[Vegan-commits] r1998 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Nov 13 15:33:01 CET 2011
Author: gsimpson
Date: 2011-11-13 15:33:01 +0100 (Sun, 13 Nov 2011)
New Revision: 1998
Modified:
www/NEWS.html
Log:
more clean up of extraneous p tags, missing closing li tags, plus change EM tag to em tags, and replace i tags with em tags
Modified: www/NEWS.html
===================================================================
--- www/NEWS.html 2011-11-13 14:22:47 UTC (rev 1997)
+++ www/NEWS.html 2011-11-13 14:33:01 UTC (rev 1998)
@@ -57,325 +57,201 @@
<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.
-</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>
+ <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>
</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).
-</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>
+ <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>
</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.
-</p>
-<p>
+ <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>
</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.
-</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>
+ <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>
</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.
-</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>
+ <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).
</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.
-</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>
+ <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>
</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>.
-</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>
+ <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>
</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.
-</p>
-<p>
+ <li> <code>treeheight</code> uses much snappier code. The results
+ should be unchanged.
+ </li>
</ul>
-</p>
-
-</p>
-
-
-</body></html>
+</body>
+</html>
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