[Vegan-commits] r2483 - branches branches/2.0 branches/2.0/inst pkg/vegan/inst

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

Author: jarioksa
Date: 2013-03-19 15:22:26 +0100 (Tue, 19 Mar 2013)
New Revision: 2483

Modified:
   branches/2.0/DESCRIPTION
   branches/2.0/inst/ChangeLog
   branches/vegan_releases.txt
   pkg/vegan/inst/NEWS.Rd
Log:
vegan 2.0-7 released to CRAN

Modified: branches/2.0/DESCRIPTION
===================================================================
--- branches/2.0/DESCRIPTION	2013-03-19 09:34:36 UTC (rev 2482)
+++ branches/2.0/DESCRIPTION	2013-03-19 14:22:26 UTC (rev 2483)
@@ -1,6 +1,6 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 2.0-7
+Version: 2.0-8
 Date: March 19, 2013
 Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, 
    Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, 

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2013-03-19 09:34:36 UTC (rev 2482)
+++ branches/2.0/inst/ChangeLog	2013-03-19 14:22:26 UTC (rev 2483)
@@ -2,8 +2,14 @@
 
 VEGAN RELEASE VERSIONS at http://cran.r-project.org/
 
-Version 2.0-7 (opened February 17, 2013)
+Version 2.0-8 (opened March 19, 2013)
 
+	* version 2.0-7 may be the last release in 2.0 series, and the
+	next release version may be a major upgrade 2.2-0 (this
+	information may change if there is a need for a 2.0 release).
+	
+Version 2.0-7 (released March 19, 2013)
+
 	* merge r2476: take back part of 2434 and return matrix from
 	wcmdscale unless eigenvalues are requested.
 	* merge r2469, 2470: do not use u.eig & v.eig.

Modified: branches/vegan_releases.txt
===================================================================
--- branches/vegan_releases.txt	2013-03-19 09:34:36 UTC (rev 2482)
+++ branches/vegan_releases.txt	2013-03-19 14:22:26 UTC (rev 2483)
@@ -13,6 +13,7 @@
 
 vegan release: revision (date) directory at vegan-forge
 
+2.0-7:   r2482 (Tue, 19 Mar 2013) branches/2.0
 2.0-6:   r2429 (Mon, 11 Feb 2013) branches/2.0
 2.0-5:   r2315 (Mon, 8 Oct 2012)  branches/2.0
 2.0-4:	 r2222 (Mon, 18 Jun 2012) branches/2.0

Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd	2013-03-19 09:34:36 UTC (rev 2482)
+++ pkg/vegan/inst/NEWS.Rd	2013-03-19 14:22:26 UTC (rev 2483)
@@ -2,6 +2,69 @@
 \title{vegan News}
 \encoding{UTF-8}
 
+\section{Changes in version 2.0.7}{
+
+  \subsection{NEW FUNCTIONS}{
+    \itemize{
+
+      \item \code{tabasco()} is a new function for graphical display
+      of community data matrix.  Technically it is an interface to \R
+      \code{heatmap}, but its use is closer to \pkg{vegan} function
+      \code{vegemite}. The function can reorder the community data
+      matrix similarly as \code{vegemite}, for instance, by ordination
+      results. Unlike \code{heatmap}, it only displays dendrograms if
+      supplied by the user, and it defaults to re-order the
+      dendrograms by correspondence analysis.  Species are ordered to
+      match site ordering or like determined by the user.
+
+    }
+  } % new functions
+
+  \subsection{BUG FIXES}{
+    \itemize{
+
+      \item Function \code{fitspecaccum(..., model = "asymp")} fitted
+      logistic model instead of asymptotic model (or the same as 
+      \code{model = "logis"}).
+
+      \item \code{nestedtemp()} failed with very sparse data (fill
+      \eqn{< 0.38}\%).
+
+    }
+  } % bug fixes 
+
+  \subsection{NEW FEATURES}{
+    \itemize{
+
+      \item The \code{plot} function for constrained ordination
+      results (\code{cca}, \code{rda}, \code{capscale}) gained
+      argument \code{axis.bp} (defaults \code{TRUE}) which can be used
+      to suppress axis scale for biplot arrays.
+
+      \item Number of iterations in nonmetric multidimensional scaling
+      (NMDS) can be set with keyword \code{maxit} (defaults
+      \code{200}) in \code{metaMDS}.
+
+    }
+  } % new features
+
+  \subsection{DEPRECATED}{
+
+    \itemize{
+
+      \item The result objects of \code{cca}, \code{rda} and
+      \code{capscale} will no longer have scores \code{u.eig},
+      \code{v.eig} and \code{wa.eig} in the future versions of
+      \pkg{vegan}. This change does not influence normal usage,
+      because \pkg{vegan} functions do not need these items.  However,
+      external scripts and packages may need changes in the future
+      versions of \pkg{vegan}.
+
+    }   
+  } % deprecated
+
+} % vegan 2.0-7
+
 \section{Changes in version 2.0-6}{
 
   \subsection{BUG FIXES}{