[Vegan-commits] r2010 - branches/2.0/R branches/2.0/inst branches/2.0/inst/doc www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Nov 20 12:21:06 CET 2011
Author: jarioksa
Date: 2011-11-20 12:21:05 +0100 (Sun, 20 Nov 2011)
New Revision: 2010
Modified:
branches/2.0/R/metaMDSdist.R
branches/2.0/inst/
branches/2.0/inst/ChangeLog
branches/2.0/inst/NEWS.Rd
branches/2.0/inst/doc/FAQ-vegan.texi
www/NEWS.html
Log:
merge r2004 (metaMDS(..., noshare=0) fix) and r2007 (FAQ update)
Modified: branches/2.0/R/metaMDSdist.R
===================================================================
--- branches/2.0/R/metaMDSdist.R 2011-11-19 06:54:26 UTC (rev 2009)
+++ branches/2.0/R/metaMDSdist.R 2011-11-20 11:21:05 UTC (rev 2010)
@@ -49,7 +49,7 @@
maxdis <- abs(distfun(matrix(c(7,0,0,3), 2, 2),
method = distance, ...) - 1) < 1e-4
if ((isTRUE(noshare) && any(tmp <- no.shared(comm))) ||
- (noshare > 0 &&
+ (!is.logical(noshare) && noshare >= 0 &&
sum(tmp <- no.shared(comm))/length(dis) > noshare)) {
if (trace)
cat("Using step-across dissimilarities:\n")
Property changes on: branches/2.0/inst
___________________________________________________________________
Deleted: svn:mergeinfo
-
Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog 2011-11-19 06:54:26 UTC (rev 2009)
+++ branches/2.0/inst/ChangeLog 2011-11-20 11:21:05 UTC (rev 2010)
@@ -4,6 +4,9 @@
Version 2.0-3 (opened November 13, 2011)
+ * merge r2007: FAQ update for arrow scaling.
+ * merge r2004: metaMDS(..., noshare=0) triggers stepacross(), but
+ 'noshare = FALSE' never does.
* merge r2001: explain scaling of arrows in envfit() plot() --
this looks like being a FAQ.
Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd 2011-11-19 06:54:26 UTC (rev 2009)
+++ branches/2.0/inst/NEWS.Rd 2011-11-20 11:21:05 UTC (rev 2010)
@@ -2,6 +2,20 @@
\title{vegan News}
\encoding{UTF-8}
+\section{Changes in version 2.0-3}{
+ \subsection{NEW FEATURES}{
+ \itemize{
+
+ \item \code{metaMDS} argument \code{noshare = 0} is now
+ regarded as a numeric threshold that always triggers extended
+ dissimilarities (\code{stepacross}), instead of being treated
+ as synonymous with \code{noshare = FALSE} which always
+ suppresses extended dissimilarities.
+
+ }
+ } % end new features
+} % end version 2.0-3
+
\section{Changes in version 2.0-2}{
\subsection{BUG FIXES}{
\itemize{
@@ -23,12 +37,13 @@
triggering of step-across in \code{capscale(..., metaMDSdist =
TRUE)}.
- \item \code{adonis} contained a minor bug resulting from incomplete
- implementation of a speed-up that did not affect the results. In
- fixing this bug, a further bug was identified in transposing the hat
- matrices. This second bug was only active following fixing of the
- first bug. In fixing both bugs, a speed-up in the internal f.test()
- function is fully realised. Reported by Nicholas Lewin-Koh.
+ \item \code{adonis} contained a minor bug resulting from
+ incomplete implementation of a speed-up that did not affect the
+ results. In fixing this bug, a further bug was identified in
+ transposing the hat matrices. This second bug was only active
+ following fixing of the first bug. In fixing both bugs, a
+ speed-up in the internal f.test() function is fully
+ realised. Reported by Nicholas Lewin-Koh.
}
} % end bug fixes
Modified: branches/2.0/inst/doc/FAQ-vegan.texi
===================================================================
--- branches/2.0/inst/doc/FAQ-vegan.texi 2011-11-19 06:54:26 UTC (rev 2009)
+++ branches/2.0/inst/doc/FAQ-vegan.texi 2011-11-20 11:21:05 UTC (rev 2010)
@@ -497,23 +497,30 @@
@node How are environmental arrows scaled?, I want to use Helmert or sum contrasts, Class variables and dummies, Ordination
@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.
+The printed output of @code{envfit} gives the direction cosines which
+are the coordinates of unit length arrows. For plotting, these are
+scaled by their correlation (square roots of column @code{r2}). You can
+see the scaled lengths of @code{envfit} arrows using command
+ at code{scores}.
-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.
+The scaled environmental vectors from @code{envfit} and the arrows for
+continuous environmental variables in constrained ordination
+(@code{cca}, @code{rda}, @code{capscale}) are adjusted 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 want change the scaling of the arrows, you can use @code{text}
+(plotting arrows and text) or @code{points} (plotting only arrows)
+functions for constrained ordination. These functions have argument
+ at 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 @code{biplot}
+scores.
+
An unexported function @code{ordiArrowMul} is used to find the scaling
for the current plot. You can use this function to see how arrows would
be scaled:
Modified: www/NEWS.html
===================================================================
--- www/NEWS.html 2011-11-19 06:54:26 UTC (rev 2009)
+++ www/NEWS.html 2011-11-20 11:21:05 UTC (rev 2010)
@@ -2,256 +2,442 @@
<html><head><title>R: vegan News</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<link rel="stylesheet" type="text/css" href="R.css">
-</head>
-<body>
+</head><body>
-<table width="100%" summary="page for NEWS">
- <tr><td>NEWS</td><td align="right">R Documentation</td></tr>
-</table>
+<table width="100%" summary="page for NEWS"><tr><td>NEWS</td><td align="right">R Documentation</td></tr></table>
<h2>vegan News</h2>
+<h3>Changes in version 2.0-3</h3>
+
+<p>
+
+
+<h4>NEW FEATURES</h4>
+
+<p>
+
+</p>
+<p>
+<ul>
+<li> <code>metaMDS</code> argument <code>noshare = 0</code> is now
+regarded as a numeric threshold that always triggers extended
+dissimilarities (<code>stepacross</code>), instead of being treated
+as synonymous with <code>noshare = FALSE</code> which always
+suppresses extended dissimilarities.
+</p>
+<p>
+</ul>
+
+</p>
+
+</p>
+
+
<h3>Changes in version 2.0-2</h3>
+<p>
+
+
<h4>BUG FIXES</h4>
+
+<p>
+
+</p>
+<p>
<ul>
- <li> Function <code>capscale</code> failed if constrained component
- had zero rank. This happened most likely in partial models when
- the conditions aliased constraints. The problem was observed in
- <code>anova(..., by ="margin")</code> which uses partial models to
- analyses the marginal effects, and was reported in an email
- message to
- <a href="https://stat.ethz.ch/pipermail/r-help/2011-October/293077.html">R-News mailing list</a>.
- </li>
- <li><code>stressplot</code> and <code>goodness</code> sometimes failed when
- <code>metaMDS</code> was based on <code>isoMDS</code> (<span class="pkg">MASS</span> package)
- because <code>metaMDSdist</code> did not use the same defaults for
- step-across (extended) dissimilarities as <code>metaMDS(...,
- engine = "isoMDS")</code>. The change of defaults can also influence
- triggering of step-across in <code>capscale(..., metaMDSdist =
- TRUE)</code>.
- <li><code>adonis</code> contained a minor bug resulting from incomplete
- implementation of a speed-up that did not affect the results. In
- fixing this bug, a further bug was identified in transposing the hat
- matrices. This second bug was only active following fixing of the
- first bug. In fixing both bugs, a speed-up in the internal f.test()
- function is fully realised. Reported by Nicholas Lewin-Koh.
- </li>
+<li> Function <code>capscale</code> failed if constrained component
+had zero rank. This happened most likely in partial models when
+the conditions aliased constraints. The problem was observed in
+<code>anova(..., by ="margin")</code> which uses partial models to
+analyses the marginal effects, and was reported in an email
+message to
+<a href="https://stat.ethz.ch/pipermail/r-help/2011-October/293077.html">R-News
+mailing list</a>.
+</p>
+<p>
+</li>
+<li><code>stressplot</code> and <code>goodness</code> sometimes failed when
+<code>metaMDS</code> was based on <code>isoMDS</code> (<span class="pkg">MASS</span> package)
+because <code>metaMDSdist</code> did not use the same defaults for
+step-across (extended) dissimilarities as <code>metaMDS(...,
+ engine = "isoMDS")</code>. The change of defaults can also influence
+triggering of step-across in <code>capscale(..., metaMDSdist =
+ TRUE)</code>.
+</p>
+<p>
+</li>
+<li><code>adonis</code> contained a minor bug resulting from
+incomplete implementation of a speed-up that did not affect the
+results. In fixing this bug, a further bug was identified in
+transposing the hat matrices. This second bug was only active
+following fixing of the first bug. In fixing both bugs, a
+speed-up in the internal f.test() function is fully
+realised. Reported by Nicholas Lewin-Koh.
+</p>
+<p>
</ul>
+</p>
+
+</p>
+<p>
+
+
<h4>NEW FEATURES</h4>
+<p>
+
+</p>
+<p>
<ul>
- <li> <code>ordiarrows</code> and <code>ordisegments</code> gained argument
- <code>order.by</code> that gives a variable to sort points within
- <code>groups</code>. Earlier the points were assumed to be in order.
- </li>
- <li>Function <code>ordispider</code> invisibly returns the
- coordinates to which the points were connected. Typically these
- are class centroids of each point, but for constrained ordination
- with no <code>groups</code> they are the LC scores.
- </li>
+<li> <code>ordiarrows</code> and <code>ordisegments</code> gained argument
+<code>order.by</code> that gives a variable to sort points within
+<code>groups</code>. Earlier the points were assumed to be in order.
+</p>
+<p>
+</li>
+<li>Function <code>ordispider</code> invisibly returns the
+coordinates to which the points were connected. Typically these
+are class centroids of each point, but for constrained ordination
+with no <code>groups</code> they are the LC scores.
+</p>
+<p>
</ul>
+
+</p>
+
+</p>
+<p>
+</p>
+
<h3>Changes in version 2.0-1</h3>
+<p>
+
+
<h4>NEW FUNCTIONS</h4>
+<p>
+
+</p>
+<p>
<ul>
- <li> <code>clamtest</code>: new function to classify species as
- generalists and specialists in two distinct habitats (CLAM test of
- Chazdon et al., <em>Ecology</em> 92, 1332–1343; 2011). The test is
- based on multinomial distribution of individuals in two habitat
- types or sampling units, and it is applicable only to count data
- with no over-dispersion.
- </li>
- <li><code>as.preston</code> gained <code>plot</code> and <code>lines</code>
- methods, and <code>as.fisher</code> gained <code>plot</code> method (which
- also can add items to existing plots). These are similar as
- <code>plot</code> and <code>lines</code> for <code>prestonfit</code> and
- <code>fisherfit</code>, but display only data without the fitted lines.
- </li>
- <li><code>raupcrick</code>: new function to implement Raup-Crick
- dissimilarity as a probability of number of co-occurring species
- with occurrence probabilities proportional to species
- frequencies. <span class="pkg">Vegan</span> has Raup-Crick index as a choice in
- <code>vegdist</code>, but that uses equal sampling probabilities for
- species and analytic equations. The new <code>raupcrick</code>
- function uses simulation with <code>oecosimu</code>. The function
- follows Chase et al. (2011) <em>Ecosphere</em> 2:art24
- [<a href="http://www.esajournals.org/doi/abs/10.1890/ES10-00117.1">doi:10.1890/ES10-00117.1</a>],
- and was developed with the consultation of Brian Inouye.
- </li>
+<li> <code>clamtest</code>: new function to classify species as
+generalists and specialists in two distinct habitats (CLAM test of
+Chazdon et al., <EM>Ecology</EM> 92, 1332–1343; 2011). The test is
+based on multinomial distribution of individuals in two habitat
+types or sampling units, and it is applicable only to count data
+with no over-dispersion.
+</p>
+<p>
+</li>
+<li><code>as.preston</code> gained <code>plot</code> and <code>lines</code>
+methods, and <code>as.fisher</code> gained <code>plot</code> method (which
+also can add items to existing plots). These are similar as
+<code>plot</code> and <code>lines</code> for <code>prestonfit</code> and
+<code>fisherfit</code>, but display only data without the fitted lines.
+</p>
+<p>
+</li>
+<li><code>raupcrick</code>: new function to implement Raup-Crick
+dissimilarity as a probability of number of co-occurring species
+with occurrence probabilities proportional to species
+frequencies. <span class="pkg">Vegan</span> has Raup-Crick index as a choice in
+<code>vegdist</code>, but that uses equal sampling probabilities for
+species and analytic equations. The new <code>raupcrick</code>
+function uses simulation with <code>oecosimu</code>. The function
+follows Chase et al. (2011) <EM>Ecosphere</EM> 2:art24
+[<a href="http://www.esajournals.org/doi/abs/10.1890/ES10-00117.1">doi:10.1890/ES10-00117.1</a>],
+and was developed with the consultation of Brian Inouye.
+</p>
+<p>
</ul>
+</p>
+
+</p>
+<p>
+
+
<h4>BUG FIXES</h4>
+<p>
+
+</p>
+<p>
<ul>
- <li> Function <code>meandist</code> could scramble items and give
- wrong results, especially when the <code>grouping</code> was
- numerical. The problem was reported by Dr Miguel Alvarez
- (Univ. Bonn).
- </li>
- <li><code>metaMDS</code> did not reset <code>tries</code> when a new model
- was started with a <code>previous.best</code> solution from a different
- model.
- </li>
- <li>Function <code>permatswap</code> for community null models using
- quantitative swap never swapped items in a <em>2 by 2</em>
- submatrix if all cells were filled.
- </li>
- <li>The result from <code>permutest.cca</code> could not be
- <code>update</code>d because of a ‘<span class="file">NAMESPACE</span>’ issue.
- </li>
- <li><font face="Courier New,Courier" color="#666666"><b>R</b></font> 2.14.0 changed so that it does not accept using
- <code>sd()</code> function for matrices (which was the behaviour at
- least since <font face="Courier New,Courier" color="#666666"><b>R</b></font> 1.0-0), and several <span class="pkg">vegan</span> functions were
- changed to adapt to this change (<code>rda</code>, <code>capscale</code>,
- <code>simulate</code> methods for <code>rda</code>, <code>cca</code> and
- <code>capscale</code>). The change in <font face="Courier New,Courier" color="#666666"><b>R</b></font> 2.14.0 does not influence the
- results but you probably wish to upgrade <span class="pkg">vegan</span> to
- avoid annoying warnings.
- </li>
+<li> Function <code>meandist</code> could scramble items and give
+wrong results, especially when the <code>grouping</code> was
+numerical. The problem was reported by Dr Miguel Alvarez
+(Univ. Bonn).
+</p>
+<p>
+</li>
+<li><code>metaMDS</code> did not reset <code>tries</code> when a new model
+was started with a <code>previous.best</code> solution from a different
+model.
+</p>
+<p>
+</li>
+<li>Function <code>permatswap</code> for community null models using
+quantitative swap never swapped items in a <i>2 by 2</i>
+submatrix if all cells were filled.
+</p>
+<p>
+</li>
+<li>The result from <code>permutest.cca</code> could not be
+<code>update</code>d because of a ‘<span class="file">NAMESPACE</span>’ issue.
+</p>
+<p>
+</li>
+<li><font face="Courier New,Courier" color="#666666"><b>R</b></font> 2.14.0 changed so that it does not accept using
+<code>sd()</code> function for matrices (which was the behaviour at
+least since <font face="Courier New,Courier" color="#666666"><b>R</b></font> 1.0-0), and several <span class="pkg">vegan</span> functions were
+changed to adapt to this change (<code>rda</code>, <code>capscale</code>,
+<code>simulate</code> methods for <code>rda</code>, <code>cca</code> and
+<code>capscale</code>). The change in <font face="Courier New,Courier" color="#666666"><b>R</b></font> 2.14.0 does not influence the
+results but you probably wish to upgrade <span class="pkg">vegan</span> to avoid
+annoying warnings.
+</p>
+<p>
</ul>
+
+</p>
+
+</p>
+<p>
+
<h4>ANALYSES</h4>
+<p>
+
+</p>
+<p>
<ul>
- <li> <code>nesteddisc</code> is slacker and hence faster when trying
- to optimize the statistic for tied column frequencies. Tracing
- showed that in most cases an improved ordering was found rather
- early in tries, and the results are equally good in most cases.
- </li>
+<li> <code>nesteddisc</code> is slacker and hence faster when trying
+to optimize the statistic for tied column frequencies. Tracing
+showed that in most cases an improved ordering was found rather
+early in tries, and the results are equally good in most cases.
+</p>
+<p>
</ul>
+</p>
+
+</p>
+<p>
+</p>
+
+
<h3>Changes in version 2.0-0</h3>
+<p>
+
+
<h4>GENERAL</h4>
+<p>
+
+</p>
+<p>
<ul>
- <li> Peter Minchin joins the <span class="pkg">vegan</span> team.
- </li>
- <li><span class="pkg">vegan</span> implements standard <font face="Courier New,Courier" color="#666666"><b>R</b></font> ‘<span class="file">NAMESPACE</span>’. In
- general, <code>S3</code> methods are not exported which means that you
- cannot directly use or see contents of functions like
- <code>cca.default</code>, <code>plot.cca</code> or <code>anova.ccabyterm</code>. To
- use these functions you should rely on <font face="Courier New,Courier" color="#666666"><b>R</b></font> delegation and simply
- use <code>cca</code> and for its result objects use <code>plot</code> and
- <code>anova</code> without suffix <code>.cca</code>. To see the contents of
- the function you can use <code>:::</code>, such as
- <code>vegan:::cca.default</code>. This change may break packages,
- documents or scripts that rely on non-exported names.
- </li>
- <li><span class="pkg">vegan</span> depends on the <span class="pkg">permute</span> package. This
- package provides powerful tools for restricted permutation
- schemes. All <span class="pkg">vegan</span> permutation will gradually move to use
- <span class="pkg">permute</span>, but currently only <code>betadisper</code> uses the new
- feature.
- </li>
+<li> Peter Minchin joins the <span class="pkg">vegan</span> team.
+</p>
+<p>
+</li>
+<li><span class="pkg">vegan</span> implements standard <font face="Courier New,Courier" color="#666666"><b>R</b></font> ‘<span class="file">NAMESPACE</span>’. In
+general, <code>S3</code> methods are not exported which means that you
+cannot directly use or see contents of functions like
+<code>cca.default</code>, <code>plot.cca</code> or <code>anova.ccabyterm</code>. To
+use these functions you should rely on <font face="Courier New,Courier" color="#666666"><b>R</b></font> delegation and simply
+use <code>cca</code> and for its result objects use <code>plot</code> and
+<code>anova</code> without suffix <code>.cca</code>. To see the contents of
+the function you can use <code>:::</code>, such as
+<code>vegan:::cca.default</code>. This change may break packages,
+documents or scripts that rely on non-exported names.
+</p>
+<p>
+</li>
+<li><span class="pkg">vegan</span> depends on the <span class="pkg">permute</span> package. This
+package provides powerful tools for restricted permutation
+schemes. All <span class="pkg">vegan</span> permutation will gradually move to use
+<span class="pkg">permute</span>, but currently only <code>betadisper</code> uses the new
+feature.
+</p>
+<p>
</ul>
+</p>
+
+</p>
+<p>
+
+
<h4>NEW FUNCTIONS</h4>
+<p>
+
+</p>
+<p>
<ul>
- <li> <code>monoMDS</code>: a new function for non-metric
- multidimensional scaling (NMDS). This function replaces
- <code>MASS::isoMDS</code> as the default method in
- <code>metaMDS</code>. Major advantages of <code>monoMDS</code> are that it
- has ‘weak’ (‘primary’) tie treatment which means
- that it can split tied observed dissimilarities. ‘Weak’
- tie treatment improves ordination of heterogeneous data sets,
- because maximum dissimilarities of <i>1</i> can be split. In
- addition to global NMDS, <code>monoMDS</code> can perform local and
- hybrid NMDS and metric MDS. It can also handle missing and zero
- dissimilarities. Moreover, <code>monoMDS</code> is faster than
- previous alternatives. The function uses <code>Fortran</code> code
- written by Peter Minchin.
- </li>
- <li><code>MDSrotate</code> a new function to replace
- <code>metaMDSrotate</code>. This function can rotate both
- <code>metaMDS</code> and <code>monoMDS</code> results so that the first
- axis is parallel to an environmental vector.
- </li>
- <li><code>eventstar</code> finds the minimum of the evenness profile
- on the Tsallis entropy, and uses this to find the corresponding
- values of diversity, evenness and numbers equivalent following
- Mendes et al. (<em>Ecography</em> 31, 450-456; 2008). The code was
- contributed by Eduardo Ribeira Cunha and Heloisa Beatriz Antoniazi
- Evangelista and adapted to <span class="pkg">vegan</span> by Peter
- Solymos.
- </li>
- <li><code>fitspecaccum</code> fits non-linear regression models to
- the species accumulation results from <code>specaccum</code>. The
- function can use new self-starting species accumulation models
- in <span class="pkg">vegan</span> or other self-starting non-linear
- regression models in <font face="Courier New,Courier" color="#666666"><b>R</b></font>.
- The function can fit Arrhenius, Gleason, Gitay, Lomolino
- (in <span class="pkg">vegan</span>), asymptotic, Gompertz,
- Michaelis-Menten, logistic and Weibull (in base <font face="Courier New,Courier" color="#666666"><b>R</b></font>) models. The
- function has <code>plot</code> and <code>predict</code> methods.
- </li>
- <li>Self-starting non-linear species accumulation models
- <code>SSarrhenius</code>, <code>SSgleason</code>, <code>SSgitay</code> and
- <code>SSlomolino</code>. These can be used with <code>fitspecaccum</code> or
- directly in non-linear regression with <code>nls</code>. These functions
- were implemented because they were found good for species-area
- models by Dengler (<em>J. Biogeogr.</em> 36, 728-744; 2009).
+<li> <code>monoMDS</code>: a new function for non-metric
+multidimensional scaling (NMDS). This function replaces
+<code>MASS::isoMDS</code> as the default method in
+<code>metaMDS</code>. Major advantages of <code>monoMDS</code> are that it
+has ‘weak’ (‘primary’) tie treatment which means
+that it can split tied observed dissimilarities. ‘Weak’
+tie treatment improves ordination of heterogeneous data sets,
+because maximum dissimilarities of <i>1</i> can be split. In
+addition to global NMDS, <code>monoMDS</code> can perform local and
+hybrid NMDS and metric MDS. It can also handle missing and zero
+dissimilarities. Moreover, <code>monoMDS</code> is faster than
+previous alternatives. The function uses <code>Fortran</code> code
+written by Peter Minchin.
+</p>
+<p>
+</li>
+<li><code>MDSrotate</code> a new function to replace
+<code>metaMDSrotate</code>. This function can rotate both <code>metaMDS</code>
+and <code>monoMDS</code> results so that the first axis is parallel to
+an environmental vector.
+</p>
+<p>
+</li>
+<li><code>eventstar</code> finds the minimum of the evenness profile
+on the Tsallis entropy, and uses this to find the corresponding
+values of diversity, evenness and numbers equivalent following
+Mendes et al. (<EM>Ecography</EM> 31, 450-456; 2008). The code was
+contributed by Eduardo Ribeira Cunha and Heloisa Beatriz Antoniazi
+Evangelista and adapted to <span class="pkg">vegan</span> by Peter Solymos.
+</p>
+<p>
+</li>
+<li><code>fitspecaccum</code> fits non-linear regression models to
+the species accumulation results from <code>specaccum</code>. The
+function can use new self-starting species accumulation models
+in <span class="pkg">vegan</span> or other self-starting non-linear regression
+models in <font face="Courier New,Courier" color="#666666"><b>R</b></font>. The function can fit Arrhenius, Gleason, Gitay,
+Lomolino (in <span class="pkg">vegan</span>), asymptotic, Gompertz,
+Michaelis-Menten, logistic and Weibull (in base <font face="Courier New,Courier" color="#666666"><b>R</b></font>) models. The
+function has <code>plot</code> and <code>predict</code> methods.
+</p>
+<p>
+</li>
+<li>Self-starting non-linear species accumulation models
+<code>SSarrhenius</code>, <code>SSgleason</code>, <code>SSgitay</code> and
+<code>SSlomolino</code>. These can be used with <code>fitspecaccum</code> or
+directly in non-linear regression with <code>nls</code>. These functions
+were implemented because they were found good for species-area
+models by Dengler (<EM>J. Biogeogr.</EM> 36, 728-744; 2009).
+</p>
+<p>
</ul>
+</p>
+
+</p>
+<p>
+
+
<h4>NEW FEATURES</h4>
+<p>
+
+</p>
+<p>
<ul>
- <li> <code>adonis</code>, <code>anosim</code>, <code>meandist</code> and
- <code>mrpp</code> warn on negative dissimilarities, and
- <code>betadisper</code> refuses to analyse them. All these functions
- expect dissimilarities, and giving something else (like
- correlations) probably is a user error.
- </li>
- <li><code>betadisper</code> uses restricted permutation of the
- <span class="pkg">permute</span> package.
- </li>
- <li><code>metaMDS</code> uses <code>monoMDS</code> as its default ordination
- engine. Function gains new argument <code>engine</code> that can be used
- to alternatively select <code>MASS::isoMDS</code>. The default is not
- to use <code>stepacross</code> with <code>monoMDS</code> because its
- ‘weak’ tie treatment can cope with tied maximum
- dissimilarities of one. However, <code>stepacross</code> is the default
- with <code>isoMDS</code> because it cannot handle adequately these tied
- maximum dissimilarities.
- </li>
- <li><code>specaccum</code> gained <code>predict</code> method which uses
- either linear or spline interpolation for data between observed
- points. Extrapolation is possible with spline interpolation, but
- may make little sense.
- </li>
- <li><code>specpool</code> can handle missing values or empty factor
- levels in the grouping factor <code>pool</code>. Now also checks that
- the length of the <code>pool</code> matches the number of
- observations.
- </li>
+<li> <code>adonis</code>, <code>anosim</code>, <code>meandist</code> and
+<code>mrpp</code> warn on negative dissimilarities, and
+<code>betadisper</code> refuses to analyse them. All these functions
+expect dissimilarities, and giving something else (like
+correlations) probably is a user error.
+</p>
+<p>
+</li>
+<li><code>betadisper</code> uses restricted permutation of the
+<span class="pkg">permute</span> package.
+</p>
+<p>
+</li>
+<li><code>metaMDS</code> uses <code>monoMDS</code> as its default ordination
+engine. Function gains new argument <code>engine</code> that can be used
+to alternatively select <code>MASS::isoMDS</code>. The default is not
+to use <code>stepacross</code> with <code>monoMDS</code> because its
+‘weak’ tie treatment can cope with tied maximum
+dissimilarities of one. However, <code>stepacross</code> is the default
+with <code>isoMDS</code> because it cannot handle adequately these tied
+maximum dissimilarities.
+</p>
+<p>
+</li>
+<li><code>specaccum</code> gained <code>predict</code> method which uses
+either linear or spline interpolation for data between observed
+points. Extrapolation is possible with spline interpolation, but
+may make little sense.
+</p>
+<p>
+</li>
+<li><code>specpool</code> can handle missing values or empty factor
+levels in the grouping factor <code>pool</code>. Now also checks that
+the length of the <code>pool</code> matches the number of
+observations.
+</p>
+<p>
</ul>
+</p>
+
+</p>
+<p>
+
+
<h4>DEPRECATED AND DEFUNCT</h4>
+<p>
+
+</p>
+<p>
<ul>
- <li> <code>metaMDSrotate</code> was replaced with <code>MDSrotate</code>
- that can also handle the results of <code>monoMDS</code>.
- </li>
- <li><code>permuted.index2</code> and other “new” permutation
- code was removed in favour of the <span class="pkg">permute</span> package.
- This code was not intended for normal use, but packages depending on that
- code in <span class="pkg">vegan</span> should instead depend on
- <span class="pkg">permute</span>.
- </li>
+<li> <code>metaMDSrotate</code> was replaced with <code>MDSrotate</code>
+that can also handle the results of <code>monoMDS</code>.
+</p>
+<p>
+</li>
+<li><code>permuted.index2</code> and other “new” permutation
+code was removed in favour of the <span class="pkg">permute</span> package. This code
+was not intended for normal use, but packages depending on that
+code in <span class="pkg">vegan</span> should instead depend on <span class="pkg">permute</span>.
+</p>
+<p>
</ul>
+
+</p>
+<p>
+</p>
+
+</p>
+<p>
+
<h4>ANALYSES</h4>
+<p>
+
+</p>
+<p>
<ul>
- <li> <code>treeheight</code> uses much snappier code. The results
- should be unchanged.
- </li>
+<li> <code>treeheight</code> uses much snappier code. The results
+should be unchanged.
+</p>
+<p>
</ul>
-</body>
-</html>
+</p>
+
+</p>
+
+
+</body></html>
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