Changes in version 2.0-4}{
+
+  \subsection{BUG FIXES}{
+    \itemize{
+    
+      \item \code{adipart} assumed constant gamma diversity in
+        simulations when assessing the \eqn{P}-value.  This could give
+        biased results if the null model produces variable gamma
+        diversities and option \code{weights = "prop"} is used.  The
+        default null model (\code{"r2dtable"}) and the default option
+        (\code{weights = "unif"}) were analysed correctly.
+
+      \item \code{anova(<prc-object>, by = "axis")} and other
+        \code{by} cases failed due to \file{NAMESPACE} issues.
+
+      \item \code{clamtest} wrongly used frequencies instead of the
+        counts when calculating sample coverage.  No detectable
+        differences were produced when rerunning examples from Chazdon
+        et al. 2011 and \pkg{vegan} help page.
+
+      \item \code{envfit} failed with unused factor levels.
+
+      \item \code{predict} for \code{cca} results with \code{type =
+        "response"} or \code{type = "working"} failed with
+        \code{newdata} if the number of rows did not match with the
+        original data.  Now the \code{newdata} is ignored if it has a
+        wrong number of rows.  The number of rows must match because
+        the results in \code{cca} must be weighted by original row
+        totals.  The problem did not concern \code{rda} or
+        \code{capscale} results which do not need row weights.
+        Reported by Glenn De'ath.
+    
+    }
+  }% end bug fixes
+
+  \subsection{NEW FEATURES}{
+    \itemize{
+
+      \item Functions for diversity partitioning (\code{adipart},
+        \code{hiersimu} and \code{multipart}) have now \code{formula}
+        and \code{default} methods.  The \code{formula} method is
+        identical to the previous functions, but the \code{default}
+        method can take two matrices as input. 
+
+ 	Functions \code{adipart} and \code{multipart} can be used for
+ 	fast and easy overall partitioning to alpha, beta and gamma
+ 	diversities by omitting the argument describing the hierarchy.
+
+      \item The method in \code{betadisper} is biased with small
+        sample sizes.  The effects of the bias are strongest with
+        unequal sample sizes. A bias adjusted version was developed by
+        Adrian Stier and Ben Bolker, and can be invoked with argument
+        \code{bias.adjust} (defaults to \code{FALSE}).
+
+      \item \code{bioenv} accepts dissimilarities (or square matrices
+        that can be interpreted as dissimilarities) as an alternative to
+        community data.  This allows using other dissimilarities than
+        those available in \code{vegdist}.
+
+      \item \code{plot} function for \code{envfit} results gained new
+        argument \code{bg} that can be used to set background colour for
+        plotted labels.
+
+      \item \code{msoplot} is more configurable, and allows, for
+        instance, setting y-axis limits.
+
+      \item Hulls and ellipses are now filled using semitransparent
+        colours in \code{ordihull} and \code{ordiellipse}, and the
+        user can set the degree of transparency with a new argument
+        \code{alpha}.  The filled shapes are used when these functions
+        are called with argument \code{draw = "polygon"}.  Function
+        \code{ordihull} puts labels (with argument \code{label = TRUE})
+        now in the real polygon centre.
+
+      \item \code{ordiplot3d} returns function \code{envfit.convert}
+        and the projected location of the \code{origin}.  Together
+        these can be used to add \code{envfit} results to existing
+        \code{ordiplot3d} plots.
+
+        Equal aspect ratio cannot be set exactly in \code{ordiplot3d}
+        because underlying core routines do not allow this. Now
+        \code{ordiplot3d} sets equal axis ranges, and the documents
+        urge users to verify that the aspect ratio is reasonably equal
+        and the graph looks like a cube.  If the problems cannot be
+        solved in the future, \code{ordiplot3d} may be removed from
+        next releases of \pkg{vegan}.
+
+      \item Function \code{ordipointlabel} gained argument to
+        \code{select} only some of the items for plotting. The
+        argument can be used only with one set of points.
+
+    }
+  } % end new features 	 
+
+}%end version 2.0-4
+
 \section{Changes in version 2.0-3}{
 
   \subsection{NEW FUNCTIONS}{