[Vegan-commits] r2422 - branches/2.0/inst www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 8 09:08:21 CET 2013
Author: jarioksa
Date: 2013-02-08 09:08:20 +0100 (Fri, 08 Feb 2013)
New Revision: 2422
Modified:
branches/2.0/inst/NEWS.Rd
www/NEWS.html
Log:
expand NEWS and remove linebreaks within \code{}
Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd 2013-02-07 17:55:39 UTC (rev 2421)
+++ branches/2.0/inst/NEWS.Rd 2013-02-08 08:08:20 UTC (rev 2422)
@@ -9,39 +9,41 @@
\itemize{
\item The species scores were scaled correctly in
- \code{capscale()} only when Euclidean distances were used. Most
- graphics will change and should be redone. The function also
- now displays the value of the additive constant when argument
- \code{add = TRUE} was used.
+ \code{capscale()} only when Euclidean distances were used. Usually
+ \code{capscale()} is used with non-Euclidean distances, and in
+ these cases the scaling was wrong. Most graphics will change and
+ should be redone. The change of scaling mainly influences the
+ spread of species scores with respect to the site scores.
\item Function \code{clamtest()} failed to set the minimum
- abundance threshold in some cases. The output was wrong when
- some of the possible species groups were missing. The problems
- were reported by Richard Telford (Bergen, Norway).
+ abundance threshold in some cases. In addition, the output was
+ wrong when some of the possible species groups were missing. The
+ problems were reported by Richard Telford (Bergen, Norway).
\item Plotting an object fitted by \code{envfit()} would fail if
\code{p.max} was used and there were unused levels for one or
more factors. The unused levels could result from deletion of
- observations with missing values or simply the result of
+ observations with missing values or simply as the result of
supplying a subset of a larger data set to \code{envfit()}.
\item \code{multipart()} printed wrong information about the
analysis type (but did analysis correctly). Reported by Valerie
Coudrain.
- \item \code{oecosimu()} failed if its \code{nestedfun} returned
- a data frame. A more fundamental fix will be in \pkg{vegan}
- 2.2-0.
+ \item \code{oecosimu()} failed if its \code{nestedfun} returned a
+ data frame. A more fundamental fix will be in \pkg{vegan} 2.2-0,
+ where the structure of the \code{oecosimu()} result will change.
\item The plot of two-dimensional \code{procrustes()} solutions
often draw original axes in a wrong angle. The problem was
reported by Elizabeth Ottesen (MIT).
- \item Function \code{treedive()} for functional diversity did
- not correctly match the species names in the community data and
- classification tree when the tree contained species that did
- not occur in the data. Related function \code{treedist()} for
- phylogenetic distances did not try to match the names at all.
+ \item Function \code{treedive()} for functional or phylogenetic
+ diversity did not correctly match the species names between the
+ community data and species tree when the tree contained species
+ that did not occur in the data. Related function
+ \code{treedist()} for phylogenetic distances did not try to match
+ the names at all.
}
@@ -51,6 +53,14 @@
\itemize{
+ \item The output of \code{capscale()} displays the value of the
+ additive constant when argument \code{add = TRUE} was used.
+
+ \item \code{fitted()} functions for \code{cca()}, \code{rda()} and
+ \code{capscale()} can now return conditioned (partial) component
+ of the response: Argument \code{model} gained a new alternative
+ \code{model = "pCCA"}.
+
\item \code{dispindmorisita()} output gained a new column for
Chi-squared based probabilities that the null hypothesis (random
distribution) is true.
@@ -71,11 +81,11 @@
method.
\item \code{ordiR2step()} gained new argument \code{R2scope}
- (defaults \code{TRUE}) which can be used to turn off the
- criterion of stopping when the adjusted \eqn{R^2}{R2} of the
- current model exceeds that of the scope. This option allows
- model building when the \code{scope} would be overdetermined
- (number of predictors higher than number of observations).
+ (defaults \code{TRUE}) which can be used to turn off the criterion
+ of stopping when the adjusted \eqn{R^2}{R-squared} of the current
+ model exceeds that of the scope. This option allows model
+ building when the \code{scope} would be overdetermined (number of
+ predictors higher than number of observations).
\code{ordiR2step()} now handles partial redundancy analysis
(pRDA).
@@ -83,19 +93,21 @@
\item \code{orditorp()} gained argument \code{select} to select
the rows or columns of the results to display.
- \item \code{protest()} prints the standardized residual
- statistic \eqn{m_{12}^2}{squared m12} in addition to the squared
- Procrustes correlation \eqn{R^2}{R2}. Both were calculated, but
- only the latter was displayed.
+ \item \code{protest()} prints the standardized residual statistic
+ \eqn{m_{12}^2}{squared m12} in addition to the squared Procrustes
+ correlation \eqn{R^2}{R-squared}. Both were calculated, but only
+ the latter was displayed.
Permutation tests are much faster in \code{protest()}. Instead
of calling repeatedly \code{procrustes()}, the goodness of fit
- statistic is evaluated within then function.
+ statistic is evaluated within the function.
\item \code{wcmdscale()} gained methods for \code{print},
\code{plot} etc. of the results. These methods are only used if
- the full \code{wcmdscale} result is returned with, e.g.,
- argument \code{eig = TRUE}.
+ the full \code{wcmdscale} result is returned with, e.g., argument
+ \code{eig = TRUE}. The default is still to return only a matrix of
+ scores similarly as the standard \R function \code{cmdscale()},
+ and in that case the new methods are not used.
}
@@ -110,9 +122,9 @@
\itemize{
- \item \code{anova(<cca_object>, ...)} failed with \code{by =
- "axis"} and \code{by = "term"}. The bug was reported by Dr Sven
- Neulinger (Christian Albrecht University, Kiel, Germany).
+ \item \code{anova(<cca_object>, ...)} failed with
+ \code{by = "axis"} and \code{by = "term"}. The bug was reported by
+ Dr Sven Neulinger (Christian Albrecht University, Kiel, Germany).
\item \code{radlattice} did not honour argument \code{BIC = TRUE},
but always displayed AIC.
@@ -218,8 +230,8 @@
\item \code{envfit} failed with unused factor levels.
- \item \code{predict} for \code{cca} results with \code{type =
- "response"} or \code{type = "working"} failed with
+ \item \code{predict} for \code{cca} results with
+ \code{type = "response"} or \code{type = "working"} failed with
\code{newdata} if the number of rows did not match with the
original data. Now the \code{newdata} is ignored if it has a
wrong number of rows. The number of rows must match because
@@ -395,10 +407,10 @@
\item \code{stressplot} and \code{goodness} sometimes failed when
\code{metaMDS} was based on \code{isoMDS} (\pkg{MASS} package)
because \code{metaMDSdist} did not use the same defaults for
- step-across (extended) dissimilarities as \code{metaMDS(...,
- engine = "isoMDS")}. The change of defaults can also influence
- triggering of step-across in \code{capscale(..., metaMDSdist =
- TRUE)}.
+ step-across (extended) dissimilarities as
+ \code{metaMDS(..., engine = "isoMDS")}. The change of defaults can
+ also influence 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
Modified: www/NEWS.html
===================================================================
--- www/NEWS.html 2013-02-07 17:55:39 UTC (rev 2421)
+++ www/NEWS.html 2013-02-08 08:08:20 UTC (rev 2422)
@@ -19,22 +19,23 @@
<ul>
<li><p> The species scores were scaled correctly in
-<code>capscale()</code> only when Euclidean distances were used. Most
-graphics will change and should be redone. The function also
-now displays the value of the additive constant when argument
-<code>add = TRUE</code> was used.
+<code>capscale()</code> only when Euclidean distances were used. Usually
+<code>capscale()</code> is used with non-Euclidean distances, and in
+these cases the scaling was wrong. Most graphics will change and
+should be redone. The change of scaling mainly influences the
+spread of species scores with respect to the site scores.
</p>
</li>
<li><p> Function <code>clamtest()</code> failed to set the minimum
-abundance threshold in some cases. The output was wrong when
-some of the possible species groups were missing. The problems
-were reported by Richard Telford (Bergen, Norway).
+abundance threshold in some cases. In addition, the output was
+wrong when some of the possible species groups were missing. The
+problems were reported by Richard Telford (Bergen, Norway).
</p>
</li>
<li><p> Plotting an object fitted by <code>envfit()</code> would fail if
<code>p.max</code> was used and there were unused levels for one or
more factors. The unused levels could result from deletion of
-observations with missing values or simply the result of
+observations with missing values or simply as the result of
supplying a subset of a larger data set to <code>envfit()</code>.
</p>
</li>
@@ -43,9 +44,9 @@
Coudrain.
</p>
</li>
-<li> <p><code>oecosimu()</code> failed if its <code>nestedfun</code> returned
-a data frame. A more fundamental fix will be in <span class="pkg">vegan</span>
-2.2-0.
+<li> <p><code>oecosimu()</code> failed if its <code>nestedfun</code> returned a
+data frame. A more fundamental fix will be in <span class="pkg">vegan</span> 2.2-0,
+where the structure of the <code>oecosimu()</code> result will change.
</p>
</li>
<li><p> The plot of two-dimensional <code>procrustes()</code> solutions
@@ -53,11 +54,12 @@
reported by Elizabeth Ottesen (MIT).
</p>
</li>
-<li><p> Function <code>treedive()</code> for functional diversity did
-not correctly match the species names in the community data and
-classification tree when the tree contained species that did
-not occur in the data. Related function <code>treedist()</code> for
-phylogenetic distances did not try to match the names at all.
+<li><p> Function <code>treedive()</code> for functional or phylogenetic
+diversity did not correctly match the species names between the
+community data and species tree when the tree contained species
+that did not occur in the data. Related function
+<code>treedist()</code> for phylogenetic distances did not try to match
+the names at all.
</p>
</li></ul>
@@ -69,6 +71,16 @@
<ul>
+<li><p> The output of <code>capscale()</code> displays the value of the
+additive constant when argument <code>add = TRUE</code> was used.
+</p>
+</li>
+<li> <p><code>fitted()</code> functions for <code>cca()</code>, <code>rda()</code> and
+<code>capscale()</code> can now return conditioned (partial) component
+of the response: Argument <code>model</code> gained a new alternative
+<code>model = "pCCA"</code>.
+</p>
+</li>
<li> <p><code>dispindmorisita()</code> output gained a new column for
Chi-squared based probabilities that the null hypothesis (random
distribution) is true.
@@ -93,11 +105,11 @@
</p>
</li>
<li> <p><code>ordiR2step()</code> gained new argument <code>R2scope</code>
-(defaults <code>TRUE</code>) which can be used to turn off the
-criterion of stopping when the adjusted <i>R2</i> of the
-current model exceeds that of the scope. This option allows
-model building when the <code>scope</code> would be overdetermined
-(number of predictors higher than number of observations).
+(defaults <code>TRUE</code>) which can be used to turn off the criterion
+of stopping when the adjusted <i>R-squared</i> of the current
+model exceeds that of the scope. This option allows model
+building when the <code>scope</code> would be overdetermined (number of
+predictors higher than number of observations).
</p>
<p><code>ordiR2step()</code> now handles partial redundancy analysis
(pRDA).
@@ -107,20 +119,22 @@
the rows or columns of the results to display.
</p>
</li>
-<li> <p><code>protest()</code> prints the standardized residual
-statistic <i>squared m12</i> in addition to the squared
-Procrustes correlation <i>R2</i>. Both were calculated, but
-only the latter was displayed.
+<li> <p><code>protest()</code> prints the standardized residual statistic
+<i>squared m12</i> in addition to the squared Procrustes
+correlation <i>R-squared</i>. Both were calculated, but only
+the latter was displayed.
</p>
<p>Permutation tests are much faster in <code>protest()</code>. Instead
of calling repeatedly <code>procrustes()</code>, the goodness of fit
-statistic is evaluated within then function.
+statistic is evaluated within the function.
</p>
</li>
<li> <p><code>wcmdscale()</code> gained methods for <code>print</code>,
<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 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>,
+and in that case the new methods are not used.
</p>
</li></ul>
@@ -137,9 +151,9 @@
<ul>
-<li> <p><code>anova(<cca_object>, ...)</code> failed with <code>by =
- "axis"</code> and <code>by = "term"</code>. The bug was reported by Dr Sven
-Neulinger (Christian Albrecht University, Kiel, Germany).
+<li> <p><code>anova(<cca_object>, ...)</code> failed with
+<code>by = "axis"</code> and <code>by = "term"</code>. The bug was reported by
+Dr Sven Neulinger (Christian Albrecht University, Kiel, Germany).
</p>
</li>
<li> <p><code>radlattice</code> did not honour argument <code>BIC = TRUE</code>,
@@ -267,8 +281,8 @@
<li> <p><code>envfit</code> failed with unused factor levels.
</p>
</li>
-<li> <p><code>predict</code> for <code>cca</code> results with <code>type =
- "response"</code> or <code>type = "working"</code> failed with
+<li> <p><code>predict</code> for <code>cca</code> results with
+<code>type = "response"</code> or <code>type = "working"</code> failed with
<code>newdata</code> if the number of rows did not match with the
original data. Now the <code>newdata</code> is ignored if it has a
wrong number of rows. The number of rows must match because
@@ -485,10 +499,10 @@
<li> <p><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>.
+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>
</li>
<li> <p><code>adonis</code> contained a minor bug resulting from
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