[Vegan-commits] r1729 - pkg/vegan/inst

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

Author: jarioksa
Date: 2011-08-18 13:33:33 +0200 (Thu, 18 Aug 2011)
New Revision: 1729

Added:
   pkg/vegan/inst/NEWS.Rd
Removed:
   pkg/vegan/inst/NEWS
Modified:
   pkg/vegan/inst/ChangeLog
Log:
add NEWS.Rd for version 2.0-in-spe

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-08-18 08:56:45 UTC (rev 1728)
+++ pkg/vegan/inst/ChangeLog	2011-08-18 11:33:33 UTC (rev 1729)
@@ -8,6 +8,13 @@
 	2011. 
 
 	* NAMESPACE: export pasteCall for analogue.
+
+	* NEWS: added file NEWS.Rd for vegan release 2.0 news in Rd format.
+	Keeping neat formatting of this file may be challenging to many
+	text editors, but it is worth trying. This file should list the
+	important items for regular vegan users, whereas this ChangeLog
+	should explain the changes to other vegan developers. The
+	vegandocs() function is not yet adapted to the NEWS.Rd.
 	
 Version 1.91-0 (closed August 18, 2011)
 

Deleted: pkg/vegan/inst/NEWS
===================================================================
--- pkg/vegan/inst/NEWS	2011-08-18 08:56:45 UTC (rev 1728)
+++ pkg/vegan/inst/NEWS	2011-08-18 11:33:33 UTC (rev 1729)
@@ -1,3 +0,0 @@
-The NEWS are only available for the release versions of vegan: 
-This is a development version. Use vegandocs("ChangeLog") to see 
-changes in the development version.

Added: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd	                        (rev 0)
+++ pkg/vegan/inst/NEWS.Rd	2011-08-18 11:33:33 UTC (rev 1729)
@@ -0,0 +1,95 @@
+\name{NEWS}
+\title{vegan News}
+\encoding{UTF-8}
+
+\section{CHANGES IN VEGAN VERSION 2.0}{
+
+  \subsection{GENERAL}{
+    \itemize{
+
+      \item Peter Minchin joins the \pkg{vegan} team.
+
+      \item \pkg{vegan} implements standard \R \code{NAMESPACE}. In
+      general, \code{S3} methods are not exported which means that you
+      cannot directly use or see contents of functions like
+      \code{cca.default}, \code{plot.cca} or \code{anova.cca}. To use
+      these functions you should rely on \R delegation and simply use
+      \code{cca} and for its result objects use \code{plot} and
+      \code{anova} without suffix \code{.cca}. To see the contents of
+      the functión you can use \code{:::}, such as
+      \code{vegan:::cca.default}. This change may break packages,
+      documents or scripts that rely on non-exported names.
+
+      \item \pgk{vegan} depends on the \pkg{permute} package. This
+      package provides powerful tools for restricted permutation
+      schemes. All \pkg{vegan} permutation will gradually move to use
+      \pkg{permute}, but currently only \code{betadisper} uses the new
+      feature. 
+
+    }
+  } % end GENERAL
+  
+  \subsection{NEW FUNCTIONS}{
+    \itemize{
+
+      \item \code{monoMDS}: a new function for non-metric
+      multidimensional scaling (NMDS). This function replaces
+      \code{MASS::isoMDS} as the default method in \code{metaMDS}. Major
+      advantages of \code{monoMDS} is that it has so called
+      \sQuote{primary} or \sQuote{weak} tie treatment which means that
+      it can split tied observed dissimilarities.  \sQuote{Weak} tie
+      treatment improves ordination of heterogeneous data sets, because
+      maximum dissimilarities of \eqn{1} can be split. In addition to
+      global NMDS, \code{monoMDS} can perform local and hybrid NMDS and
+      metric MDS.  It can also handle missing and zero dissimilarities.
+      Moreover, \code{monoMDS} is faster than previous alternatives.
+      
+      \item \code{fitspecaccum} to fit non-linear regression models to
+      the species accumulation results from \code{specaccum}. The
+      function can use new self-starting species accumulation models in
+      \pkg{vegan} or other self-starting non-linear regression models in
+      \R such as \code{SSmicmen} for Michaelis-Menten models.
+
+      \item Self-starting non-linear species accumulation models
+      \code{SSarrhenius}, \code{SSgleason}, \code{SSgitay} and
+      \code{SSlomolino}. These can be used with \code{fitspecaccum} or
+      directly in non-linear regression with \code{nls}. 
+
+    }
+  } % end NEW FUNCTIONS
+
+  \subsection{NEW FEATURES}{
+    
+    \itemize{
+
+      \item \code{betadisper} uses restricted permutation of the
+      \pkg{permute} package. 
+      
+      \item \code{metaMDS} uses \code{monoMDS} as its default ordination
+      engine. Function gains new argument \code{engine} that can be used
+      to alternatively select \code{MASS::isoMDS}.  The default is not
+      to use \code{stepacross} with \code{monoMDS} because its
+      \sQuote{weak} tie treatment can cope with tied maximum
+      dissimilarities of one. However, \code{stepacross} is always used
+      with \code{isoMDS} because it cannot handle adequately these tied
+      maximum dissimilarities. 
+
+    }
+  } % end NEW FEATURES
+
+  \subsection{BUG FIXES}{
+    
+  } % end BUG FIXES
+
+  \subsection{ANALYSES}{
+    \itemize{
+
+      \item \code{treeheight} uses much snappier code. The results
+      should be unchanged.
+      
+    }
+
+  } % end ANALYSES
+    
+}% end VERSTION 2.0   
+