[Vegan-commits] r1968 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Oct 30 18:52:06 CET 2011
Author: jarioksa
Date: 2011-10-30 18:52:06 +0100 (Sun, 30 Oct 2011)
New Revision: 1968
Added:
www/FAQ-vegan.html
www/NEWS.html
Modified:
www/index.php
Log:
more info on the web page (that really should be re-done)
Added: www/FAQ-vegan.html
===================================================================
--- www/FAQ-vegan.html (rev 0)
+++ www/FAQ-vegan.html 2011-10-30 17:52:06 UTC (rev 1968)
@@ -0,0 +1,1463 @@
+<!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
+questions about R package vegan.
+This is version of $Date: 2011-02-17 11:25:56 +0200 (Thu, 17 Feb 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
+Creative Commons, 543 Howard Street, 5th Floor, San Francisco,
+California, 94105, USA.
+
+Copyright C 2008-2011 Jari Oksanen
+
+-->
+<!-- Created on October, 30 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>
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+Maintained by: Many creative people <dev at texi2html.cvshome.org>
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+<head>
+<title>vegan FAQ: vegan FAQ</title>
+
+<meta name="description" content="vegan FAQ: vegan FAQ">
+<meta name="keywords" content="vegan FAQ: vegan FAQ">
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+
+<body lang="en" bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#800080" alink="#FF0000">
+
+<a name="NOD1"></a>
+<a name="SEC_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>
+<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="settitle">vegan FAQ</h1>
+<p>This document contains answers to some of the most frequently asked
+questions about R package vegan.
+This is version of $Date: 2011-02-17 11:25:56 +0200 (Thu, 17 Feb 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></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">
+</td></tr>
+<tr><td align="left" valign="top"><a href="#SEC16">2. Ordination</a></td><td> </td><td align="left" valign="top">
+</td></tr>
+<tr><td align="left" valign="top"><a href="#SEC33">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>
+<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>
+<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"> </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">[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>
+
+<table class="menu" border="0" cellspacing="0">
+<tr><td align="left" valign="top"><a href="#SEC2">1.1 What is vegan?</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">
+</td></tr>
+<tr><td align="left" valign="top"><a href="#SEC4">1.3 How to obtain vegan 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 vegan 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">
+</td></tr>
+<tr><td align="left" valign="top"><a href="#SEC7">1.6 What other documentation is available for vegan?</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 vegan?</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 vegan?</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 vegan</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 vegan from sources?</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">
+</td></tr>
+<tr><td align="left" valign="top"><a href="#SEC13">1.12 How to report a bug in vegan?</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">
+</td></tr>
+<tr><td align="left" valign="top"><a href="#SEC15">1.14 Can I contribute to vegan?</a></td><td> </td><td align="left" valign="top">
+</td></tr>
+</table>
+
+<hr size="6">
+<a name="NOD3"></a>
+<a name="SEC2"></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>
+<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"> </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">[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 vegan? </h2>
+
+<p>Vegan is an R package for community ecologists. It contains the most
+popular methods of multivariate analysis needed in analysing ecological
+communities, and tools for diversity analysis, and other potentially
+useful functions. Vegan is not self-contained but it must be run under
+R statistical environment, and it also depends on many other R
+packages. Vegan is <a href="http://www.gnu.org/philosophy/free-sw.html, free software">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">http://www.gnu.org/licenses/gpl.html, ,GPL2 license</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="#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="#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"> </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">[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>
+
+<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
+<a href="http://www.gnu.org/philosophy/free-sw.html, free software">http://www.gnu.org/philosophy/free-sw.html, free software</a>
+distributed under a GNU-style
+<a href="http://www.gnu.org/copyleft/copyleft.html, copyleft">http://www.gnu.org/copyleft/copyleft.html, copyleft</a>, and an
+official part of the <a href="http://www.gnu.org/, GNU">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="#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="#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"> </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">[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 vegan and R? </h2>
+
+<p>Both R and latest release version of vegan can be obtained through
+<a href="http://cran.r-project.org,,CRAN">http://cran.r-project.org,,CRAN</a>. Unstable development version of
+vegan can be obtained through
+<a href="http://r-forge.r-project.org/projects/vegan/,,R-Forge">http://r-forge.r-project.org/projects/vegan/,,R-Forge</a>.
+
+</p>
+
+<hr size="6">
+<a name="NOD6"></a>
+<a name="SEC5"></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>
+<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"> </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">[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 vegan depends on? </h2>
+
+<p>Some vegan functions depend on packages <code>MASS</code>, <code>mgcv</code>,
+<code>cluster</code> and <code>lattice</code>. These all are recommended standard
+R packages that should be available in every R installation. In
+addition, some vegan functions <code>require</code> non-standard R packages.
+Vegan declares these packages only as suggested ones, and you can install vegan
+and use most of its functions without these packages. The
+non-standard packages needed by some vegan functions are:
+</p><ul class="toc">
+<li><p> Package <code>scatterplot3d</code>
+is needed by <code>ordiplot3d</code>
+
+</p></li><li><p> Package <code>rgl</code>
+is needed by <code>ordirgl</code>
+and <code>rgl.isomap</code>
+
+</p></li></ul>
+
+<hr size="6">
+<a name="NOD7"></a>
+<a name="SEC6"></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>
+<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"> </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">[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>
+
+<p>CRAN <a href="http://cran.r-project.org/src/contrib/Views/,,Task Views">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 <code>ctv</code>, 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>
+<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>
+<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"> </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">[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 vegan? </h2>
+
+<p>Vegan is a fully documented R package with standard help pages. These
+are the most authoritative sources of documentation (and as a last
+resource you can use the force and the read the source, as vegan is open
+source). Vegan package ships with other documents which can be read
+with <code>vegandocs</code> command (documented in the vegan help). The
+documents included in the vegan package are
+</p><ul class="toc">
+<li>
+<p>Vegan <code>NEWS</code> (not in the development version: only in CRAN)
+</p></li><li>
+<p>Vegan <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 vegan
+(<code>intro-vegan.pdf</code>).
+</p></li><li>
+<p>Introduction to diversity methods in vegan (<code>diversity-vegan.pdf</code>).
+</p></li><li>
+<p>Discussion on design decisions in vegan (<code>decision-vegan.pdf</code>).
+</p></li><li>
+<p>Description of variance partition procedures in function
+<code>varpart</code> (<code>partitioning.pdf</code>).
+</p></li></ul>
+
+
+<p>Web documents outside the package include:
+</p><ul class="toc">
+<li>
+<p><a href="http://vegan.r-forge.r-project.org/">http://vegan.r-forge.r-project.org/</a>: vegan 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>: vegan
+tutorial.
+
+</p></li></ul>
+
+<hr size="6">
+<a name="NOD9"></a>
+<a name="SEC8"></a>
+<table cellpadding="1" cellspacing="1" border="0">
+<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="#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"> </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">[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"> 1.7 Is there a Graphical User Interface (GUI) for vegan? </h2>
+
+<p>Roeland Kindt has made package <code>BiodiversityR</code> which provides a
+GUI for vegan. The package is available at
+<a href="http://cran.r-project.org/src/contrib/Descriptions/BiodiversityR.html,,CRAN">http://cran.r-project.org/src/contrib/Descriptions/BiodiversityR.html,,CRAN</a>.
+It is not a mere GUI for vegan, but adds some new functions and
+complements vegan functions in order to provide a
+workbench for biodiversity analysis. You can install <code>BiodiversityR</code> using
+<code>install.packages("BiodiversityR")</code> or graphical package
+management menu in R. The GUI works on Windows, MacOS X and Linux.
+
+</p><hr size="6">
+<a name="NOD10"></a>
+<a name="SEC9"></a>
+<table cellpadding="1" cellspacing="1" border="0">
+<tr><td valign="middle" align="left">[<a href="#SEC8" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC10" 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"> </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">[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"> 1.8 How to cite vegan? </h2>
+
+<p>Use command <code>citation("vegan")</code> in R to see the recommended
+citation to be used in publications.
+
+</p><hr size="6">
+<a name="NOD11"></a>
+<a name="SEC10"></a>
+<table cellpadding="1" cellspacing="1" border="0">
+<tr><td valign="middle" align="left">[<a href="#SEC9" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC11" 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"> </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">[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"> 1.9 Version numbering in vegan </h2>
+
+<p>From version 1.10-0, vegan is developed at
+<a href="http://r-forge.r-project.org/projects/vegan/,,R-Forge">http://r-forge.r-project.org/projects/vegan/,,R-Forge</a> and there
+is a general progression of version numbers mixed with stable (at
+<a href="http://cran.r-project.org,,CRAN">http://cran.r-project.org,,CRAN</a>) and devel versions (at
+<a href="http://r-forge.r-project.org/projects/vegan/,,R-Forge">http://r-forge.r-project.org/projects/vegan/,,R-Forge</a>).
+
+</p><p>Vegan version numbers are of type x.y-z, where number y is odd for
+stable release versions at <a href="http://cran.r-project.org,,CRAN">http://cran.r-project.org,,CRAN</a> and
+even for unstable release versions at
+<a href="http://r-forge.r-project.org/projects/vegan,,F-Forge">http://r-forge.r-project.org/projects/vegan,,F-Forge</a>.
+
+</p><hr size="6">
+<a name="NOD12"></a>
+<a name="SEC11"></a>
+<table cellpadding="1" cellspacing="1" border="0">
+<tr><td valign="middle" align="left">[<a href="#SEC10" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC12" 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"> </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">[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"> 1.10 How to build vegan from sources? </h2>
+
+<p>In general, you do not need to build vegan from sources, but binary
+builds of release versions are available through
+<a href="http://cran.r-project.org/,,CRAN">http://cran.r-project.org/,,CRAN</a> for Windows and MacOS X. If you
+use some other operating systems, you may have to use source packages.
+Vegan is a standard R package, and can be built like instructed in R
+documentation. Vegan contains source files in C and FORTRAN,
+and you need appropriate compilers (which may need more work in Windows
+and MacOS X).
+
+</p><hr size="6">
+<a name="NOD13"></a>
+<a name="SEC12"></a>
+<table cellpadding="1" cellspacing="1" border="0">
+<tr><td valign="middle" align="left">[<a href="#SEC11" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC13" 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"> </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">[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"> 1.11 Are there binaries for devel versions? </h2>
+
+<p><a href="http://r-forge.r-project.org/projects/vegan/,,R-Forge">http://r-forge.r-project.org/projects/vegan/,,R-Forge</a> runs daily
+tests on the devel package, and if passed, it builds source package
+together with Windows and MacOS X binaries. You can install those
+packages within R with command
+<code>install.packages("vegan", repos="http://r-forge.r-project.org/")</code>.
+If you use GUI menu entry, you must select or define the R-Forge
+repository.
+
+</p><hr size="6">
+<a name="NOD14"></a>
+<a name="SEC13"></a>
+<table cellpadding="1" cellspacing="1" border="0">
+<tr><td valign="middle" align="left">[<a href="#SEC12" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC14" 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"> </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">[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"> 1.12 How to report a bug in vegan? </h2>
+
+<p>If you think you have found a bug in vegan, you should report it to
+vegan maintainers or developers. The bug report should be so detailed
+that the bug can be replicated and corrected. Preferably, you should
+send an example that causes a bug. If it needs a data set that is not
+available in R, you should send a minimal data set as well. You also
+should paste the output or error message in your message. You also
+should specify which version of vegan you used.
+
+</p><p>Bug reports are welcome: they are the only way to make vegan non-buggy.
+
+</p><p>Please note that you shall not send bug reports to R mailing lists,
+since vegan is not a standard R package.
+
+</p><p>There also is a bug reporting tool at
+<a href="http://r-forge.r-project.org/projects/vegan/,,R-Forge">http://r-forge.r-project.org/projects/vegan/,,R-Forge</a>, but you
+need to register as a site user to report bugs (this is site policy).
+
+</p><hr size="6">
+<a name="NOD15"></a>
+<a name="SEC14"></a>
+<table cellpadding="1" cellspacing="1" border="0">
+<tr><td valign="middle" align="left">[<a href="#SEC13" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC15" 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"> </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">[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"> 1.13 Is it a bug or a feature? </h2>
+
+<p>It is not necessarily a bug if some function gives different
+results than you expect: That may be a deliberate design decision. It
+may be useful to check the documentation of the function to see what
+was the intended behaviour. It may also happen that function has an
+argument to switch the behaviour to match your expectation. For
+instance, function <code>vegdist</code> always calculates quantitative
+indices (when this is possible). If you expect it to calculate a
+binary index, you should use argument <code>binary = TRUE</code>.
+
+</p><hr size="6">
+<a name="NOD16"></a>
+<a name="SEC15"></a>
+<table cellpadding="1" cellspacing="1" border="0">
+<tr><td valign="middle" align="left">[<a href="#SEC14" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC16" 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"> </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">[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"> 1.14 Can I contribute to vegan? </h2>
+
+<p>Vegan is dependent on user contribution. All feedback is welcome. If
+you have problem with vegan, it may be as simple as incomplete
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/vegan -r 1968
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