[Vegan-commits] r2907 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 6 14:43:26 CET 2014
Author: jarioksa
Date: 2014-11-06 14:43:26 +0100 (Thu, 06 Nov 2014)
New Revision: 2907
Modified:
www/NEWS.html
Log:
Update NEWS.html to vegan 2.2-0
Modified: www/NEWS.html
===================================================================
--- www/NEWS.html 2014-11-06 09:17:29 UTC (rev 2906)
+++ www/NEWS.html 2014-11-06 13:43:26 UTC (rev 2907)
@@ -1,10 +1,9 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<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">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><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>
-<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 style="text-align: right;">R Documentation</td></tr></table>
<h2>vegan News</h2>
@@ -22,32 +21,31 @@
integer giving the number of parallel processes. In unix-alikes
(Mac OS, Linux) this will launch <code>"multicore"</code> processing
and in Windows it will set up <code>"snow"</code> clusters as desribed
-in the documentation of <span class="pkg">parallel</span> package. If <code>option</code>
+in the documentation of the <span class="pkg">parallel</span> package. If <code>option</code>
<code>"mc.cores"</code> is set to an integer > 1, this will be used to
automatically start parallel processing. Finally, the argument
can also be a previously set up <code>"snow"</code> cluster which will
be used both in Windows and in unix-alikes. <span class="pkg">Vegan</span> vignette
on Design decision explains the implementation (use
<code>vegandocs("decission")</code>, and <span class="pkg">parallel</span> package has more
-extensive documentation on parallel processing in <font face="Courier New,Courier" color="#666666"><b>R</b></font>.
+extensive documentation on parallel processing in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.
</p>
<p>The following function use parallel processing in analysing
-permutatin statistics: <code>adonis</code>, <code>anosim</code>,
+permutation statistics: <code>adonis</code>, <code>anosim</code>,
<code>anova.cca</code> (and <code>permutest.cca</code>), <code>mantel</code> (and
-<code>mantel.partial</code>), <code>mrpp</code>, <code>permutest.betadisper</code>
-and <code>simper</code>. In addition, <code>bioenv</code> can compare
-several candidate sets of models in paralle, <code>metaMDS</code> can
-launch several random starts in parallel, and <code>oecosimu</code>
-can evaluate test statistics for several null models in
-parallel.
+<code>mantel.partial</code>), <code>mrpp</code>, <code>ordiareatest</code>,
+<code>permutest.betadisper</code> and <code>simper</code>. In addition,
+<code>bioenv</code> can compare several candidate sets of models in
+paralle, <code>metaMDS</code> can launch several random starts in
+parallel, and <code>oecosimu</code> can evaluate test statistics for
+several null models in parallel.
</p>
</li>
-<li><p> All permutation tests are based on the <span class="pkg">permute</span>
-package which offers strong tools for restricted
-permutation. All these functions have argument
-<code>permutations</code>. The default usage of simple non-restricted
-permutations is achieved by giving a single integer number as
-its argument. Restricted permutations can be defined using the
+<li><p> All permutation tests are based on the <span class="pkg">permute</span> package
+which offers strong tools for restricted permutation. All these
+functions have argument <code>permutations</code>. The default usage of
+simple non-restricted permutations is achieved by giving a single
+integer number. Restricted permutations can be defined using the
<code>how</code> function of the <span class="pkg">permute</span> package. Finally, the
argument can be a permutation matrix where rows define
permutations. It is possible to use external or user constructed
@@ -60,13 +58,13 @@
<code>vegandocs("permutations")</code>.
</p>
<p>The following functions use the <span class="pkg">permute</span> package:
-<code>CCorA</code>, <code>adonis</code>, <code>anosim</code>, <code>anova.cca</code>
-(plus associated <code>permutest.cca</code>, <code>add1.cca</code>,
+<code>CCorA</code>, <code>adonis</code>, <code>anosim</code>, <code>anova.cca</code> (plus
+associated <code>permutest.cca</code>, <code>add1.cca</code>,
<code>drop1.cca</code>, <code>ordistep</code>, <code>ordiR2step</code>),
<code>envfit</code> (plus associated <code>factorfit</code> and
<code>vectorfit</code>), <code>mantel</code> (and <code>mantel.partial</code>),
-<code>mrpp</code>, <code>mso</code>, <code>permutest.betadisper</code>,
-<code>protest</code> and <code>simper</code>.
+<code>mrpp</code>, <code>mso</code>, <code>ordiareatest</code>,
+<code>permutest.betadisper</code>, <code>protest</code> and <code>simper</code>.
</p>
</li>
<li><p> Community null model generation has been completely
@@ -93,7 +91,7 @@
<ul>
<li> <p><span class="pkg">vegan</span> package dependencies and namespace imports
-were adapted to changes in <font face="Courier New,Courier" color="#666666"><b>R</b></font>, and no more trigger warnings and
+were adapted to changes in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>, and no more trigger warnings and
notes in package tests.
</p>
</li>
@@ -112,7 +110,7 @@
<ul>
<li><p> Function <code>dispweight</code> implements dispersion weighting
-of Clarke et al. (<EM>Marine Ecology Progress Series</EM>, 320,
+of Clarke et al. (<em>Marine Ecology Progress Series</em>, 320,
11–27). In addition, we implemented a new method for
generalized dispersion weighting <code>gdispweight</code>. Both
methods downweight species that are significantly
@@ -122,29 +120,35 @@
<li><p> New <code>hclust</code> support functions <code>reorder</code>,
<code>rev</code> and <code>scores</code>. Functions <code>reorder</code> and
<code>rev</code> are similar as these functions for <code>dendrogram</code>
-objects. However, <code>reorder</code> can use (and defaults to)
-weighted mean. In weighted mean the node average is always the
+objects in base <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>. However, <code>reorder</code> can use (and defaults
+to) weighted mean. In weighted mean the node average is always the
mean of member leaves, whereas the <code>dendrogram</code> uses always
-the unweighted means of joined branches.
+unweighted means of joined branches.
</p>
</li>
-<li> <p><code>permustats</code> to extract and inspect permutation
+<li><p> Function <code>ordiareatest</code> supplements <code>ordihull</code> and
+<code>ordiellipse</code> and provides a randomization test for the
+one-sided alternative hypothesis that convex hulls or ellipses in
+two-dimensional ordination space have smaller areas than with
+randomized groups.
+</p>
+</li>
+<li><p> Function <code>permustats</code> extracts and inspects permutation
results with support functions <code>summary</code>, <code>density</code>,
<code>densityplot</code>, <code>qqnorm</code> and <code>qqmath</code>. The
-<code>density</code> and <code>qqnorm</code> are standard <font face="Courier New,Courier" color="#666666"><b>R</b></font> tools that
-only work with one statistic, and <code>densityplot</code> and
-<code>qqmath</code> are <span class="pkg">lattice</span> graphics that work with
-univariate and multivariate statistics. The results of following
-functions can be extracted: <code>anosim</code>, <code>adonis</code>,
-<code>mantel</code> (and <code>mantel.partial</code>), <code>mrpp</code>,
-<code>oecosimu</code>, <code>permustest.cca</code> (but not the
-corresponding <code>anova</code> methods),
-<code>permutest.betadisper</code>, and <code>protest</code>.
+<code>density</code> and <code>qqnorm</code> are standard <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> tools that only
+work with one statistic, and <code>densityplot</code> and <code>qqmath</code>
+are <span class="pkg">lattice</span> graphics that work with univariate and
+multivariate statistics. The results of following functions can be
+extracted: <code>anosim</code>, <code>adonis</code>, <code>mantel</code> (and
+<code>mantel.partial</code>), <code>mrpp</code>, <code>oecosimu</code>,
+<code>permustest.cca</code> (but not the corresponding <code>anova</code>
+methods), <code>permutest.betadisper</code>, and <code>protest</code>.
</p>
</li>
-<li> <p><code>stressplot</code> functions display the ordination
-distances at given number of dimensions against original
-distances. These are a generalization of <code>stressplot</code> for
+<li> <p><code>stressplot</code> functions display the ordination distances
+at given number of dimensions against original distances. The
+method functins are similar to <code>stressplot</code> for
<code>metaMDS</code>, and always use the inherent distances of each
ordination method. The functions are available for the results
<code>capscale</code>, <code>cca</code>, <code>princomp</code>, <code>prcomp</code>,
@@ -164,7 +168,7 @@
</p>
</li>
<li> <p><code>ordiellipse</code> can handle points exactly on a line,
-including only two points.
+including only two points (with a warning).
</p>
</li>
<li><p> plotting <code>radfit</code> results for several species failed if
@@ -239,18 +243,45 @@
distance in addition to the default Euclidean.
</p>
</li>
-<li><p> User can set colours and line types in unction
+<li><p> User can set colours and line types in function
<code>rarecurve</code> for plotting rarefaction curves.
</p>
</li>
<li> <p><code>spantree</code> gained a support function <code>as.hclust</code>
-to change the minimum spannig tree into an <code>hclust</code> tree.
+to change the minimum spanning tree into an <code>hclust</code> tree.
</p>
</li>
<li> <p><code>fitspecaccum</code> can do weighted analysis. Gained
<code>lines</code> method.
</p>
</li>
+<li><p> Functions for extrapolated number of species or for the size
+of species pool using Chao method were modified following Chiu et
+al., <em>Biometrics</em> 70, 671–682 (2014).
+</p>
+<p>Incidence based <code>specpool</code> can now use (and defaults to)
+small sample correction with number of sites as the sample
+size. Function uses basic Chao extrapolation based on the ratio of
+singletons and doubletons, but switches now to bias corrected Chao
+extrapolation if there are no doubletons (species found
+twice). The variance formula for bias corrected Chao was derived
+following the supporting
+<a href="http://onlinelibrary.wiley.com/doi/10.1111/biom.12200/suppinfo">online material</a>
+and differs slightly from Chiu et al. (2014).
+</p>
+<p>The <code>poolaccum</code> function was changed similarly, but the small
+sample correction is used always.
+</p>
+<p>The abundance based <code>estimateR</code> uses bias corrected Chao
+extrapolation, but earlier it estimated its variance with classic
+Chao model. Now we use the widespread
+<a href="http://viceroy.eeb.uconn.edu/EstimateS/EstimateSPages/EstSUsersGuide/EstimateSUsersGuide.htm#AppendixB">approximate
+equation</a> for variance.
+</p>
+<p>With these changes these functions are more similar to
+<a href="http://viceroy.eeb.uconn.edu/EstimateS/EstimateSPages/EstSUsersGuide/EstimateSUsersGuide.htm#AppendixB">EstimateS</a>.
+</p>
+</li>
<li> <p><code>tabasco</code> uses now <code>reorder.hclust</code> for
<code>hclust</code> object for better ordering than previously when it
cast trees to <code>dendrogram</code> objects.
@@ -270,7 +301,7 @@
III. <code>varespec</code> and <code>dune</code> use 8-character names (4
from genus + 4 from species epithet). New data set on
phylogenetic distances for <code>dune</code> was extracted from Zanne
-et al. (<EM>Nature</EM>, 2014).
+et al. (<em>Nature</em> 506, 89–92; 2014).
</p>
</li>
<li><p> User configurable plots for <code>rarecurve</code>.
@@ -295,13 +326,13 @@
</p>
</li>
<li> <p><code>commsimulator</code> is deprecated. Replace
-<code>commsimulator(x, method)</code> with <code>simulate(nullmodel(x,
- method))</code>.
+<code>commsimulator(x, method)</code> with
+<code>simulate(nullmodel(x, method))</code>.
</p>
</li>
<li> <p><code>density</code> and <code>densityplot</code> for permutation
-results: use <code>permustats</code> with its <code>density</code> and
-<code>densityplot</code> method.
+results are deprecated: use <code>permustats</code> with its
+<code>density</code> and <code>densityplot</code> method.
</p>
</li></ul>
@@ -402,11 +433,11 @@
<ul>
<li><p> This version is released due to changes in programming
-interface and testing procedures in <font face="Courier New,Courier" color="#666666"><b>R</b></font> 3.0.2. If you are using an
-older version of <font face="Courier New,Courier" color="#666666"><b>R</b></font>, there is no need to upgrade <span class="pkg">vegan</span>. There
+interface and testing procedures in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.2. If you are using an
+older version of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>, there is no need to upgrade <span class="pkg">vegan</span>. There
are no new features nor bug fixes. The only user-visible changes
are in documentation and in output messages and formatting. Because
-of <font face="Courier New,Courier" color="#666666"><b>R</b></font> changes, this version is dependent on <font face="Courier New,Courier" color="#666666"><b>R</b></font> version 2.14.0
+of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> changes, this version is dependent on <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> version 2.14.0
or newer and on <span class="pkg">lattice</span> package.
</p>
</li></ul>
@@ -422,7 +453,7 @@
<ul>
<li><p> This is a maintenance release that fixes some issues
-raised by changed in <font face="Courier New,Courier" color="#666666"><b>R</b></font> toolset for processing vignettes. In
+raised by changed in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> toolset for processing vignettes. In
the same we also fix some typographic issues in the vignettes.
</p>
</li></ul>
@@ -468,7 +499,7 @@
<ul>
<li> <p><code>tabasco()</code> is a new function for graphical display
-of community data matrix. Technically it is an interface to <font face="Courier New,Courier" color="#666666"><b>R</b></font>
+of community data matrix. Technically it is an interface to <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>
<code>heatmap</code>, but its use is closer to <span class="pkg">vegan</span> function
<code>vegemite</code>. The function can reorder the community data
matrix similarly as <code>vegemite</code>, for instance, by ordination
@@ -657,7 +688,7 @@
<code>plot</code> etc. of the results. These methods are only used if
the full <code>wcmdscale</code> result is returned with, e.g., argument
<code>eig = TRUE</code>. The default is still to return only a matrix of
-scores similarly as the standard <font face="Courier New,Courier" color="#666666"><b>R</b></font> function <code>cmdscale()</code>,
+scores similarly as the standard <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> function <code>cmdscale()</code>,
and in that case the new methods are not used.
</p>
</li></ul>
@@ -756,13 +787,13 @@
version of LaTeX (TeXLive 2012).
</p>
</li>
-<li> <p><font face="Courier New,Courier" color="#666666"><b>R</b></font> versions later than 2.15-1 (including development
+<li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> versions later than 2.15-1 (including development
version) report warnings and errors when installing and checking
<span class="pkg">vegan</span>, and you must upgrade <span class="pkg">vegan</span> to this version.
The warnings concern functions <code>cIndexKM</code> and
<code>betadisper</code>, and the error occurs in <code>betadisper</code>.
These errors and warnings were triggered by internal changes in
-<font face="Courier New,Courier" color="#666666"><b>R</b></font>.
+<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.
</p>
</li></ul>
@@ -893,8 +924,8 @@
<li><p> Added new nestedness functions <code>nestedbetasor</code> and
<code>nestedbetajac</code> that implement multiple-site dissimilarity
indices and their decomposition into turnover and nestedness
-components following Baselga (<EM>Global Ecology and
-Biogeography</EM> 19, 134–143; 2010).
+components following Baselga (<em>Global Ecology and
+Biogeography</em> 19, 134–143; 2010).
</p>
</li>
<li><p> Added function <code>rarecurve</code> to draw rarefaction curves
@@ -904,8 +935,8 @@
</p>
</li>
<li><p> Added function <code>simper</code> that implements
-“similarity percentages” of Clarke (<EM>Australian
-Journal of Ecology</EM> 18, 117–143; 1993). The method compares
+“similarity percentages” of Clarke (<em>Australian
+Journal of Ecology</em> 18, 117–143; 1993). The method compares
two or more groups and decomposes the average between-group
Bray-Curtis dissimilarity index to contributions by individual
species. The code was developed in
@@ -977,8 +1008,8 @@
</p>
</li>
<li><p> Added Cao dissimilarity (CYd) as a new dissimilarity
-method in <code>vegdist</code> following Cao et al., <EM>Water
-Envir Res</EM> 69, 95–106 (1997). The index should be good for
+method in <code>vegdist</code> following Cao et al., <em>Water
+Envir Res</em> 69, 95–106 (1997). The index should be good for
data with high beta diversity and variable sampling
intensity. Thanks to consultation to Yong Cao (Univ Illinois,
USA).
@@ -1057,7 +1088,7 @@
<ul>
<li> <p><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
+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.
@@ -1077,7 +1108,7 @@
<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
+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>
@@ -1110,12 +1141,12 @@
<code>update</code>d because of a ‘<span class="file">NAMESPACE</span>’ issue.
</p>
</li>
-<li> <p><font face="Courier New,Courier" color="#666666"><b>R</b></font> 2.14.0 changed so that it does not accept using
+<li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 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
+least since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 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
+<code>capscale</code>). The change in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.14.0 does not influence the
results but you probably wish to upgrade <span class="pkg">vegan</span> to avoid
annoying warnings.
</p>
@@ -1149,11 +1180,11 @@
<li><p> Peter Minchin joins the <span class="pkg">vegan</span> team.
</p>
</li>
-<li> <p><span class="pkg">vegan</span> implements standard <font face="Courier New,Courier" color="#666666"><b>R</b></font> ‘<span class="file">NAMESPACE</span>’. In
+<li> <p><span class="pkg">vegan</span> implements standard <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> ‘<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 these functions you should rely on <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 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
@@ -1200,7 +1231,7 @@
<li> <p><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
+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>
@@ -1209,9 +1240,9 @@
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,
+models in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>. 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
+Michaelis-Menten, logistic and Weibull (in base <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>) models. The
function has <code>plot</code> and <code>predict</code> methods.
</p>
</li>
@@ -1220,7 +1251,7 @@
<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).
+models by Dengler (<em>J. Biogeogr.</em> 36, 728-744; 2009).
</p>
</li></ul>
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