[Vegan-commits] r2939 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Mar 12 14:56:16 CET 2015
Author: jarioksa
Date: 2015-03-12 14:56:16 +0100 (Thu, 12 Mar 2015)
New Revision: 2939
Modified:
www/NEWS.html
Log:
Update NEWS in preparation of 2.2-2 release
Modified: www/NEWS.html
===================================================================
--- www/NEWS.html 2015-03-12 07:28:07 UTC (rev 2938)
+++ www/NEWS.html 2015-03-12 13:56:16 UTC (rev 2939)
@@ -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>
@@ -12,12 +11,79 @@
+<h4>BUG FIXES</h4>
+
+
+<ul>
+<li><p> Constrained ordination functions <code>cca</code>, <code>rda</code> and
+<code>capscale</code> are now more robust. Scoping of data set names and
+variable names is much improved. This should fix numerous
+long-standing problems, for instance those reported by Benedicte
+Bachelot (in email) and Richard Telford (in Twitter), as well as
+issues <a href="https://github.com/vegandevs/vegan/issues/16">#16</a>
+and <a href="https://github.com/vegandevs/vegan/issues/100">#100</a> in
+GitHub.
+</p>
+</li>
+<li><p> Ordination functions <code>cca</code> and <code>rda</code> silently
+accepted dissimilarities as input although their analysis makes
+no sense with these methods. Dissimilarities should be analysed
+with distance-based redundancy analysis (<code>capscale</code>).
+</p>
+</li>
+<li><p> The variance of the conditional component was over-estimated
+in <code>goodness</code> of <code>rda</code> results, and results were wrong
+for partial RDA. The problems were reported in an
+<a href="https://stat.ethz.ch/pipermail/r-sig-ecology/2015-March/004936.html">R-sig-ecology</a>
+message by Christoph von Redwitz.
+</p>
+</li></ul>
+
+
+
+
+<h4>WINDOWS</h4>
+
+
+<ul>
+<li> <p><code>orditkplot</code> did not add file type identifier to saved
+graphics in Windows although that is required. The problem only
+concerned Windows OS.
+</p>
+</li></ul>
+
+
+
+
<h4>NEW FEATURES</h4>
<ul>
+<li> <p><code>goodness</code> function for constrained ordination
+(<code>cca</code>, <code>rda</code>, <code>capscale</code>) was redesigned. Function
+gained argument <code>addprevious</code> to add the variation explained
+by previous ordination components to axes when <code>statistic =
+ "explained"</code>. With this option, <code>model = "CCA"</code> will include
+the variation explained by partialled-out conditions, and
+<code>model = "CA"</code> will include the accumulated variation
+explained by conditions and constraints. The former behaviour was
+<code>addprevious = TRUE</code> for <code>model = "CCA"</code>, and
+<code>addprevious = FALSE</code> for <code>model = "CA"</code>. The argument
+will have no effect when <code>statistic = "distance"</code>, but this
+will always show the residual distance after all previous
+components. Formerly it displayed the residual distance only for
+the currently analysed model.
+</p>
+</li>
+<li><p> Functions <code>ordiArrowMul</code> and <code>ordiArrowTextXY</code> are
+exported and can be used in normal interactive sessions. These
+functions are used to scale a bunch arrows to fit ordination
+graphics, and formerly they were internal functions used within
+other <span class="pkg">vegan</span> functions.
+</p>
+</li>
<li><p> The <code>varpart</code> plots of four-component models were
-redesigned following Legendre, Borcard & Roberts <EM>Ecology</EM>
+redesigned following Legendre, Borcard & Roberts <em>Ecology</em>
93, 1234–1240 (2012), and they use now four ellipses instead of
three circles and two rectangles. The components are now labelled
in plots, and the circles and ellipses can be easily filled with
@@ -39,7 +105,7 @@
<li><p> This is a maintenance release to avoid warning messages
caused by changes in CRAN repository. The namespace usage is also
more stringent to avoid warnings and notes in development versions
-of <font face="Courier New,Courier" color="#666666"><b>R</b></font>.
+of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.
</p>
</li></ul>
@@ -84,7 +150,7 @@
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),
+<em>Biometrics</em> 70, 671–682 (2014),
<a href="http://onlinelibrary.wiley.com/doi/10.1111/biom.12200/suppinfo">online
supplementary material</a>.
</p>
@@ -131,7 +197,7 @@
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 <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
permutation statistics: <code>adonis</code>, <code>anosim</code>,
@@ -194,7 +260,7 @@
<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>
@@ -213,7 +279,7 @@
<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
@@ -223,7 +289,7 @@
<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 <font face="Courier New,Courier" color="#666666"><b>R</b></font>. However, <code>reorder</code> can use (and defaults
+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
unweighted means of joined branches.
@@ -239,7 +305,7 @@
<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 <font face="Courier New,Courier" color="#666666"><b>R</b></font> tools that only
+<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
@@ -360,7 +426,7 @@
</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
@@ -404,7 +470,7 @@
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>.
@@ -536,11 +602,11 @@
<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>
@@ -556,7 +622,7 @@
<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>
@@ -602,7 +668,7 @@
<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
@@ -791,7 +857,7 @@
<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>
@@ -890,13 +956,13 @@
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>
@@ -1027,8 +1093,8 @@
<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
@@ -1038,8 +1104,8 @@
</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
@@ -1111,8 +1177,8 @@
</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).
@@ -1191,7 +1257,7 @@
<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.
@@ -1211,7 +1277,7 @@
<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>
@@ -1244,12 +1310,12 @@
<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>
@@ -1283,11 +1349,11 @@
<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
@@ -1334,7 +1400,7 @@
<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>
@@ -1343,9 +1409,9 @@
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>
@@ -1354,7 +1420,7 @@
<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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