[Vegan-commits] r1730 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2011-08-18 15:48:10 +0200 (Thu, 18 Aug 2011)
New Revision: 1730

Modified:
   pkg/vegan/R/vegandocs.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/inst/NEWS.Rd
Log:
vegandocs shows NEWS

Modified: pkg/vegan/R/vegandocs.R
===================================================================
--- pkg/vegan/R/vegandocs.R	2011-08-18 11:33:33 UTC (rev 1729)
+++ pkg/vegan/R/vegandocs.R	2011-08-18 13:48:10 UTC (rev 1730)
@@ -1,4 +1,4 @@
-"vegandocs" <-
+`vegandocs` <-
     function (doc = c("NEWS", "ChangeLog", "FAQ-vegan.pdf", "intro-vegan.pdf",
               "diversity-vegan.pdf", "decision-vegan.pdf",
               "partitioning.pdf")) 
@@ -9,8 +9,9 @@
         if (.Platform$OS.type == "windows")
             shell.exec(doc)
         else system(paste(getOption("pdfviewer"), doc, "&"))
-    }
-    else {
+    } else if (doc == "NEWS") {
+        file.show(Rd2txt(file.path(path.package("vegan"), "NEWS.Rd"), tempfile()))
+    } else {
         file.show(system.file(package="vegan", doc))
     } 
 }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-08-18 11:33:33 UTC (rev 1729)
+++ pkg/vegan/inst/ChangeLog	2011-08-18 13:48:10 UTC (rev 1730)
@@ -13,8 +13,10 @@
 	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.
+	should explain the changes to other vegan developers. vegandocs()
+	uses a kluge to show the text formatted NEWS file -- I really do
+	not understand why R core decided to use NEWS format that is not
+	intended to be human readable but is very difficult to access. 
 	
 Version 1.91-0 (closed August 18, 2011)
 

Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd	2011-08-18 11:33:33 UTC (rev 1729)
+++ pkg/vegan/inst/NEWS.Rd	2011-08-18 13:48:10 UTC (rev 1730)
@@ -2,13 +2,13 @@
 \title{vegan News}
 \encoding{UTF-8}
 
-\section{CHANGES IN VEGAN VERSION 2.0}{
+\section{CHANGES IN VEGAN VERSION 2.0 beta}{
 
   \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
@@ -19,19 +19,19 @@
       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
+      
+      \item \pkg{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
@@ -49,19 +49,19 @@
       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. 
       
@@ -73,17 +73,17 @@
       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.