[Vegan-commits] r2384 - pkg/vegan/inst/doc www

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Jan 22 18:55:06 CET 2013 

Author: jarioksa
Date: 2013-01-22 18:55:06 +0100 (Tue, 22 Jan 2013)
New Revision: 2384

Modified:
   pkg/vegan/inst/doc/FAQ-vegan.texi
   www/FAQ-vegan.html
Log:
new FAQ entries: Mac usage, finding ordination scores

Modified: pkg/vegan/inst/doc/FAQ-vegan.texi
===================================================================
--- pkg/vegan/inst/doc/FAQ-vegan.texi	2013-01-21 12:56:26 UTC (rev 2383)
+++ pkg/vegan/inst/doc/FAQ-vegan.texi	2013-01-22 17:55:06 UTC (rev 2384)
@@ -81,6 +81,7 @@
 * How to cite @pkg{vegan}?::    
 * How to build @pkg{vegan} from sources?::  
 * Are there binaries for devel versions?::  
+* Can I use @pkg{vegan} in Mac?::  
 * How to report a bug in @pkg{vegan}?::  
 * Is it a bug or a feature?::   
 * Can I contribute to @pkg{vegan}?::  
@@ -231,7 +232,7 @@
 and you need appropriate compilers (which may need more work in Windows
 and MacOS X).
 
- at node Are there binaries for devel versions?, How to report a bug in @pkg{vegan}?, How to build @pkg{vegan} from sources?, Introduction
+ at node Are there binaries for devel versions?, Can I use @pkg{vegan} in Mac?, How to build @pkg{vegan} from sources?, Introduction
 @section Are there binaries for devel versions?
 
 @uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge} runs daily
@@ -242,7 +243,20 @@
 If you use GUI menu entry, you must select or define the R-Forge
 repository. 
 
- at node How to report a bug in @pkg{vegan}?, Is it a bug or a feature?, Are there binaries for devel versions?, Introduction
+ at node Can I use @pkg{vegan} in Mac?, How to report a bug in @pkg{vegan}?, Are there binaries for devel versions?, Introduction
+ at section Can I use @pkg{vegan} in Mac?
+
+Yes, you can, and @pkg{vegan} binaries are available for Mac through
+ at uref{http://cran.r-project.org,,CRAN}. However, in some cases you may
+need to install extra tools packages available in
+ at uref{http://cran.r-project.org/bin/macosx/tools/,,MacOS tools} pages:
+If you use function such as @code{orditkplot} that need @code{Tcl/Tk}
+you may need to install @code{tcltk} package.  If you use @pkg{vegan}
+binaries from other places than from
+ at uref{http://cran.r-project.org,,CRAN}, you may also need to install
+ at code{gfortran} package.
+
+ at node How to report a bug in @pkg{vegan}?, Is it a bug or a feature?, Can I use @pkg{vegan} in Mac?, Introduction
 @section How to report a bug in @pkg{vegan}?
 
 If you think you have found a bug in @pkg{vegan}, you should report it to
@@ -317,6 +331,7 @@
 * I get zero stress but no convergent solutions in @code{metaMDS}::  
 * Zero dissimilarities in isoMDS::  
 * I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores::  
+* Where can I find numerical scores of ordination axes?::  
 * How the RDA results are scaled?::  
 * cca fails with ``data.frame expected'' or ``"site.env" missing''::  
 * Variance explained by ordination axes::  
@@ -423,7 +438,7 @@
 the kluge (or work harder with your data). Usually it is better to use
 @code{monoMDS}.
 
- at node I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores, How the RDA results are scaled?, Zero dissimilarities in isoMDS, Ordination
+ at node I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores, Where can I find numerical scores of ordination axes?, Zero dissimilarities in isoMDS, Ordination
 @section I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores
 
 Claims like this have indeed been at large in the Internet, but they are
@@ -437,9 +452,22 @@
 are strictly Euclidean, it is correct to use @pkg{vegan} functions
 @code{envfit} and @code{ordisurf} with @acronym{NMDS} results.
 
+ at node Where can I find numerical scores of ordination axes?, How the RDA results are scaled?, I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores, Ordination
+ at section Where can I find numerical scores of ordination axes?
 
+Normally you can use function @code{scores} to extract ordination scores
+for any ordination method. The @code{scores} function can also find
+ordination scores for many non- at pkg{vegan} functions such as for
+ at code{prcomp} and @code{princomp} and for some @pkg{ade4} functions.
 
- at node How the RDA results are scaled?, cca fails with ``data.frame expected'' or ``"site.env" missing'', I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores, Ordination
+In some cases the ordination result object stores raw scores, and
+the axes are also scaled appropriate when you access them with
+ at code{scores}.  For instance, in @code{cca} and @code{rda} the
+ordination object has only so-called normalized scores, and they are
+scaled for ordination plots or for other use when they are accessed with
+ at code{scores}. 
+
+ at node How the RDA results are scaled?, cca fails with ``data.frame expected'' or ``"site.env" missing'', Where can I find numerical scores of ordination axes?, Ordination
 @section How the @acronym{RDA} results are scaled?
 
 The scaling or @acronym{RDA} results indeed differ from most other

Modified: www/FAQ-vegan.html
===================================================================
--- www/FAQ-vegan.html	2013-01-21 12:56:26 UTC (rev 2383)
+++ www/FAQ-vegan.html	2013-01-22 17:55:06 UTC (rev 2384)
@@ -1,9 +1,10 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html401/loose.dtd">
 <html>
-<!-- This document contains answers to some of the most frequently asked
+<!--This document contains answers to some of the most frequently asked
 questions about R package vegan. 
-This is version of $Date: 2012-05-27 18:10:14 +0300 (Sun, 27 May 2012) $.
+This is version of $Date: 2013-01-07 12:58:43 +0200 (Mon, 07 Jan 2013) $.
 
+
 This work is licensed under the Creative Commons Attribution 3.0
 License. To view a copy of this license, visit
 http://creativecommons.org/licenses/by/3.0/ or send a letter to
@@ -12,29 +13,29 @@
 
 Copyright C 2008-2012 Jari Oksanen
 
- -->
-<!-- Created on January 7, 2013 by texi2html 1.82
-texi2html was written by: 
-            Lionel Cons <Lionel.Cons at cern.ch> (original author)
+-->
+<!-- Created on January, 22 2013 by texi2html 1.70 -->
+<!--
+Written by: Lionel Cons <Lionel.Cons at cern.ch> (original author)
             Karl Berry  <karl at freefriends.org>
             Olaf Bachmann <obachman at mathematik.uni-kl.de>
             and many others.
-Maintained by: Many creative people.
-Send bugs and suggestions to <texi2html-bug at nongnu.org>
+Maintained by: Many creative people <dev at texi2html.cvshome.org>
+Send bugs and suggestions to <users at texi2html.cvshome.org>
+
 -->
 <head>
-<title>vegan FAQ</title>
+<title>vegan FAQ: vegan FAQ</title>
 
-<meta name="description" content="vegan FAQ">
-<meta name="keywords" content="vegan FAQ">
+<meta name="description" content="vegan FAQ: vegan FAQ">
+<meta name="keywords" content="vegan FAQ: vegan FAQ">
 <meta name="resource-type" content="document">
 <meta name="distribution" content="global">
-<meta name="Generator" content="texi2html 1.82">
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<meta name="Generator" content="texi2html 1.70">
+<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
 <style type="text/css">
 <!--
 a.summary-letter {text-decoration: none}
-blockquote.smallquotation {font-size: smaller}
 pre.display {font-family: serif}
 pre.format {font-family: serif}
 pre.menu-comment {font-family: serif}
@@ -43,8 +44,6 @@
 pre.smallexample {font-size: smaller}
 pre.smallformat {font-family: serif; font-size: smaller}
 pre.smalllisp {font-size: smaller}
-span.roman {font-family:serif; font-weight:normal;}
-span.sansserif {font-family:sans-serif; font-weight:normal;}
 ul.toc {list-style: none}
 -->
 </style>
@@ -54,112 +53,116 @@
 
 <body lang="en" bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#800080" alink="#FF0000">
 
-<a name="Top"></a>
+<a name="NOD1"></a>
+<a name="SEC_Top"></a>
 <table cellpadding="1" cellspacing="1" border="0">
-<tr><td valign="middle" align="left">[<a href="#Top" title="Cover (top) of document">Top</a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
 <td valign="middle" align="left">[Contents]</td>
 <td valign="middle" align="left">[Index]</td>
 <td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
 </tr></table>
-<a name="vegan-FAQ"></a>
 <h1 class="settitle"><strong>vegan</strong> FAQ</h1>
 <p>This document contains answers to some of the most frequently asked
 questions about R package <strong>vegan</strong>. 
-This is version of $Date: 2012-05-27 18:10:14 +0300 (Sun, 27 May 2012) $.
-</p>
-<blockquote><p>This work is licensed under the Creative Commons Attribution 3.0
+This is version of $Date: 2013-01-07 12:58:43 +0200 (Mon, 07 Jan 2013) $.
+
+</p><blockquote>
+<p>This work is licensed under the Creative Commons Attribution 3.0
 License. To view a copy of this license, visit
 <a href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</a> or send a letter to
 Creative Commons, 543 Howard Street, 5th Floor, San Francisco,
 California, 94105, USA.
-</p>
-<p>Copyright © 2008-2012 Jari Oksanen
+
+</p><p>Copyright © 2008-2012 Jari Oksanen
 </p></blockquote>
 
 
 
 
+
 <table class="menu" border="0" cellspacing="0">
-<tr><td align="left" valign="top"><a href="#Introduction">1. Introduction</a></td><td>  </td><td align="left" valign="top">                
+<tr><td align="left" valign="top"><a href="#SEC1">1. Introduction</a></td><td>  </td><td align="left" valign="top">                
 </td></tr>
-<tr><td align="left" valign="top"><a href="#Ordination">2. Ordination</a></td><td>  </td><td align="left" valign="top">                  
+<tr><td align="left" valign="top"><a href="#SEC17">2. Ordination</a></td><td>  </td><td align="left" valign="top">                  
 </td></tr>
-<tr><td align="left" valign="top"><a href="#Other-analysis-methods">3. Other analysis methods</a></td><td>  </td><td align="left" valign="top">     
+<tr><td align="left" valign="top"><a href="#SEC40">3. Other analysis methods</a></td><td>  </td><td align="left" valign="top">     
 </td></tr>
 </table>
 
 <hr size="1">
-<a name="Introduction"></a>
+<a name="NOD2"></a>
+<a name="SEC1"></a>
 <table cellpadding="1" cellspacing="1" border="0">
-<tr><td valign="middle" align="left">[<a href="#Top" title="Previous section in reading order"> < </a>]</td>
-<td valign="middle" align="left">[<a href="#What-is-vegan_003f" title="Next section in reading order"> > </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC_Top" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC2" title="Next section in reading order"> > </a>]</td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Top" title="Beginning of this chapter or previous chapter"> << </a>]</td>
-<td valign="middle" align="left">[<a href="#Top" title="Up section"> Up </a>]</td>
-<td valign="middle" align="left">[<a href="#Ordination" title="Next chapter"> >> </a>]</td>
+<td valign="middle" align="left">[ << ]</td>
+<td valign="middle" align="left">[<a href="#SEC_Top" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC17" title="Next chapter"> >> </a>]</td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
 <td valign="middle" align="left">[Contents]</td>
 <td valign="middle" align="left">[Index]</td>
 <td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
 </tr></table>
-<a name="Introduction-1"></a>
-<h1 class="chapter">1. Introduction</h1>
+<h1 class="chapter"> 1. Introduction </h1>
 
 <table class="menu" border="0" cellspacing="0">
-<tr><td align="left" valign="top"><a href="#What-is-vegan_003f">1.1 What is <strong>vegan</strong>?</a></td><td>  </td><td align="left" valign="top">        
+<tr><td align="left" valign="top"><a href="#SEC2">1.1 What is <strong>vegan</strong>?</a></td><td>  </td><td align="left" valign="top">        
 </td></tr>
-<tr><td align="left" valign="top"><a href="#What-is-R_003f">1.2 What is R?</a></td><td>  </td><td align="left" valign="top">                  
+<tr><td align="left" valign="top"><a href="#SEC3">1.2 What is R?</a></td><td>  </td><td align="left" valign="top">                  
 </td></tr>
-<tr><td align="left" valign="top"><a href="#How-to-obtain-vegan-and-R_003f">1.3 How to obtain <strong>vegan</strong> and R?</a></td><td>  </td><td align="left" valign="top">  
+<tr><td align="left" valign="top"><a href="#SEC4">1.3 How to obtain <strong>vegan</strong> and R?</a></td><td>  </td><td align="left" valign="top">  
 </td></tr>
-<tr><td align="left" valign="top"><a href="#What-R-packages-vegan-depends-on_003f">1.4 What R packages <strong>vegan</strong> depends on?</a></td><td>  </td><td align="left" valign="top">  
+<tr><td align="left" valign="top"><a href="#SEC5">1.4 What R packages <strong>vegan</strong> depends on?</a></td><td>  </td><td align="left" valign="top">  
 </td></tr>
-<tr><td align="left" valign="top"><a href="#What-other-packages-are-available-for-ecologists_003f">1.5 What other packages are available for ecologists?</a></td><td>  </td><td align="left" valign="top">  
+<tr><td align="left" valign="top"><a href="#SEC6">1.5 What other packages are available for ecologists?</a></td><td>  </td><td align="left" valign="top">  
 </td></tr>
-<tr><td align="left" valign="top"><a href="#What-other-documentation-is-available-for-vegan_003f">1.6 What other documentation is available for <strong>vegan</strong>?</a></td><td>  </td><td align="left" valign="top">  
+<tr><td align="left" valign="top"><a href="#SEC7">1.6 What other documentation is available for <strong>vegan</strong>?</a></td><td>  </td><td align="left" valign="top">  
 </td></tr>
-<tr><td align="left" valign="top"><a href="#Is-there-a-Graphical-User-Interface-_0028GUI_0029-for-vegan_003f">1.7 Is there a Graphical User Interface (GUI) for <strong>vegan</strong>?</a></td><td>  </td><td align="left" valign="top">  
+<tr><td align="left" valign="top"><a href="#SEC8">1.7 Is there a Graphical User Interface (GUI) for <strong>vegan</strong>?</a></td><td>  </td><td align="left" valign="top">  
 </td></tr>
-<tr><td align="left" valign="top"><a href="#How-to-cite-vegan_003f">1.8 How to cite <strong>vegan</strong>?</a></td><td>  </td><td align="left" valign="top">    
+<tr><td align="left" valign="top"><a href="#SEC9">1.8 How to cite <strong>vegan</strong>?</a></td><td>  </td><td align="left" valign="top">    
 </td></tr>
-<tr><td align="left" valign="top"><a href="#How-to-build-vegan-from-sources_003f">1.9 How to build <strong>vegan</strong> from sources?</a></td><td>  </td><td align="left" valign="top">  
+<tr><td align="left" valign="top"><a href="#SEC10">1.9 How to build <strong>vegan</strong> from sources?</a></td><td>  </td><td align="left" valign="top">  
 </td></tr>
-<tr><td align="left" valign="top"><a href="#Are-there-binaries-for-devel-versions_003f">1.10 Are there binaries for devel versions?</a></td><td>  </td><td align="left" valign="top">  
+<tr><td align="left" valign="top"><a href="#SEC11">1.10 Are there binaries for devel versions?</a></td><td>  </td><td align="left" valign="top">  
 </td></tr>
-<tr><td align="left" valign="top"><a href="#How-to-report-a-bug-in-vegan_003f">1.11 How to report a bug in <strong>vegan</strong>?</a></td><td>  </td><td align="left" valign="top">  
+<tr><td align="left" valign="top"><a href="#SEC12">1.11 Can I use <strong>vegan</strong> in Mac?</a></td><td>  </td><td align="left" valign="top">  
 </td></tr>
-<tr><td align="left" valign="top"><a href="#Is-it-a-bug-or-a-feature_003f">1.12 Is it a bug or a feature?</a></td><td>  </td><td align="left" valign="top">   
+<tr><td align="left" valign="top"><a href="#SEC13">1.12 How to report a bug in <strong>vegan</strong>?</a></td><td>  </td><td align="left" valign="top">  
 </td></tr>
-<tr><td align="left" valign="top"><a href="#Can-I-contribute-to-vegan_003f">1.13 Can I contribute to <strong>vegan</strong>?</a></td><td>  </td><td align="left" valign="top">  
+<tr><td align="left" valign="top"><a href="#SEC14">1.13 Is it a bug or a feature?</a></td><td>  </td><td align="left" valign="top">   
 </td></tr>
-<tr><td align="left" valign="top"><a href="#Can-I-have-write-access-to-vegan-repository_003f">1.14 Can I have write access to <strong>vegan</strong> repository?</a></td><td>  </td><td align="left" valign="top">  
+<tr><td align="left" valign="top"><a href="#SEC15">1.14 Can I contribute to <strong>vegan</strong>?</a></td><td>  </td><td align="left" valign="top">  
 </td></tr>
+<tr><td align="left" valign="top"><a href="#SEC16">1.15 Can I have write access to <strong>vegan</strong> repository?</a></td><td>  </td><td align="left" valign="top">  
+</td></tr>
 </table>
 
 <hr size="6">
-<a name="What-is-vegan_003f"></a>
+<a name="NOD3"></a>
+<a name="SEC2"></a>
 <table cellpadding="1" cellspacing="1" border="0">
-<tr><td valign="middle" align="left">[<a href="#Introduction" title="Previous section in reading order"> < </a>]</td>
-<td valign="middle" align="left">[<a href="#What-is-R_003f" title="Next section in reading order"> > </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC1" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC3" title="Next section in reading order"> > </a>]</td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Beginning of this chapter or previous chapter"> << </a>]</td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Up section"> Up </a>]</td>
-<td valign="middle" align="left">[<a href="#Ordination" title="Next chapter"> >> </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Beginning of this chapter or previous chapter"> << </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC17" title="Next chapter"> >> </a>]</td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
 <td valign="middle" align="left">[Contents]</td>
 <td valign="middle" align="left">[Index]</td>
 <td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
 </tr></table>
-<a name="What-is-vegan_003f-1"></a>
-<h2 class="section">1.1 What is <strong>vegan</strong>?</h2>
+<h2 class="section"> 1.1 What is <strong>vegan</strong>? </h2>
 
 <p><strong>Vegan</strong> is an R package for community ecologists. It contains the most
 popular methods of multivariate analysis needed in analysing ecological
@@ -168,96 +171,96 @@
 R statistical environment, and it also depends on many other R
 packages. <strong>Vegan</strong> is <a href="http://www.gnu.org/philosophy/free-sw.html">free software</a> and distributed under
 <a href="http://www.gnu.org/licenses/gpl.html">GPL2 license</a>.
-</p>
-<hr size="6">
-<a name="What-is-R_003f"></a>
+
+</p><hr size="6">
+<a name="NOD4"></a>
+<a name="SEC3"></a>
 <table cellpadding="1" cellspacing="1" border="0">
-<tr><td valign="middle" align="left">[<a href="#What-is-vegan_003f" title="Previous section in reading order"> < </a>]</td>
-<td valign="middle" align="left">[<a href="#How-to-obtain-vegan-and-R_003f" title="Next section in reading order"> > </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC2" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC4" title="Next section in reading order"> > </a>]</td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Beginning of this chapter or previous chapter"> << </a>]</td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Up section"> Up </a>]</td>
-<td valign="middle" align="left">[<a href="#Ordination" title="Next chapter"> >> </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Beginning of this chapter or previous chapter"> << </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC17" title="Next chapter"> >> </a>]</td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
 <td valign="middle" align="left">[Contents]</td>
 <td valign="middle" align="left">[Index]</td>
 <td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
 </tr></table>
-<a name="What-is-R_003f-1"></a>
-<h2 class="section">1.2 What is R?</h2>
+<h2 class="section"> 1.2 What is R? </h2>
 
 <p>R is a system for statistical computation and graphics.  It consists of
 a language plus a run-time environment with graphics, a debugger, access
 to certain system functions, and the ability to run programs stored in
 script files.
-</p>
-<p>R has a home page at <a href="http://www.R-project.org/">http://www.R-project.org/</a>.  It is
+
+</p><p>R has a home page at <a href="http://www.R-project.org/">http://www.R-project.org/</a>.  It is
 <a href="http://www.gnu.org/philosophy/free-sw.html">free software</a>
-distributed under a <acronym>GNU</acronym>-style
+distributed under a GNU-style
 <a href="http://www.gnu.org/copyleft/copyleft.html">copyleft</a>, and an
-official part of the <a href="http://www.gnu.org/"><acronym>GNU</acronym></a> project
-(“<acronym>GNU</acronym> S”).
-</p>
-<hr size="6">
-<a name="How-to-obtain-vegan-and-R_003f"></a>
+official part of the <a href="http://www.gnu.org/">GNU</a> project
+("GNU S").
+
+</p><hr size="6">
+<a name="NOD5"></a>
+<a name="SEC4"></a>
 <table cellpadding="1" cellspacing="1" border="0">
-<tr><td valign="middle" align="left">[<a href="#What-is-R_003f" title="Previous section in reading order"> < </a>]</td>
-<td valign="middle" align="left">[<a href="#What-R-packages-vegan-depends-on_003f" title="Next section in reading order"> > </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC3" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC5" title="Next section in reading order"> > </a>]</td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Beginning of this chapter or previous chapter"> << </a>]</td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Up section"> Up </a>]</td>
-<td valign="middle" align="left">[<a href="#Ordination" title="Next chapter"> >> </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Beginning of this chapter or previous chapter"> << </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC17" title="Next chapter"> >> </a>]</td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
 <td valign="middle" align="left">[Contents]</td>
 <td valign="middle" align="left">[Index]</td>
 <td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
 </tr></table>
-<a name="How-to-obtain-vegan-and-R_003f-1"></a>
-<h2 class="section">1.3 How to obtain <strong>vegan</strong> and R?</h2>
+<h2 class="section"> 1.3 How to obtain <strong>vegan</strong> and R? </h2>
 
 <p>Both R and latest release version of <strong>vegan</strong> can be obtained through
 <a href="http://cran.r-project.org">CRAN</a>. Unstable development version of
 <strong>vegan</strong> can be obtained through
 <a href="http://r-forge.r-project.org/projects/vegan/">R-Forge</a>.
+
 </p>
 
-
 <hr size="6">
-<a name="What-R-packages-vegan-depends-on_003f"></a>
+<a name="NOD6"></a>
+<a name="SEC5"></a>
 <table cellpadding="1" cellspacing="1" border="0">
-<tr><td valign="middle" align="left">[<a href="#How-to-obtain-vegan-and-R_003f" title="Previous section in reading order"> < </a>]</td>
-<td valign="middle" align="left">[<a href="#What-other-packages-are-available-for-ecologists_003f" title="Next section in reading order"> > </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC4" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC6" title="Next section in reading order"> > </a>]</td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Beginning of this chapter or previous chapter"> << </a>]</td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Up section"> Up </a>]</td>
-<td valign="middle" align="left">[<a href="#Ordination" title="Next chapter"> >> </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Beginning of this chapter or previous chapter"> << </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC17" title="Next chapter"> >> </a>]</td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
 <td valign="middle" align="left">[Contents]</td>
 <td valign="middle" align="left">[Index]</td>
 <td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
 </tr></table>
-<a name="What-R-packages-vegan-depends-on_003f-1"></a>
-<h2 class="section">1.4 What R packages <strong>vegan</strong> depends on?</h2>
+<h2 class="section"> 1.4 What R packages <strong>vegan</strong> depends on? </h2>
 
 <p><strong>Vegan</strong> depends on the <strong>permute</strong> package which will provide
 advanced and flexible permutation routines for vegan (but currently only
 a small part of functions use <strong>permute</strong>). The <strong>permute</strong> package
 is developed together with <strong>vegan</strong> in
 <a href="http://vegan.r-forge.r-project.org/">R-Forge</a>. 
-</p>
-<p>Some individual <strong>vegan</strong> functions depend on packages <strong>MASS</strong>,
+
+</p><p>Some individual <strong>vegan</strong> functions depend on packages <strong>MASS</strong>,
 <strong>mgcv</strong>, <strong>cluster</strong>, <strong>lattice</strong> and <strong>tcltk</strong>.  These all are
 base or recommended R packages that should be available in every R
 installation.  In addition, some <strong>vegan</strong> functions <code>require</code>
@@ -265,62 +268,62 @@
 suggested ones, and you can install <strong>vegan</strong> and use most of its
 functions without these packages.  The non-standard packages needed by
 some <strong>vegan</strong> functions are:
-</p><ul>
-<li> Package <strong>scatterplot3d</strong>
+</p><ul class="toc">
+<li><p> Package <strong>scatterplot3d</strong>
 is needed by <code>ordiplot3d</code>
 
-</li><li> Package <strong>rgl</strong>
+</p></li><li><p> Package <strong>rgl</strong>
 is needed by <code>ordirgl</code>
 and <code>rgl.isomap</code>
 
-</li></ul>
+</p></li></ul>
 
 <hr size="6">
-<a name="What-other-packages-are-available-for-ecologists_003f"></a>
+<a name="NOD7"></a>
+<a name="SEC6"></a>
 <table cellpadding="1" cellspacing="1" border="0">
-<tr><td valign="middle" align="left">[<a href="#What-R-packages-vegan-depends-on_003f" title="Previous section in reading order"> < </a>]</td>
-<td valign="middle" align="left">[<a href="#What-other-documentation-is-available-for-vegan_003f" title="Next section in reading order"> > </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC5" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC7" title="Next section in reading order"> > </a>]</td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Beginning of this chapter or previous chapter"> << </a>]</td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Up section"> Up </a>]</td>
-<td valign="middle" align="left">[<a href="#Ordination" title="Next chapter"> >> </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Beginning of this chapter or previous chapter"> << </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC17" title="Next chapter"> >> </a>]</td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
 <td valign="middle" align="left">[Contents]</td>
 <td valign="middle" align="left">[Index]</td>
 <td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
 </tr></table>
-<a name="What-other-packages-are-available-for-ecologists_003f-1"></a>
-<h2 class="section">1.5 What other packages are available for ecologists?</h2>
+<h2 class="section"> 1.5 What other packages are available for ecologists? </h2>
 
-<p><acronym>CRAN</acronym> <a href="http://cran.r-project.org/src/contrib/Views/">Task Views</a> include entries like <code>Environmetrics</code>, <code>Multivariate</code>
+<p>CRAN <a href="http://cran.r-project.org/src/contrib/Views/">Task Views</a> include entries like <code>Environmetrics</code>, <code>Multivariate</code>
 and <code>Spatial</code> that describe several useful packages and functions.
 If you install R package <strong>ctv</strong>, you can inspect Task Views from your
 R session, and automatically install sets of most important packages.
-</p>
-<hr size="6">
-<a name="What-other-documentation-is-available-for-vegan_003f"></a>
+
+</p><hr size="6">
+<a name="NOD8"></a>
+<a name="SEC7"></a>
 <table cellpadding="1" cellspacing="1" border="0">
-<tr><td valign="middle" align="left">[<a href="#What-other-packages-are-available-for-ecologists_003f" title="Previous section in reading order"> < </a>]</td>
-<td valign="middle" align="left">[<a href="#Is-there-a-Graphical-User-Interface-_0028GUI_0029-for-vegan_003f" title="Next section in reading order"> > </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC6" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC8" title="Next section in reading order"> > </a>]</td>
 <td valign="middle" align="left">   </td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Beginning of this chapter or previous chapter"> << </a>]</td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Up section"> Up </a>]</td>
-<td valign="middle" align="left">[<a href="#Ordination" title="Next chapter"> >> </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Beginning of this chapter or previous chapter"> << </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Up section"> Up </a>]</td>
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/vegan -r 2384

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