[Vegan-commits] r1975 - pkg/vegan/inst pkg/vegan/inst/doc www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Oct 31 19:23:01 CET 2011
Author: jarioksa
Date: 2011-10-31 19:23:01 +0100 (Mon, 31 Oct 2011)
New Revision: 1975
Modified:
pkg/vegan/inst/ChangeLog
pkg/vegan/inst/doc/FAQ-vegan.texi
www/FAQ-vegan.html
Log:
fix mark-up and add new entries to FAQ
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2011-10-31 16:58:22 UTC (rev 1974)
+++ pkg/vegan/inst/ChangeLog 2011-10-31 18:23:01 UTC (rev 1975)
@@ -4,6 +4,11 @@
Version 2.1-6 (opened October 30, 2011)
+ * FAQ: correct mark-up of hyper links (@uref{} instead of @url{}),
+ add new entries on RDA scaling, scaling of NMDS stress and scaling
+ of environmental arrows in cca/rda/capscale/envfit, plus some
+ minor updates of old entries.
+
* ordispider: returns invisibly the coordinates to which each
point is connected. Triggered by an email query of this
functionality.
Modified: pkg/vegan/inst/doc/FAQ-vegan.texi
===================================================================
--- pkg/vegan/inst/doc/FAQ-vegan.texi 2011-10-31 16:58:22 UTC (rev 1974)
+++ pkg/vegan/inst/doc/FAQ-vegan.texi 2011-10-31 18:23:01 UTC (rev 1975)
@@ -17,7 +17,7 @@
@quotation
This work is licensed under the Creative Commons Attribution 3.0
License. To view a copy of this license, visit
- at url{http://creativecommons.org/licenses/by/3.0/} or send a letter to
+ at uref{http://creativecommons.org/licenses/by/3.0/} or send a letter to
Creative Commons, 543 Howard Street, 5th Floor, San Francisco,
California, 94105, USA.
@@ -66,7 +66,7 @@
@chapter Introduction
@menu
-* What is vegan?::
+* What is vegan?::
* What is R?::
* How to obtain vegan and R?::
* What R packages vegan depends on?::
@@ -113,9 +113,9 @@
@section How to obtain vegan and R?
Both R and latest release version of vegan can be obtained through
- at url{http://cran.r-project.org,,CRAN}. Unstable development version of
+ at uref{http://cran.r-project.org,,CRAN}. Unstable development version of
vegan can be obtained through
- at url{http://r-forge.r-project.org/projects/vegan/,,R-Forge}.
+ at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge}.
@@ -143,7 +143,7 @@
@node What other packages are available for ecologists?, What other documentation is available for vegan?, What R packages vegan depends on?, Introduction
@section What other packages are available for ecologists?
- at acronym{CRAN} @url{http://cran.r-project.org/src/contrib/Views/,,Task
+ at acronym{CRAN} @uref{http://cran.r-project.org/src/contrib/Views/,,Task
Views} include entries like @code{Environmetrics}, @code{Multivariate}
and @code{Spatial} that describe several useful packages and
functions. If you install R package @code{ctv}, you can
@@ -161,7 +161,7 @@
documents included in the vegan package are
@itemize
@item
-Vegan @code{NEWS} (not in the development version: only in CRAN)
+Vegan @code{NEWS}
@item
Vegan @code{ChangeLog}.
@item
@@ -183,9 +183,9 @@
@itemize
@item
- at url{http://vegan.r-forge.r-project.org/}: vegan homepage.
+ at uref{http://vegan.r-forge.r-project.org/}: vegan homepage.
@item
- at url{http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf}: vegan
+ at uref{http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf}: vegan
tutorial.
@end itemize
@@ -195,7 +195,7 @@
Roeland Kindt has made package @code{BiodiversityR} which provides a
GUI for vegan. The package is available at
- at url{http://cran.r-project.org/src/contrib/Descriptions/BiodiversityR.html,,CRAN}.
+ at uref{http://cran.r-project.org/src/contrib/Descriptions/BiodiversityR.html,,CRAN}.
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} using
@@ -212,22 +212,22 @@
@section Version numbering in vegan
From version 1.10-0, vegan is developed at
- at url{http://r-forge.r-project.org/projects/vegan/,,R-Forge} and there
+ 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 url{http://cran.r-project.org,,CRAN}) and devel versions (at
- at url{http://r-forge.r-project.org/projects/vegan/,,R-Forge}).
+ at uref{http://cran.r-project.org,,CRAN}) and devel versions (at
+ at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge}).
Vegan version numbers are of type x.y-z, where number y is odd for
-stable release versions at @url{http://cran.r-project.org,,CRAN} and
+stable release versions at @uref{http://cran.r-project.org,,CRAN} and
even for unstable release versions at
- at url{http://r-forge.r-project.org/projects/vegan,,R-Forge}.
+ at uref{http://r-forge.r-project.org/projects/vegan,,R-Forge}.
@node How to build vegan from sources?, Are there binaries for devel versions?, Version numbering in vegan, Introduction
@section How to build vegan from sources?
In general, you do not need to build vegan from sources, but binary
builds of release versions are available through
- at url{http://cran.r-project.org/,,CRAN} for Windows and MacOS X. If you
+ at uref{http://cran.r-project.org/,,CRAN} 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 @acronym{FORTRAN},
@@ -237,7 +237,7 @@
@node Are there binaries for devel versions?, How to report a bug in vegan?, How to build vegan from sources?, Introduction
@section Are there binaries for devel versions?
- at url{http://r-forge.r-project.org/projects/vegan/,,R-Forge} runs daily
+ at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge} 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
@@ -262,7 +262,7 @@
since vegan is not a standard R package.
There also is a bug reporting tool at
- at url{http://r-forge.r-project.org/projects/vegan/,,R-Forge}, but you
+ at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge}, but you
need to register as a site user to report bugs (this is site policy).
@node Is it a bug or a feature?, Can I contribute to vegan?, How to report a bug in vegan?, Introduction
@@ -301,11 +301,14 @@
* I have only numeric and positive data but vegan still complaints::
* Can you analyse binary or cover class data?::
* Why dissimilarities in vegan differ from other sources?::
+* Why NMDS stress is sometimes 0.1 and sometimes 10?::
* Zero dissimilarities in isoMDS::
+* How the RDA results are scaled?::
* cca fails with ``data.frame expected'' or ``"site.env" missing''::
* Variance explained by ordination axes::
* Is it possible to have passive points in ordination?::
* Class variables and dummies::
+* How are environmental arrows scaled?::
* I want to use Helmert or sum contrasts::
* What are aliased variables and how to see them?::
* Plotting aliased variables::
@@ -338,7 +341,7 @@
analysis) that need count data. These methods check that input data are
integers, but they may be fooled by cover class data.
- at node Why dissimilarities in vegan differ from other sources?, Zero dissimilarities in isoMDS, Can you analyse binary or cover class data?, Ordination
+ at node Why dissimilarities in vegan differ from other sources?, Why NMDS stress is sometimes 0.1 and sometimes 10?, Can you analyse binary or cover class data?, Ordination
@section Why dissimilarities in vegan differ from other sources?
Most commonly the reason is that other software use presence--absence
@@ -352,20 +355,47 @@
Another reason may be that indices indeed are defined differently,
because people use same names for different indices.
- at node Zero dissimilarities in isoMDS, cca fails with ``data.frame expected'' or ``"site.env" missing'', Why dissimilarities in vegan differ from other sources?, Ordination
+ at node Why NMDS stress is sometimes 0.1 and sometimes 10?, Zero dissimilarities in isoMDS, Why dissimilarities in vegan differ from other sources?, Ordination
+ at section Why @acronym{NMDS} stress is sometimes 0.1 and sometimes 10?
+
+Stress is a proportional measure of badness of fit. The proportions can
+be expressed either as parts of one or as percents. Function
+ at code{isoMDS} (MASS package) uses percents, and function @code{monoMDS}
+(vegan package) uses proprotions, and therefore the same stress is 100
+times higher in @code{isoMDS}. The results of @code{goodness} function
+also depend on the definition of stress, and the same @code{goodness} is
+100 times higher in @code{isoMDS} than in @code{monoMDS}. Both of these
+conventions are equally correct.
+
+ at node Zero dissimilarities in isoMDS, How the RDA results are scaled?, Why NMDS stress is sometimes 0.1 and sometimes 10?, Ordination
@section Zero dissimilarities in isoMDS
-You can use argument @code{zerodist = "add"} in @code{metaMDS} or
- at code{metaMDSdist} to handle zero dissimilarities. With this argument,
-zero dissimilarities are replace with a small above zero value, and they
-can be handled in @code{isoMDS}. This is a kluge, and some people do
-not like this. A more principal solution is to remove duplicate sites
-using R command @code{unique}. However, after some standardizations or
-with some dissimilarity indices, originally non-unique sites can have
-zero dissimilarity, and you have to resort to the kluge (or work
-harder with your data).
+Function @code{metaMDS} uses function @code{monoMDS} as its default
+method for @acronym{NMDS}, and this function can handle zero
+dissimilarities. The alternative function @code{isoMDS} was the only
+choice before vegan 2.0-0, and it cannot handle zero dissimilarities. If
+you want to use @code{isoMDS}, you can use argument @code{zerodist =
+"add"} in @code{metaMDS} to handle zero dissimilarities. With this
+argument, zero dissimilarities are replaced with a small above zero
+value, and they can be handled in @code{isoMDS}. This is a kluge, and
+some people do not like this. A more principal solution is to remove
+duplicate sites using R command @code{unique}. However, after some
+standardizations or with some dissimilarity indices, originally
+non-unique sites can have zero dissimilarity, and you have to resort to
+the kluge (or work harder with your data). Usually it is better to use
+ at code{monoMDS}.
- at node cca fails with ``data.frame expected'' or ``"site.env" missing'', Variance explained by ordination axes, Zero dissimilarities in isoMDS, Ordination
+ at node How the RDA results are scaled?, cca fails with ``data.frame expected'' or ``"site.env" missing'', Zero dissimilarities in isoMDS, Ordination
+ at section How the @acronym{RDA} results are scaled?
+
+The scaling or @acronym{RDA} results indeed differ from most other
+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 vegan'' that you can read with
+vegan command @code{vegandocs("decision")}.
+
+ at 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''
This is not a vegan error message, but it comes from the @code{cca}
@@ -451,7 +481,7 @@
row 3 ``passive'': @code{dune[3,] <- 0.001*dune[3,]}.
- at node Class variables and dummies, I want to use Helmert or sum contrasts, Is it possible to have passive points in ordination?, Ordination
+ at node Class variables and dummies, How are environmental arrows scaled?, Is it possible to have passive points in ordination?, Ordination
@section Class variables and dummies
You should define a class variable as an R @code{factor}, and vegan will
@@ -466,11 +496,28 @@
contrasts. Both of these contrasts explained in standard R
documentation.
-You should never make your own dummy variables, but you should use
-standard R factors. R will internally change these factors into
-dummies in a consistent and correct way.
- at node I want to use Helmert or sum contrasts, What are aliased variables and how to see them?, Class variables and dummies, Ordination
+ at node How are environmental arrows scaled?, I want to use Helmert or sum contrasts, Class variables and dummies, Ordination
+ at section How are environmental arrows scaled?
+
+Arrows for continuous environmental variables in constrained ordination
+(@code{cca}, @code{rda}, @code{capscale}) and fitted environmental
+vectors from @code{envfit} are scaled to fill the current graph. The
+lengths of arrows do not have fixed meaning with respect to the points
+(species, sites), but they can only compared against each other, and
+therefore only their relative lengths are important.
+
+If you really want change the scaling of the arrows, you can use
+ at code{text} (plotting arrows and text) or @code{points} (plotting only
+arrows) functions for constrained ordination. These functions have
+argument @code{arrow.mul} which sets the multiplier. The @code{plot}
+function for @code{envfit} also has the @code{arrow.mul} argument to set
+the arrow multiplier. If you save the invisible result of the
+constrained ordination @code{plot} command, you can see the value of the
+currently used @code{arrow.mul} which is saved as an attribute of
+ at code{biplot} scores.
+
+ at node I want to use Helmert or sum contrasts, What are aliased variables and how to see them?, How are environmental arrows scaled?, Ordination
@section I want to use Helmert or sum contrasts
@code{vegan} uses standard R utilities for defining
@@ -508,11 +555,10 @@
@code{anova.cca}, @code{mantel}, @code{mrpp}, @code{envfit} and
@code{protest}.
-Vegan has an alternative permutation function @code{permuted.index2}
-which allows restricted permutation designs for time series, line
-transects, spatial grids and blocking factors. However, that function is
-not developed at the moment. Vegan is going to switch to using a
-separate package (permute) for permutations.
+Vegan will move to use permute package in all its permutation tests, but
+currently this package is only used in @code{permutest.betadisper}. The
+permute package will allow restricted permutation designs for time
+series, line transects, spatial grids and blocking factors.
@node How to use different plotting symbols in ordination graphics?, How to avoid cluttered ordination graphs?, Constrained permutations in vegan, Ordination
@section How to use different plotting symbols in ordination graphics?
Modified: www/FAQ-vegan.html
===================================================================
--- www/FAQ-vegan.html 2011-10-31 16:58:22 UTC (rev 1974)
+++ www/FAQ-vegan.html 2011-10-31 18:23:01 UTC (rev 1975)
@@ -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: 2011-02-17 11:25:56 +0200 (Thu, 17 Feb 2011) $.
+This is version of $Date: 2011-10-31 18:58:22 +0200 (Mon, 31 Oct 2011) $.
This work is licensed under the Creative Commons Attribution 3.0
@@ -14,7 +14,7 @@
Copyright C 2008-2011 Jari Oksanen
-->
-<!-- Created on October, 30 2011 by texi2html 1.70 -->
+<!-- Created on October, 31 2011 by texi2html 1.70 -->
<!--
Written by: Lionel Cons <Lionel.Cons at cern.ch> (original author)
Karl Berry <karl at freefriends.org>
@@ -64,7 +64,7 @@
<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) $.
+This is version of $Date: 2011-10-31 18:58:22 +0200 (Mon, 31 Oct 2011) $.
</p><blockquote>
<p>This work is licensed under the Creative Commons Attribution 3.0
@@ -85,7 +85,7 @@
</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">
+<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>
@@ -167,8 +167,8 @@
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>.
+packages. Vegan 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>
@@ -197,10 +197,10 @@
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>
+<a href="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
+<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">
@@ -225,9 +225,9 @@
<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
+<a href="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>.
+<a href="http://r-forge.r-project.org/projects/vegan/">R-Forge</a>.
</p>
@@ -290,7 +290,7 @@
</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>
+<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 <code>ctv</code>, you can
inspect Task Views from your R session, and automatically install sets
@@ -325,7 +325,7 @@
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>Vegan <code>NEWS</code>
</p></li><li>
<p>Vegan <code>ChangeLog</code>.
</p></li><li>
@@ -376,7 +376,7 @@
<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>.
+<a href="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
@@ -429,15 +429,15 @@
<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
+<a href="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>).
+<a href="http://cran.r-project.org">CRAN</a>) and devel versions (at
+<a href="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
+stable release versions at <a href="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>.
+<a href="http://r-forge.r-project.org/projects/vegan">R-Forge</a>.
</p><hr size="6">
<a name="NOD12"></a>
@@ -462,7 +462,7 @@
<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
+<a href="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,
@@ -490,7 +490,7 @@
</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
+<p><a href="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
@@ -533,7 +533,7 @@
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
+<a href="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">
@@ -610,7 +610,7 @@
<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="#SEC_Top" title="Up section"> Up </a>]</td>
-<td valign="middle" align="left">[<a href="#SEC33" title="Next chapter"> >> </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC36" title="Next chapter"> >> </a>]</td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left"> </td>
@@ -629,32 +629,38 @@
</td></tr>
<tr><td align="left" valign="top"><a href="#SEC19">2.3 Why dissimilarities in vegan differ from other sources?</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC20">2.4 Zero dissimilarities in isoMDS</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#SEC20">2.4 Why NMDS stress is sometimes 0.1 and sometimes 10?</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC21">2.5 cca fails with "data.frame expected" or ""site.env" missing"</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#SEC21">2.5 Zero dissimilarities in isoMDS</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC22">2.6 Variance explained by ordination axes.</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#SEC22">2.6 How the RDA results are scaled?</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC23">2.7 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="#SEC23">2.7 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="#SEC24">2.8 Class variables and dummies</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#SEC24">2.8 Variance explained by ordination axes.</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC25">2.9 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="#SEC25">2.9 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="#SEC26">2.10 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="#SEC26">2.10 Class variables and dummies</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC27">2.11 Plotting aliased variables</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#SEC27">2.11 How are environmental arrows scaled?</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC28">2.12 Constrained permutations in vegan</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#SEC28">2.12 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="#SEC29">2.13 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="#SEC29">2.13 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="#SEC30">2.14 How to avoid cluttered ordination graphs?</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#SEC30">2.14 Plotting aliased variables</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC31">2.15 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="#SEC31">2.15 Constrained permutations in vegan</a></td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top"><a href="#SEC32">2.16 Can I zoom into an ordination plot?</a></td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top"><a href="#SEC32">2.16 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="#SEC33">2.17 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="#SEC34">2.18 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="#SEC35">2.19 Can I zoom into an ordination plot?</a></td><td> </td><td align="left" valign="top">
+</td></tr>
</table>
<hr size="6">
@@ -666,7 +672,7 @@
<td valign="middle" align="left"> </td>
<td valign="middle" align="left">[<a href="#SEC16" title="Beginning of this chapter or previous chapter"> << </a>]</td>
<td valign="middle" align="left">[<a href="#SEC16" title="Up section"> Up </a>]</td>
-<td valign="middle" align="left">[<a href="#SEC33" title="Next chapter"> >> </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC36" title="Next chapter"> >> </a>]</td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left"> </td>
@@ -683,9 +689,9 @@
data. Most common reasons for non-numeric data are that row names were
read as a non-numeric variable instead of being used as row names (check
argument <code>row.names</code> in reading the data), or that the column names
-were interpted as data (check argument <code>header = TRUE</code> in reading
+were interpreted as data (check argument <code>header = TRUE</code> in reading
the data). Another common reason is that you had empty cells in your
-input data, and these were interprted as missing values.
+input data, and these were interpreted as missing values.
</p><hr size="6">
<a name="NOD19"></a>
@@ -696,7 +702,7 @@
<td valign="middle" align="left"> </td>
<td valign="middle" align="left">[<a href="#SEC16" title="Beginning of this chapter or previous chapter"> << </a>]</td>
<td valign="middle" align="left">[<a href="#SEC16" title="Up section"> Up </a>]</td>
-<td valign="middle" align="left">[<a href="#SEC33" title="Next chapter"> >> </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC36" title="Next chapter"> >> </a>]</td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left"> </td>
@@ -723,7 +729,7 @@
<td valign="middle" align="left"> </td>
<td valign="middle" align="left">[<a href="#SEC16" title="Beginning of this chapter or previous chapter"> << </a>]</td>
<td valign="middle" align="left">[<a href="#SEC16" title="Up section"> Up </a>]</td>
-<td valign="middle" align="left">[<a href="#SEC33" title="Next chapter"> >> </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC36" title="Next chapter"> >> </a>]</td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left"> </td>
@@ -755,7 +761,7 @@
<td valign="middle" align="left"> </td>
<td valign="middle" align="left">[<a href="#SEC16" title="Beginning of this chapter or previous chapter"> << </a>]</td>
<td valign="middle" align="left">[<a href="#SEC16" title="Up section"> Up </a>]</td>
-<td valign="middle" align="left">[<a href="#SEC33" title="Next chapter"> >> </a>]</td>
+<td valign="middle" align="left">[<a href="#SEC36" title="Next chapter"> >> </a>]</td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left"> </td>
<td valign="middle" align="left"> </td>
@@ -765,17 +771,16 @@
<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"> 2.4 Zero dissimilarities in isoMDS </h2>
+<h2 class="section"> 2.4 Why NMDS stress is sometimes 0.1 and sometimes 10? </h2>
-<p>You can use argument <code>zerodist = "add"</code> in <code>metaMDS</code> or
-<code>metaMDSdist</code> to handle zero dissimilarities. With this argument,
-zero dissimilarities are replace with a small above zero value, and they
-can be handled in <code>isoMDS</code>. This is a kluge, and some people do
-not like this. A more principal solution is to remove duplicate sites
-using R command <code>unique</code>. However, after some standardizations or
-with some dissimilarity indices, originally non-unique sites can have
-zero dissimilarity, and you have to resort to the kluge (or work
-harder with your data).
+<p>Stress is a proportional measure of badness of fit. The proportions can
+be expressed either as parts of one or as percents. Function
+<code>isoMDS</code> (MASS package) uses percents, and function <code>monoMDS</code>
+(vegan package) uses proprotions, and therefore the same stress is 100
+times higher in <code>isoMDS</code>. The results of <code>goodness</code> function
+also depend on the definition of stress, and the same <code>goodness</code> is
+100 times higher in <code>isoMDS</code> than in <code>monoMDS</code>. Both of these
+conventions are equally correct.
</p><hr size="6">
<a name="NOD22"></a>
@@ -786,7 +791,7 @@
<td valign="middle" align="left"> </td>
<td valign="middle" align="left">[<a href="#SEC16" title="Beginning of this chapter or previous chapter"> << </a>]</td>
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/vegan -r 1975
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