[Vegan-commits] r2200 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun May 27 16:57:20 CEST 2012
Author: jarioksa
Date: 2012-05-27 16:57:20 +0200 (Sun, 27 May 2012)
New Revision: 2200
Modified:
www/FAQ-vegan.html
Log:
update html FAQ for r2199
Modified: www/FAQ-vegan.html
===================================================================
--- www/FAQ-vegan.html 2012-05-27 14:55:57 UTC (rev 2199)
+++ www/FAQ-vegan.html 2012-05-27 14:57:20 UTC (rev 2200)
@@ -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: 2012-05-24 15:08:01 +0300 (Thu, 24 May 2012) $.
+This is version of $Date: 2012-05-27 17:55:57 +0300 (Sun, 27 May 2012) $.
+
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 May 24, 2012 by texi2html 1.82
-texi2html was written by:
- Lionel Cons <Lionel.Cons at cern.ch> (original author)
+-->
+<!-- Created on May, 27 2012 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}
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-->
</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: 2012-05-24 15:08:01 +0300 (Thu, 24 May 2012) $.
-</p>
-<blockquote><p>This work is licensed under the Creative Commons Attribution 3.0
+This is version of $Date: 2012-05-27 17:55:57 +0300 (Sun, 27 May 2012) $.
+
+</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="#SEC15">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="#SEC36">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="#SEC15" 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 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="#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 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-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 Can I contribute to <strong>vegan</strong>?</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="#SEC15" 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
@@ -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"> < </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="#SEC15" 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="#SEC15" 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="#SEC15" 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>
@@ -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"> < </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="#SEC15" 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>
+<td valign="middle" align="left">[<a href="#SEC15" 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-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>
-<a href="http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf">http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf</a>: <strong>vegan</strong>
+<p><a href="http://vegan.r-forge.r-project.org/">http://vegan.r-forge.r-project.org/</a>: <strong>vegan</strong> homepage.
+</p></li><li>
+<p><a href="http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf">http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf</a>: <strong>vegan</strong>
tutorial.
-</li></ul>
+</p></li></ul>
<hr size="6">
-<a name="Is-there-a-Graphical-User-Interface-_0028GUI_0029-for-vegan_003f"></a>
+<a name="NOD9"></a>
+<a name="SEC8"></a>
<table cellpadding="1" cellspacing="1" border="0">
-<tr><td valign="middle" align="left">[<a href="#What-other-documentation-is-available-for-vegan_003f" title="Previous section in reading order"> < </a>]</td>
-<td valign="middle" align="left">[<a href="#How-to-cite-vegan_003f" title="Next section in reading order"> > </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#SEC7" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC9" 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="#SEC15" 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="Is-there-a-Graphical-User-Interface-_0028GUI_0029-for-vegan_003f-1"></a>
-<h2 class="section">1.7 Is there a Graphical User Interface (GUI) for <strong>vegan</strong>?</h2>
+<h2 class="section"> 1.7 Is there a Graphical User Interface (GUI) for <strong>vegan</strong>? </h2>
<p>Roeland Kindt has made package <strong>BiodiversityR</strong> which provides a
GUI for <strong>vegan</strong>. The package is available at
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/vegan -r 2200
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