[Vegan-commits] r2920 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Dec 12 10:01:27 CET 2014
Author: jarioksa
Date: 2014-12-12 10:01:27 +0100 (Fri, 12 Dec 2014)
New Revision: 2920
Modified:
www/NEWS.html
Log:
update NEWS.html
Modified: www/NEWS.html
===================================================================
--- www/NEWS.html 2014-12-12 08:59:36 UTC (rev 2919)
+++ www/NEWS.html 2014-12-12 09:01:27 UTC (rev 2920)
@@ -1,9 +1,10 @@
-<!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" />
+<!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">
</head><body>
-<table width="100%" summary="page for NEWS"><tr><td>NEWS</td><td style="text-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>
@@ -40,9 +41,19 @@
<ul>
-<li> <p><code>linestack</code> accepts now expressions (such as
-mathematical notation) as labels.
+<li> <p><code>estimateR</code> uses a more exact variance formula for
+bias-corrected Chao estimate of extrapolated number of
+species. The new formula may be unpublished, but it was derived
+following the guidelines of Chiu, Wang, Walther & Chao,
+<EM>Biometrics</EM> 70, 671–682 (2014),
+<a href="http://onlinelibrary.wiley.com/doi/10.1111/biom.12200/suppinfo">online
+supplementary material</a>.
</p>
+</li>
+<li> <p><code>linestack</code> accepts now expressions as labels. This
+allows using mathematical symbols and formula given as
+mathematical expressions.
+</p>
</li></ul>
@@ -69,7 +80,7 @@
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 <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.
+extensive documentation on parallel processing in <font face="Courier New,Courier" color="#666666"><b>R</b></font>.
</p>
<p>The following function use parallel processing in analysing
permutation statistics: <code>adonis</code>, <code>anosim</code>,
@@ -132,7 +143,7 @@
<ul>
<li> <p><span class="pkg">vegan</span> package dependencies and namespace imports
-were adapted to changes in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>, and no more trigger warnings and
+were adapted to changes in <font face="Courier New,Courier" color="#666666"><b>R</b></font>, and no more trigger warnings and
notes in package tests.
</p>
</li>
@@ -151,7 +162,7 @@
<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
@@ -161,7 +172,7 @@
<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 in base <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>. However, <code>reorder</code> can use (and defaults
+objects in base <font face="Courier New,Courier" color="#666666"><b>R</b></font>. 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
unweighted means of joined branches.
@@ -177,7 +188,7 @@
<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 <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> tools that only
+<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
@@ -298,7 +309,7 @@
</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).
+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
@@ -342,7 +353,7 @@
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> 506, 89–92; 2014).
+et al. (<EM>Nature</EM> 506, 89–92; 2014).
</p>
</li>
<li><p> User configurable plots for <code>rarecurve</code>.
@@ -474,11 +485,11 @@
<ul>
<li><p> This version is released due to changes in programming
-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
+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
are no new features nor bug fixes. The only user-visible changes
are in documentation and in output messages and formatting. Because
-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
+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
or newer and on <span class="pkg">lattice</span> package.
</p>
</li></ul>
@@ -494,7 +505,7 @@
<ul>
<li><p> This is a maintenance release that fixes some issues
-raised by changed in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> toolset for processing vignettes. In
+raised by changed in <font face="Courier New,Courier" color="#666666"><b>R</b></font> toolset for processing vignettes. In
the same we also fix some typographic issues in the vignettes.
</p>
</li></ul>
@@ -540,7 +551,7 @@
<ul>
<li> <p><code>tabasco()</code> is a new function for graphical display
-of community data matrix. Technically it is an interface to <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>
+of community data matrix. Technically it is an interface to <font face="Courier New,Courier" color="#666666"><b>R</b></font>
<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
@@ -729,7 +740,7 @@
<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 <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> function <code>cmdscale()</code>,
+scores similarly as the standard <font face="Courier New,Courier" color="#666666"><b>R</b></font> function <code>cmdscale()</code>,
and in that case the new methods are not used.
</p>
</li></ul>
@@ -828,13 +839,13 @@
version of LaTeX (TeXLive 2012).
</p>
</li>
-<li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> versions later than 2.15-1 (including development
+<li> <p><font face="Courier New,Courier" color="#666666"><b>R</b></font> 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
-<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.
+<font face="Courier New,Courier" color="#666666"><b>R</b></font>.
</p>
</li></ul>
@@ -965,8 +976,8 @@
<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
@@ -976,8 +987,8 @@
</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
@@ -1049,8 +1060,8 @@
</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).
@@ -1129,7 +1140,7 @@
<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.
@@ -1149,7 +1160,7 @@
<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>
@@ -1182,12 +1193,12 @@
<code>update</code>d because of a ‘<span class="file">NAMESPACE</span>’ issue.
</p>
</li>
-<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
+<li> <p><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 <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
+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 <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.14.0 does not influence the
+<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>
@@ -1221,11 +1232,11 @@
<li><p> Peter Minchin joins the <span class="pkg">vegan</span> team.
</p>
</li>
-<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
+<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
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 <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> delegation and simply
+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
@@ -1272,7 +1283,7 @@
<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>
@@ -1281,9 +1292,9 @@
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 <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>. The function can fit Arrhenius, Gleason, Gitay,
+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 <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>) models. The
+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>
</li>
@@ -1292,7 +1303,7 @@
<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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