[Vegan-commits] r2007 - pkg/vegan/inst/doc www

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Nov 17 18:50:15 CET 2011


Author: jarioksa
Date: 2011-11-17 18:50:15 +0100 (Thu, 17 Nov 2011)
New Revision: 2007

Modified:
   pkg/vegan/inst/doc/FAQ-vegan.texi
   www/FAQ-vegan.html
Log:
futher FAQ clarification on arrow scaling

Modified: pkg/vegan/inst/doc/FAQ-vegan.texi
===================================================================
--- pkg/vegan/inst/doc/FAQ-vegan.texi	2011-11-16 17:34:35 UTC (rev 2006)
+++ pkg/vegan/inst/doc/FAQ-vegan.texi	2011-11-17 17:50:15 UTC (rev 2007)
@@ -497,23 +497,30 @@
 @node How are environmental arrows scaled?, I want to use Helmert or sum contrasts, Class variables and dummies, Ordination
 @section How are environmental arrows scaled?
 
-Arrows for continuous environmental variables in constrained ordination
-(@code{cca}, @code{rda}, @code{capscale}) and fitted environmental
-vectors from @code{envfit} are scaled to fill the current graph.  The
-lengths of arrows do not have fixed meaning with respect to the points
-(species, sites), but they can only compared against each other, and
-therefore only their relative lengths are important. 
+The printed output of @code{envfit} gives the direction cosines which
+are the coordinates of unit length arrows. For plotting, these are
+scaled by their correlation (square roots of column @code{r2}). You can
+see the scaled lengths of @code{envfit} arrows using command
+ at code{scores}.
 
-If you really want change the scaling of the arrows, you can use
- at code{text} (plotting arrows and text) or @code{points} (plotting only
-arrows) functions for constrained ordination. These functions have
-argument @code{arrow.mul} which sets the multiplier.  The @code{plot}
-function for @code{envfit} also has the @code{arrow.mul} argument to set
-the arrow multiplier.  If you save the invisible result of the
-constrained ordination @code{plot} command, you can see the value of the
-currently used @code{arrow.mul} which is saved as an attribute of
- at code{biplot} scores. 
+The scaled environmental vectors from @code{envfit} and the arrows for
+continuous environmental variables in constrained ordination
+(@code{cca}, @code{rda}, @code{capscale}) are adjusted to fill the
+current graph.  The lengths of arrows do not have fixed meaning with
+respect to the points (species, sites), but they can only compared
+against each other, and therefore only their relative lengths are
+important.
 
+If you want change the scaling of the arrows, you can use @code{text}
+(plotting arrows and text) or @code{points} (plotting only arrows)
+functions for constrained ordination. These functions have argument
+ at code{arrow.mul} which sets the multiplier.  The @code{plot} function
+for @code{envfit} also has the @code{arrow.mul} argument to set the
+arrow multiplier.  If you save the invisible result of the constrained
+ordination @code{plot} command, you can see the value of the currently
+used @code{arrow.mul} which is saved as an attribute of @code{biplot}
+scores.
+
 An unexported function @code{ordiArrowMul} is used to find the scaling
 for the current plot. You can use this function to see how arrows would
 be scaled:

Modified: www/FAQ-vegan.html
===================================================================
--- www/FAQ-vegan.html	2011-11-16 17:34:35 UTC (rev 2006)
+++ www/FAQ-vegan.html	2011-11-17 17:50:15 UTC (rev 2007)
@@ -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: 2011-11-01 21:26:52 +0200 (Tue, 01 Nov 2011) $.
+This is version of $Date: 2011-11-02 16:29:50 +0200 (Wed, 02 Nov 2011) $.
 
+
 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 2008-2011 Jari Oksanen
 
- -->
-<!-- Created on November 2, 2011 by texi2html 1.82
-texi2html was written by: 
-            Lionel Cons <Lionel.Cons at cern.ch> (original author)
+-->
+<!-- Created on November, 17 2011 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>
@@ -54,110 +53,112 @@
 
 <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: 2011-11-01 21:26:52 +0200 (Tue, 01 Nov 2011) $.
-</p>
-<blockquote><p>This work is licensed under the Creative Commons Attribution 3.0
+This is version of $Date: 2011-11-02 16:29:50 +0200 (Wed, 02 Nov 2011) $.
+
+</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 &copy; 2008-2011 Jari Oksanen
+
+</p><p>Copyright &copy; 2008-2011 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>&nbsp;&nbsp;</td><td align="left" valign="top">                
+<tr><td align="left" valign="top"><a href="#SEC1">1. Introduction</a></td><td>&nbsp;&nbsp;</td><td align="left" valign="top">                
 </td></tr>
-<tr><td align="left" valign="top"><a href="#Ordination">2. Ordination</a></td><td>&nbsp;&nbsp;</td><td align="left" valign="top">                  
+<tr><td align="left" valign="top"><a href="#SEC15">2. Ordination</a></td><td>&nbsp;&nbsp;</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>&nbsp;&nbsp;</td><td align="left" valign="top">     
+<tr><td align="left" valign="top"><a href="#SEC35">3. Other analysis methods</a></td><td>&nbsp;&nbsp;</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"> &lt; </a>]</td>
-<td valign="middle" align="left">[<a href="#What-is-vegan_003f" title="Next section in reading order"> &gt; </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC_Top" title="Previous section in reading order"> &lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC2" title="Next section in reading order"> &gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
-<td valign="middle" align="left">[<a href="#Top" title="Beginning of this chapter or previous chapter"> &lt;&lt; </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"> &gt;&gt; </a>]</td>
+<td valign="middle" align="left">[ &lt;&lt; ]</td>
+<td valign="middle" align="left">[<a href="#SEC_Top" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC15" title="Next chapter"> &gt;&gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</td><td align="left" valign="top">                  
+<tr><td align="left" valign="top"><a href="#SEC3">1.2 What is R?</a></td><td>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</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>&nbsp;&nbsp;</td><td align="left" valign="top">  
+<tr><td align="left" valign="top"><a href="#SEC12">1.11 How to report a bug in <strong>vegan</strong>?</a></td><td>&nbsp;&nbsp;</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>&nbsp;&nbsp;</td><td align="left" valign="top">   
+<tr><td align="left" valign="top"><a href="#SEC13">1.12 Is it a bug or a feature?</a></td><td>&nbsp;&nbsp;</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>&nbsp;&nbsp;</td><td align="left" valign="top">  
+<tr><td align="left" valign="top"><a href="#SEC14">1.13 Can I contribute to <strong>vegan</strong>?</a></td><td>&nbsp;&nbsp;</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"> &lt; </a>]</td>
-<td valign="middle" align="left">[<a href="#What-is-R_003f" title="Next section in reading order"> &gt; </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC1" title="Previous section in reading order"> &lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC3" title="Next section in reading order"> &gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Beginning of this chapter or previous chapter"> &lt;&lt; </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"> &gt;&gt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Beginning of this chapter or previous chapter"> &lt;&lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC15" title="Next chapter"> &gt;&gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </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
@@ -166,96 +167,96 @@
 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"> &lt; </a>]</td>
-<td valign="middle" align="left">[<a href="#How-to-obtain-vegan-and-R_003f" title="Next section in reading order"> &gt; </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC2" title="Previous section in reading order"> &lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC4" title="Next section in reading order"> &gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Beginning of this chapter or previous chapter"> &lt;&lt; </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"> &gt;&gt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Beginning of this chapter or previous chapter"> &lt;&lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC15" title="Next chapter"> &gt;&gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </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
-(&ldquo;<acronym>GNU</acronym> S&rdquo;).
-</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
+(&quot;GNU S&quot;).
+
+</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"> &lt; </a>]</td>
-<td valign="middle" align="left">[<a href="#What-R-packages-vegan-depends-on_003f" title="Next section in reading order"> &gt; </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC3" title="Previous section in reading order"> &lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC5" title="Next section in reading order"> &gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Beginning of this chapter or previous chapter"> &lt;&lt; </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"> &gt;&gt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Beginning of this chapter or previous chapter"> &lt;&lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC15" title="Next chapter"> &gt;&gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </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"> &lt; </a>]</td>
-<td valign="middle" align="left">[<a href="#What-other-packages-are-available-for-ecologists_003f" title="Next section in reading order"> &gt; </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC4" title="Previous section in reading order"> &lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC6" title="Next section in reading order"> &gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Beginning of this chapter or previous chapter"> &lt;&lt; </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"> &gt;&gt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Beginning of this chapter or previous chapter"> &lt;&lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC15" title="Next chapter"> &gt;&gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </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>
@@ -263,62 +264,62 @@
 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"> &lt; </a>]</td>
-<td valign="middle" align="left">[<a href="#What-other-documentation-is-available-for-vegan_003f" title="Next section in reading order"> &gt; </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC5" title="Previous section in reading order"> &lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC7" title="Next section in reading order"> &gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Beginning of this chapter or previous chapter"> &lt;&lt; </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"> &gt;&gt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Beginning of this chapter or previous chapter"> &lt;&lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC15" title="Next chapter"> &gt;&gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </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"> &lt; </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"> &gt; </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC6" title="Previous section in reading order"> &lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC8" title="Next section in reading order"> &gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
-<td valign="middle" align="left">[<a href="#Introduction" title="Beginning of this chapter or previous chapter"> &lt;&lt; </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"> &gt;&gt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Beginning of this chapter or previous chapter"> &lt;&lt; </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC1" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC15" title="Next chapter"> &gt;&gt; </a>]</td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </td>
 <td valign="middle" align="left"> &nbsp; </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-documentation-is-available-for-vegan_003f-1"></a>
-<h2 class="section">1.6 What other documentation is available for <strong>vegan</strong>?</h2>
+<h2 class="section"> 1.6 What other documentation is available for <strong>vegan</strong>? </h2>
 
 <p><strong>Vegan</strong> is a fully documented R package with standard help pages.  These
 are the most authoritative sources of documentation (and as a last
@@ -326,56 +327,56 @@
 source).  <strong>Vegan</strong> package ships with other documents which can be read
 with <code>vegandocs</code> command (documented in the <strong>vegan</strong> help).  The
 documents included in the <strong>vegan</strong> package are
-</p><ul>
+</p><ul class="toc">
 <li>
-<strong>Vegan</strong> <code>NEWS</code>
-</li><li> 
-<strong>Vegan</strong> <code>ChangeLog</code>.
-</li><li>
-This document (<code>FAQ-vegan.pdf</code>).
-</li><li>
-Short introduction to basic ordination methods in <strong>vegan</strong>
+<p><strong>Vegan</strong> <code>NEWS</code>
+</p></li><li> 
+<p><strong>Vegan</strong> <code>ChangeLog</code>.
+</p></li><li>
+<p>This document (<code>FAQ-vegan.pdf</code>).
+</p></li><li>
+<p>Short introduction to basic ordination methods in <strong>vegan</strong>
 (<code>intro-vegan.pdf</code>).
-</li><li>
-Introduction to diversity methods in <strong>vegan</strong> (<code>diversity-vegan.pdf</code>).
-</li><li> 
-Discussion on design decisions in <strong>vegan</strong> (<code>decision-vegan.pdf</code>).
-</li><li>
-Description of variance partition procedures in function
+</p></li><li>
+<p>Introduction to diversity methods in <strong>vegan</strong> (<code>diversity-vegan.pdf</code>).
+</p></li><li> 
+<p>Discussion on design decisions in <strong>vegan</strong> (<code>decision-vegan.pdf</code>).
+</p></li><li>
+<p>Description of variance partition procedures in function
 <code>varpart</code> (<code>partitioning.pdf</code>).
-</li></ul>
+</p></li></ul>
 
 
 <p>Web documents outside the package include:
-</p><ul>
+</p><ul class="toc">
 <li>
-<a href="http://vegan.r-forge.r-project.org/">http://vegan.r-forge.r-project.org/</a>: <strong>vegan</strong> homepage.
-</li><li>
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/vegan -r 2007


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