[Vegan-commits] r2430 - branches pkg/vegan pkg/vegan/inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Feb 11 13:36:04 CET 2013
Author: jarioksa
Date: 2013-02-11 13:36:04 +0100 (Mon, 11 Feb 2013)
New Revision: 2430
Modified:
branches/vegan_releases.txt
pkg/vegan/DESCRIPTION
pkg/vegan/inst/ChangeLog
pkg/vegan/inst/NEWS.Rd
Log:
wrap up vegan_2.0-6 for CRAN
Modified: branches/vegan_releases.txt
===================================================================
--- branches/vegan_releases.txt 2013-02-11 07:36:50 UTC (rev 2429)
+++ branches/vegan_releases.txt 2013-02-11 12:36:04 UTC (rev 2430)
@@ -13,6 +13,7 @@
vegan release: revision (date) directory at vegan-forge
+2.0-6: r2429 (Mon, 11 Feb 2013) branches/2.0
2.0-5: r2315 (Mon, 8 Oct 2012) branches/2.0
2.0-4: r2222 (Mon, 18 Jun 2012) branches/2.0
2.0-3: r2119 (Sat, 03 Mar 2012) branches/2.0
Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION 2013-02-11 07:36:50 UTC (rev 2429)
+++ pkg/vegan/DESCRIPTION 2013-02-11 12:36:04 UTC (rev 2430)
@@ -1,7 +1,7 @@
Package: vegan
Title: Community Ecology Package
-Version: 2.1-25
-Date: February 2, 2013
+Version: 2.1-26
+Date: February 11, 2013
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2013-02-11 07:36:50 UTC (rev 2429)
+++ pkg/vegan/inst/ChangeLog 2013-02-11 12:36:04 UTC (rev 2430)
@@ -2,8 +2,13 @@
VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
-Version 2.1-25 (opened February 2, 2013)
+Version 2.1-26 (opened February 11, 2013)
+ * New version opened with the release of vegan_2.0-6 on February
+ 11, 2013.
+
+Version 2.1-25 (closed February 11, 2013)
+
* FAQ: new entry on impossibility of using random effects in cca,
rda, capscale & adonis, and telling how to do this
approximately. Please comment and correct.
Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd 2013-02-11 07:36:50 UTC (rev 2429)
+++ pkg/vegan/inst/NEWS.Rd 2013-02-11 12:36:04 UTC (rev 2430)
@@ -2,15 +2,129 @@
\title{vegan News}
\encoding{UTF-8}
+\section{Changes in version 2.0-6}{
+
+ \subsection{BUG FIXES}{
+
+ \itemize{
+
+ \item The species scores were scaled wrongly in
+ \code{capscale()}. They were scaled correctly only when Euclidean
+ distances were used, but usually \code{capscale()} is used with
+ non-Euclidean distances. 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. In addition, the output was
+ wrong when some of the possible species groups were missing. Both
+ 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 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 the 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,
+ 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 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.
+
+ }
+
+ } % bug fixes
+
+ \subsection{NEW FEATURES}{
+
+ \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.
+
+ \item \code{metaMDS()} and \code{monoMDS()} have new default
+ convergence criteria. Most importantly, scale factor of the
+ gradient (\code{sfgrmin}) is stricter. The former limit was too
+ slack with large data sets and iterations stopped early without
+ getting close to the solution. In addition, \code{scores()}
+ ignore now requests to dimensions beyond those calculated
+ instead of failing, and \code{scores()} for \code{metaMDS()}
+ results do not drop dimensions.
+
+ \item \code{msoplot()} gained \code{legend} argument for
+ positioning the legend.
+
+ \item Nestedness function \code{nestednodf()} gained a \code{plot}
+ 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}{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).
+
+ \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}{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 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 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.
+
+ }
+
+ } % new features
+
+
+} % end 2.0-6
+
\section{Changes in version 2.0-5}{
\subsection{BUG FIXES}{
\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.
@@ -116,8 +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
@@ -293,10 +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
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