[Vegan-commits] r2606 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Sep 6 15:32:11 CEST 2013
Author: jarioksa
Date: 2013-09-06 15:32:11 +0200 (Fri, 06 Sep 2013)
New Revision: 2606
Modified:
www/FAQ-vegan.html
Log:
web page of updated FAQ
Modified: www/FAQ-vegan.html
===================================================================
--- www/FAQ-vegan.html 2013-09-06 13:29:19 UTC (rev 2605)
+++ www/FAQ-vegan.html 2013-09-06 13:32:11 UTC (rev 2606)
@@ -2,7 +2,7 @@
<html>
<!-- This document contains answers to some of the most frequently asked
questions about R package vegan.
-This is version of $Date: 2013-01-22 19:55:06 +0200 (Tue, 22 Jan 2013) $.
+This is version of $Date: 2013-09-06 16:29:19 +0300 (Fri, 06 Sep 2013) $.
This work is licensed under the Creative Commons Attribution 3.0
License. To view a copy of this license, visit
@@ -13,7 +13,7 @@
Copyright C 2008-2013 Jari Oksanen
-->
-<!-- Created on February 5, 2013 by texi2html 1.82
+<!-- Created on September 6, 2013 by texi2html 1.82
texi2html was written by:
Lionel Cons <Lionel.Cons at cern.ch> (original author)
Karl Berry <karl at freefriends.org>
@@ -65,7 +65,7 @@
<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: 2013-01-22 19:55:06 +0200 (Tue, 22 Jan 2013) $.
+This is version of $Date: 2013-09-06 16:29:19 +0300 (Fri, 06 Sep 2013) $.
</p>
<blockquote><p>This work is licensed under the Creative Commons Attribution 3.0
License. To view a copy of this license, visit
@@ -682,32 +682,34 @@
</td></tr>
<tr><td align="left" valign="top"><a href="#cca-fails-with-_0060_0060data_002eframe-expected_0027_0027-or-_0060_0060_0022site_002eenv_0022-missing_0027_0027">2.10 cca fails with “data.frame expected” or “"site.env" missing”</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#Variance-explained-by-ordination-axes">2.11 Variance explained by ordination axes.</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#Ordination-fails-with-_0060_0060Error-in-La_002esvd_0027_0027">2.11 Ordination fails with “Error in La.svd”</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#Can-I-have-random-effects-in-constrained-ordination-or-in-adonis_003f">2.12 Can I have random effects in constrained ordination or in <code>adonis</code>?</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#Variance-explained-by-ordination-axes">2.12 Variance explained by ordination axes.</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#Is-it-possible-to-have-passive-points-in-ordination_003f">2.13 Is it possible to have passive points in ordination?</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#Can-I-have-random-effects-in-constrained-ordination-or-in-adonis_003f">2.13 Can I have random effects in constrained ordination or in <code>adonis</code>?</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#Class-variables-and-dummies">2.14 Class variables and dummies</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#Is-it-possible-to-have-passive-points-in-ordination_003f">2.14 Is it possible to have passive points in ordination?</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#How-are-environmental-arrows-scaled_003f">2.15 How are environmental arrows scaled?</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#Class-variables-and-dummies">2.15 Class variables and dummies</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#I-want-to-use-Helmert-or-sum-contrasts">2.16 I want to use Helmert or sum contrasts</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#How-are-environmental-arrows-scaled_003f">2.16 How are environmental arrows scaled?</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#What-are-aliased-variables-and-how-to-see-them_003f">2.17 What are aliased variables and how to see them?</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#I-want-to-use-Helmert-or-sum-contrasts">2.17 I want to use Helmert or sum contrasts</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#Plotting-aliased-variables">2.18 Plotting aliased variables</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#What-are-aliased-variables-and-how-to-see-them_003f">2.18 What are aliased variables and how to see them?</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#Constrained-permutations-in-vegan">2.19 Constrained permutations in <strong>vegan</strong></a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#Plotting-aliased-variables">2.19 Plotting aliased variables</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#How-to-use-different-plotting-symbols-in-ordination-graphics_003f">2.20 How to use different plotting symbols in ordination graphics?</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#Constrained-permutations-in-vegan">2.20 Constrained permutations in <strong>vegan</strong></a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#How-to-avoid-cluttered-ordination-graphs_003f">2.21 How to avoid cluttered ordination graphs?</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#How-to-use-different-plotting-symbols-in-ordination-graphics_003f">2.21 How to use different plotting symbols in ordination graphics?</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#Can-I-flip-an-axis-in-ordination-diagram_003f">2.22 Can I flip an axis in ordination diagram?</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#How-to-avoid-cluttered-ordination-graphs_003f">2.22 How to avoid cluttered ordination graphs?</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#Can-I-zoom-into-an-ordination-plot_003f">2.23 Can I zoom into an ordination plot?</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#Can-I-flip-an-axis-in-ordination-diagram_003f">2.23 Can I flip an axis in ordination diagram?</a></td><td> </td><td align="left" valign="top">
</td></tr>
+<tr><td align="left" valign="top"><a href="#Can-I-zoom-into-an-ordination-plot_003f">2.24 Can I zoom into an ordination plot?</a></td><td> </td><td align="left" valign="top">
+</td></tr>
</table>
<hr size="6">
@@ -1004,7 +1006,7 @@
<a name="cca-fails-with-_0060_0060data_002eframe-expected_0027_0027-or-_0060_0060_0022site_002eenv_0022-missing_0027_0027"></a>
<table cellpadding="1" cellspacing="1" border="0">
<tr><td valign="middle" align="left">[<a href="#How-the-RDA-results-are-scaled_003f" title="Previous section in reading order"> < </a>]</td>
-<td valign="middle" align="left">[<a href="#Variance-explained-by-ordination-axes" title="Next section in reading order"> > </a>]</td>
+<td valign="middle" align="left">[<a href="#Ordination-fails-with-_0060_0060Error-in-La_002esvd_0027_0027" title="Next section in reading order"> > </a>]</td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left">[<a href="#Ordination" title="Beginning of this chapter or previous chapter"> << </a>]</td>
<td valign="middle" align="left">[<a href="#Ordination" title="Up section"> Up </a>]</td>
@@ -1030,9 +1032,49 @@
<code>detach(package:ade4)</code>.
</p>
<hr size="6">
+<a name="Ordination-fails-with-_0060_0060Error-in-La_002esvd_0027_0027"></a>
+<table cellpadding="1" cellspacing="1" border="0">
+<tr><td valign="middle" align="left">[<a href="#cca-fails-with-_0060_0060data_002eframe-expected_0027_0027-or-_0060_0060_0022site_002eenv_0022-missing_0027_0027" title="Previous section in reading order"> < </a>]</td>
+<td valign="middle" align="left">[<a href="#Variance-explained-by-ordination-axes" title="Next section in reading order"> > </a>]</td>
+<td valign="middle" align="left"> </td>
+<td valign="middle" align="left">[<a href="#Ordination" title="Beginning of this chapter or previous chapter"> << </a>]</td>
+<td valign="middle" align="left">[<a href="#Ordination" title="Up section"> Up </a>]</td>
+<td valign="middle" align="left">[<a href="#Other-analysis-methods" 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">[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="Ordination-fails-with-_0060_0060Error-in-La_002esvd_0027_0027-1"></a>
+<h2 class="section">2.11 Ordination fails with “Error in La.svd”</h2>
+
+<p>Constrained ordination (<code>cca</code>, <code>rda</code>, <code>capscale</code>) will
+sometimes fail with error message
+<code>Error in La.svd(x, nu, nv): error code 1 from Lapack routine 'dgesdd'.</code>
+</p>
+<p>It seems that the basic problem is in the <code>svd</code> function of
+<code>LAPACK</code> that is used for numerical analysis in R. <code>LAPACK</code>
+is an external library that is beyond the control of package developers
+and R core team so that these problems may be unsolvable. It seems that
+the problems with the LAPACK code are so common that even the help page
+of <code>svd</code> warns about them
+</p>
+<p>Reducing the range of constraints (environmental variables) helps
+sometimes. For instance, multiplying constraints by a constant < 1. This
+rescaling does not influence the numerical results of constrained
+ordination, but it can complicate further analyses when values of
+constraints are needed, because the same scaling must be applied
+there. We can only hope that this problem is fixed in the future
+versions of R and <code>LAPACK</code>.
+</p>
+<hr size="6">
<a name="Variance-explained-by-ordination-axes"></a>
<table cellpadding="1" cellspacing="1" border="0">
-<tr><td valign="middle" align="left">[<a href="#cca-fails-with-_0060_0060data_002eframe-expected_0027_0027-or-_0060_0060_0022site_002eenv_0022-missing_0027_0027" title="Previous section in reading order"> < </a>]</td>
+<tr><td valign="middle" align="left">[<a href="#Ordination-fails-with-_0060_0060Error-in-La_002esvd_0027_0027" title="Previous section in reading order"> < </a>]</td>
<td valign="middle" align="left">[<a href="#Can-I-have-random-effects-in-constrained-ordination-or-in-adonis_003f" title="Next section in reading order"> > </a>]</td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left">[<a href="#Ordination" title="Beginning of this chapter or previous chapter"> << </a>]</td>
@@ -1048,7 +1090,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="Variance-explained-by-ordination-axes_002e"></a>
-<h2 class="section">2.11 Variance explained by ordination axes.</h2>
+<h2 class="section">2.12 Variance explained by ordination axes.</h2>
<p>In general, <strong>vegan</strong> does not directly give any statistics on the
“variance explained” by ordination axes or by the constrained axes.
@@ -1125,7 +1167,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="Can-I-have-random-effects-in-constrained-ordination-or-in-adonis_003f-1"></a>
-<h2 class="section">2.12 Can I have random effects in constrained ordination or in <code>adonis</code>?</h2>
+<h2 class="section">2.13 Can I have random effects in constrained ordination or in <code>adonis</code>?</h2>
<p>No. Strictly speaking, this is impossible. However, you can define
models that respond to similar goals as random effects models, although
@@ -1182,7 +1224,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="Is-it-possible-to-have-passive-points-in-ordination_003f-1"></a>
-<h2 class="section">2.13 Is it possible to have passive points in ordination?</h2>
+<h2 class="section">2.14 Is it possible to have passive points in ordination?</h2>
<p><strong>Vegan</strong> does not have a concept of passive points, or a point that should
only little influence the ordination results. However, you can add
@@ -1217,7 +1259,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="Class-variables-and-dummies-1"></a>
-<h2 class="section">2.14 Class variables and dummies</h2>
+<h2 class="section">2.15 Class variables and dummies</h2>
<p>You should define a class variable as an R <code>factor</code>, and <strong>vegan</strong> will
automatically handle them with formula interface. You also can define
@@ -1251,7 +1293,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="How-are-environmental-arrows-scaled_003f-1"></a>
-<h2 class="section">2.15 How are environmental arrows scaled?</h2>
+<h2 class="section">2.16 How are environmental arrows scaled?</h2>
<p>The printed output of <code>envfit</code> gives the direction cosines which
are the coordinates of unit length arrows. For plotting, these are
@@ -1305,7 +1347,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="I-want-to-use-Helmert-or-sum-contrasts-1"></a>
-<h2 class="section">2.16 I want to use Helmert or sum contrasts</h2>
+<h2 class="section">2.17 I want to use Helmert or sum contrasts</h2>
<p><code><strong>vegan</strong></code> uses standard R utilities for defining
contrasts. The default in standard installations is to use treatment
@@ -1332,7 +1374,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="What-are-aliased-variables-and-how-to-see-them_003f-1"></a>
-<h2 class="section">2.17 What are aliased variables and how to see them?</h2>
+<h2 class="section">2.18 What are aliased variables and how to see them?</h2>
<p>Aliased variable has no information because it can be expressed with
the help of other variables. Such variables are automatically removed
@@ -1362,7 +1404,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="Plotting-aliased-variables-1"></a>
-<h2 class="section">2.18 Plotting aliased variables</h2>
+<h2 class="section">2.19 Plotting aliased variables</h2>
<p>You can fit vectors or class centroids for aliased variables using
<code>envfit</code> function. The <code>envfit</code> function uses weighted
@@ -1388,7 +1430,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="Constrained-permutations-in-vegan-1"></a>
-<h2 class="section">2.19 Constrained permutations in <strong>vegan</strong></h2>
+<h2 class="section">2.20 Constrained permutations in <strong>vegan</strong></h2>
<p>You can constrain your permutations within <code>strata</code> or levels of
factors. You can use stratified permutations in all <strong>vegan</strong>
@@ -1421,7 +1463,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="How-to-use-different-plotting-symbols-in-ordination-graphics_003f-1"></a>
-<h2 class="section">2.20 How to use different plotting symbols in ordination graphics?</h2>
+<h2 class="section">2.21 How to use different plotting symbols in ordination graphics?</h2>
<p>The default ordination <code>plot</code> function is intended for fast
plotting and it is not very configurable. To use different plotting
@@ -1451,7 +1493,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="How-to-avoid-cluttered-ordination-graphs_003f-1"></a>
-<h2 class="section">2.21 How to avoid cluttered ordination graphs?</h2>
+<h2 class="section">2.22 How to avoid cluttered ordination graphs?</h2>
<p>If there is a really high number of species or sites, the graphs often
are congested and many labels are overwritten. It may be impossible to
@@ -1523,7 +1565,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="Can-I-flip-an-axis-in-ordination-diagram_003f-1"></a>
-<h2 class="section">2.22 Can I flip an axis in ordination diagram?</h2>
+<h2 class="section">2.23 Can I flip an axis in ordination diagram?</h2>
<p>Use <code>xlim</code> or <code>ylim</code> with flipped limits. If you have model
<code>mod <- cca(dune)</code> you can flip the first axis with <code>plot(mod,
@@ -1548,7 +1590,7 @@
<td valign="middle" align="left">[<a href="#SEC_About" title="About (help)"> ? </a>]</td>
</tr></table>
<a name="Can-I-zoom-into-an-ordination-plot_003f-1"></a>
-<h2 class="section">2.23 Can I zoom into an ordination plot?</h2>
+<h2 class="section">2.24 Can I zoom into an ordination plot?</h2>
<p>You can use <code>xlim</code> and <code>ylim</code> arguments in <code>plot</code> or
<code>ordiplot</code> to zoom into ordination diagrams. Normally you must set
both <code>xlim</code> and <code>ylim</code> because ordination plots will keep the
@@ -1684,7 +1726,7 @@
</tr></table>
<h1>About This Document</h1>
<p>
- This document was generated by <em>Jari Oksanen</em> on <em>February 5, 2013</em> using <a href="http://www.nongnu.org/texi2html/"><em>texi2html 1.82</em></a>.
+ This document was generated by <em>Jari Oksanen</em> on <em>September 6, 2013</em> using <a href="http://www.nongnu.org/texi2html/"><em>texi2html 1.82</em></a>.
</p>
<p>
The buttons in the navigation panels have the following meaning:
@@ -1786,7 +1828,7 @@
<hr size="1">
<p>
<font size="-1">
- This document was generated by <em>Jari Oksanen</em> on <em>February 5, 2013</em> using <a href="http://www.nongnu.org/texi2html/"><em>texi2html 1.82</em></a>.
+ This document was generated by <em>Jari Oksanen</em> on <em>September 6, 2013</em> using <a href="http://www.nongnu.org/texi2html/"><em>texi2html 1.82</em></a>.
</font>
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