[Vegan-commits] r1982 - pkg/vegan/inst/doc www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 2 15:29:51 CET 2011
Author: jarioksa
Date: 2011-11-02 15:29:50 +0100 (Wed, 02 Nov 2011)
New Revision: 1982
Modified:
pkg/vegan/inst/doc/FAQ-vegan.texi
www/FAQ-vegan.html
Log:
remove entry on version numbers and tweak mark-up
Modified: pkg/vegan/inst/doc/FAQ-vegan.texi
===================================================================
--- pkg/vegan/inst/doc/FAQ-vegan.texi 2011-11-02 08:09:02 UTC (rev 1981)
+++ pkg/vegan/inst/doc/FAQ-vegan.texi 2011-11-02 14:29:50 UTC (rev 1982)
@@ -71,15 +71,14 @@
@chapter Introduction
@menu
-* What is @pkg{vegan}?::
+* What is @pkg{vegan}?::
* What is R?::
* How to obtain @pkg{vegan} and R?::
* What R packages @pkg{vegan} depends on?::
* What other packages are available for ecologists?::
* What other documentation is available for @pkg{vegan}?::
* Is there a Graphical User Interface (GUI) for @pkg{vegan}?::
-* How to cite @pkg{vegan}?::
-* Version numbering in @pkg{vegan}::
+* How to cite @pkg{vegan}?::
* How to build @pkg{vegan} from sources?::
* Are there binaries for devel versions?::
* How to report a bug in @pkg{vegan}?::
@@ -213,27 +212,13 @@
@code{install.packages("BiodiversityR")} or graphical package
management menu in R. The GUI works on Windows, MacOS X and Linux.
- at node How to cite @pkg{vegan}?, Version numbering in @pkg{vegan}, Is there a Graphical User Interface (GUI) for @pkg{vegan}?, Introduction
+ at node How to cite @pkg{vegan}?, How to build @pkg{vegan} from sources?, Is there a Graphical User Interface (GUI) for @pkg{vegan}?, Introduction
@section How to cite @pkg{vegan}?
Use command @code{citation("vegan")} in R to see the recommended
citation to be used in publications.
- at node Version numbering in @pkg{vegan}, How to build @pkg{vegan} from sources?, How to cite @pkg{vegan}?, Introduction
- at section Version numbering in @pkg{vegan}
-
-From version 1.10-0, @pkg{vegan} is developed at
- at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge} and there
-is a general progression of version numbers mixed with stable (at
- at uref{http://cran.r-project.org,,CRAN}) and devel versions (at
- at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge}).
-
- at pkg{Vegan} version numbers are of type x.y-z, where number y is odd for
-stable release versions at @uref{http://cran.r-project.org,,CRAN} and
-even for unstable release versions at
- at uref{http://r-forge.r-project.org/projects/vegan,,R-Forge}.
-
- at node How to build @pkg{vegan} from sources?, Are there binaries for devel versions?, Version numbering in @pkg{vegan}, Introduction
+ at node How to build @pkg{vegan} from sources?, Are there binaries for devel versions?, How to cite @pkg{vegan}?, Introduction
@section How to build @pkg{vegan} from sources?
In general, you do not need to build @pkg{vegan} from sources, but binary
@@ -403,8 +388,8 @@
software packages. The scaling of @acronym{RDA} is such a complicated
issue that it cannot be explained in this @acronym{FAQ}, but it is
explained in a separate @acronym{pdf} document on ``Design decision and
-implementation details in @pkg{vegan}'' that you can read with
- at pkg{vegan} command @code{@pkg{vegan}docs("decision")}.
+implementation details in vegan'' that you can read with @pkg{vegan}
+command @code{vegandocs("decision")}.
@node cca fails with ``data.frame expected'' or ``"site.env" missing'', Variance explained by ordination axes, How the RDA results are scaled?, Ordination
@section cca fails with ``data.frame expected'' or ``"site.env" missing''
@@ -412,9 +397,9 @@
This is not a @pkg{vegan} error message, but it comes from the
@code{cca} function in the @pkg{ade4} package. There is an unfortunate
name clash, and if you have loaded @pkg{ade4} after @pkg{vegan}, the
-ade4 version of @code{cca} will mask the @pkg{vegan} version. You can
-use the @pkg{vegan} version using command @code{vegan::cca()}. If you do
-not need package @pkg{ade4}, you can detach it with command
+ at pkg{ade4} version of @code{cca} will mask the @pkg{vegan} version. You
+can use the @pkg{vegan} version using command @code{vegan::cca()}. If
+you do not need package @pkg{ade4}, you can detach it with command
@code{detach(package:ade4)}.
@node Variance explained by ordination axes, Is it possible to have passive points in ordination?, cca fails with ``data.frame expected'' or ``"site.env" missing'', Ordination
Modified: www/FAQ-vegan.html
===================================================================
--- www/FAQ-vegan.html 2011-11-02 08:09:02 UTC (rev 1981)
+++ www/FAQ-vegan.html 2011-11-02 14:29:50 UTC (rev 1982)
@@ -1,10 +1,9 @@
<!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: 2011-10-31 20:23:01 +0200 (Mon, 31 Oct 2011) $.
+This is version of $Date: 2011-11-01 21:26:52 +0200 (Tue, 01 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
@@ -13,29 +12,29 @@
Copyright C 2008-2011 Jari Oksanen
--->
-<!-- Created on November, 1 2011 by texi2html 1.70 -->
-<!--
-Written by: Lionel Cons <Lionel.Cons at cern.ch> (original author)
+ -->
+<!-- Created on November 2, 2011 by texi2html 1.82
+texi2html was 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 <dev at texi2html.cvshome.org>
-Send bugs and suggestions to <users at texi2html.cvshome.org>
-
+Maintained by: Many creative people.
+Send bugs and suggestions to <texi2html-bug at nongnu.org>
-->
<head>
-<title>vegan FAQ: vegan FAQ</title>
+<title>vegan FAQ</title>
-<meta name="description" content="vegan FAQ: vegan FAQ">
-<meta name="keywords" content="vegan FAQ: vegan FAQ">
+<meta name="description" content="vegan FAQ">
+<meta name="keywords" content="vegan FAQ">
<meta name="resource-type" content="document">
<meta name="distribution" content="global">
-<meta name="Generator" content="texi2html 1.70">
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
+<meta name="Generator" content="texi2html 1.82">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<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}
@@ -44,6 +43,8 @@
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>
@@ -53,114 +54,110 @@
<body lang="en" bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#800080" alink="#FF0000">
-<a name="NOD1"></a>
-<a name="SEC_Top"></a>
+<a name="Top"></a>
<table cellpadding="1" cellspacing="1" border="0">
-<tr><td valign="middle" align="left">[<a href="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
+<tr><td valign="middle" align="left">[<a href="#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: 2011-10-31 20:23:01 +0200 (Mon, 31 Oct 2011) $.
-
-</p><blockquote>
-<p>This work is licensed under the Creative Commons Attribution 3.0
+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
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 © 2008-2011 Jari Oksanen
+</p>
+<p>Copyright © 2008-2011 Jari Oksanen
</p></blockquote>
-
<table class="menu" border="0" cellspacing="0">
-<tr><td align="left" valign="top"><a href="#SEC1">1. Introduction</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#Introduction">1. Introduction</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC16">2. Ordination</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#Ordination">2. Ordination</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC36">3. Other analysis methods</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#Other-analysis-methods">3. Other analysis methods</a></td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr size="1">
-<a name="NOD2"></a>
-<a name="SEC1"></a>
+<a name="Introduction"></a>
<table cellpadding="1" cellspacing="1" border="0">
-<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>
+<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>
<td valign="middle" align="left"> </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="#SEC16" title="Next chapter"> >> </a>]</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"> </td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left"> </td>
-<td valign="middle" align="left">[<a href="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#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>
-<h1 class="chapter"> 1. Introduction </h1>
+<a name="Introduction-1"></a>
+<h1 class="chapter">1. Introduction</h1>
<table class="menu" border="0" cellspacing="0">
-<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">
+<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">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC3">1.2 What is R?</a></td><td> </td><td align="left" valign="top">
+<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">
</td></tr>
-<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">
+<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">
</td></tr>
-<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">
+<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">
</td></tr>
-<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">
+<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">
</td></tr>
-<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">
+<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">
</td></tr>
-<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">
+<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">
</td></tr>
-<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">
+<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">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC10">1.9 Version numbering in <strong>vegan</strong></a></td><td> </td><td align="left" valign="top">
+<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">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC11">1.10 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="#Are-there-binaries-for-devel-versions_003f">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="#SEC12">1.11 Are there binaries for devel versions?</a></td><td> </td><td align="left" valign="top">
+<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">
</td></tr>
-<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">
+<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">
</td></tr>
-<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">
+<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">
</td></tr>
-<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>
</table>
<hr size="6">
-<a name="NOD3"></a>
-<a name="SEC2"></a>
+<a name="What-is-vegan_003f"></a>
<table cellpadding="1" cellspacing="1" border="0">
-<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>
+<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>
<td valign="middle" align="left"> </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="#SEC16" title="Next chapter"> >> </a>]</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"> </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="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#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>
-<h2 class="section"> 1.1 What is <strong>vegan</strong>? </h2>
+<a name="What-is-vegan_003f-1"></a>
+<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
@@ -169,96 +166,96 @@
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="NOD4"></a>
-<a name="SEC3"></a>
+</p>
+<hr size="6">
+<a name="What-is-R_003f"></a>
<table cellpadding="1" cellspacing="1" border="0">
-<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>
+<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>
<td valign="middle" align="left"> </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="#SEC16" title="Next chapter"> >> </a>]</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"> </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="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#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>
-<h2 class="section"> 1.2 What is R? </h2>
+<a name="What-is-R_003f-1"></a>
+<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 GNU-style
+distributed under a <acronym>GNU</acronym>-style
<a href="http://www.gnu.org/copyleft/copyleft.html">copyleft</a>, and an
-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>
+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>
<table cellpadding="1" cellspacing="1" border="0">
-<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>
+<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>
<td valign="middle" align="left"> </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="#SEC16" title="Next chapter"> >> </a>]</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"> </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="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#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>
-<h2 class="section"> 1.3 How to obtain <strong>vegan</strong> and R? </h2>
+<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>
<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="NOD6"></a>
-<a name="SEC5"></a>
+<a name="What-R-packages-vegan-depends-on_003f"></a>
<table cellpadding="1" cellspacing="1" border="0">
-<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>
+<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>
<td valign="middle" align="left"> </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="#SEC16" title="Next chapter"> >> </a>]</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"> </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="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#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>
-<h2 class="section"> 1.4 What R packages <strong>vegan</strong> depends on? </h2>
+<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>
<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>
@@ -266,62 +263,62 @@
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 class="toc">
-<li><p> Package <strong>scatterplot3d</strong>
+</p><ul>
+<li> Package <strong>scatterplot3d</strong>
is needed by <code>ordiplot3d</code>
-</p></li><li><p> Package <strong>rgl</strong>
+</li><li> Package <strong>rgl</strong>
is needed by <code>ordirgl</code>
and <code>rgl.isomap</code>
-</p></li></ul>
+</li></ul>
<hr size="6">
-<a name="NOD7"></a>
-<a name="SEC6"></a>
+<a name="What-other-packages-are-available-for-ecologists_003f"></a>
<table cellpadding="1" cellspacing="1" border="0">
-<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>
+<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>
<td valign="middle" align="left"> </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="#SEC16" title="Next chapter"> >> </a>]</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"> </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="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#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>
-<h2 class="section"> 1.5 What other packages are available for ecologists? </h2>
+<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>
-<p>CRAN <a href="http://cran.r-project.org/src/contrib/Views/">Task Views</a> include entries like <code>Environmetrics</code>, <code>Multivariate</code>
+<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>
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="NOD8"></a>
-<a name="SEC7"></a>
+</p>
+<hr size="6">
+<a name="What-other-documentation-is-available-for-vegan_003f"></a>
<table cellpadding="1" cellspacing="1" border="0">
-<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>
+<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>
<td valign="middle" align="left"> </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="#SEC16" title="Next chapter"> >> </a>]</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"> </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="#SEC_Top" title="Cover (top) of document">Top</a>]</td>
+<td valign="middle" align="left">[<a href="#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>
-<h2 class="section"> 1.6 What other documentation is available for <strong>vegan</strong>? </h2>
+<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>
<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
@@ -329,56 +326,56 @@
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
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/vegan -r 1982
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