[Vegan-commits] r2896 - pkg/vegan/inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Oct 9 10:25:19 CEST 2014
Author: jarioksa
Date: 2014-10-09 10:25:19 +0200 (Thu, 09 Oct 2014)
New Revision: 2896
Modified:
pkg/vegan/inst/ChangeLog
pkg/vegan/inst/NEWS.Rd
Log:
Squashed commit of the following:
commit 53c612015bd1acbb54f189800c62f48c48744ca7
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Wed Oct 8 14:27:22 2014 +0300
ChangeLog heading to the github time
commit af070de7f5246f53e732d6ca86c9137aa2cc77be
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Wed Oct 8 14:19:08 2014 +0300
compile ChangeLog from git logs, long afterwards
I am not sure if we need to keep ChangeLog. This needs a bit care,
because ChangeLog is essentially linear and git is a web. However,
I collected major changes from git logs to still have a ChangeLog
of major events.
commit a143de91c4d840952bdcb638119bfb9245b148f1
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Wed Oct 8 11:05:18 2014 +0300
more NEWS picked from the ChangeLog
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2014-10-08 07:43:04 UTC (rev 2895)
+++ pkg/vegan/inst/ChangeLog 2014-10-09 08:25:19 UTC (rev 2896)
@@ -1,9 +1,38 @@
-$Date$
+VEGAN DEVEL VERSIONS at https://github.com/vegandevs/vegan
-VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
+Version 2.1-43 (opened September 11, 2014)
-Version 2.1-43
+ * cca, rda, capscale: remove u.eig, v.eig and wa.eig items or
+ scores scaled by eigenvectors. We have had a warning of their
+ eventual removal since vegan 1.6-8, and now we finally did
+ so. Scaling of scores happens when scores() function access
+ normalized score items of the results.
+ * commsimulator: commented out deprecation warning at the moment,
+ because this triggered warnings in CRAN packages bipartite and
+ metacom. Contacted the maintainers of these packages, and will put
+ back the warning in 2.2-1.
+
+ * getPermuteMatrix: works also when 'strata' are
+ missing. Triggered an error in CRAN package mpmcorrelogram.
+
+ * permustats: new function to extract permutation results from
+ vegan objects, with support functions summary, density,
+ densityplot, qqnorm and qqmath. Deprecated previous density and
+ densityplot methods directly accessing the same results.
+
+ * ordirgl, ordiplot3d: 3D functions using rgl or scatterplot3d
+ packages were removed from vegan and moved to a new CRAN package
+ vegan3d (released Oct 7, 2014).
+
+ * scores.hclust: combined documentation with other hclust methods.
+
+ * scoverage: removed from vegan.
+
+ * dispweight: veganified so that uses nullmodels. Added
+ gdispweight(): a new generalized method taking any glm() formula
+ instead of one grouping.
+
* betadisper Permutation tests via the `permutest()` method
are now parallelised. The number of cores to parallelise over
is specified by argument `parallel` in common with the
@@ -13,8 +42,13 @@
was specified using `control` which is not an argument to the
`permutest()` method for `betadisper()`.
-Version 2.1-42 (opened September 4, 2014)
+ * ccanova: removed from vegan. These were backup functions of old
+ anova.cca, and were completely rewritten for new vegan.
+ * metaMDSrotate: made defunct (replaced with MDSrotate).
+
+Version 2.1-42 (closed September 11, 2014)
+
* Opened a new version to prepare release 2.2-0.
* Moved main development from R-Forge to GitHub.com.
@@ -25,9 +59,9 @@
* getPermuteMatrix: routines have a common API based on the new
function.
+
+Version 2.1-41 (closed September 4, 2014)
-Version 2.1-41 (closed September 4, 2014)
-
* ordiellipse, ordihull, ordispider: can now handle (omit) NA
cases in 'groups'. They were able to omit to NA cases in scores,
but having NA in 'groups' triggered really cryptic error
@@ -69,7 +103,7 @@
* cascadeKM: Calinski index for one group will now be NA instead
of randomly chosen Inf, -Inf or NaN which can cause confusion (see
- http://stackoverflow.com/questions/21022848/r-produces-different-result-after-io-on-file
+ http://stackoverflow.com/questions/21022848/r-produces-different-result-after-io-on-file
* ordiellipse: failed if all points were on a line. Now handles
these cases by drawing a line trhough the points, and issuing a
Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd 2014-10-08 07:43:04 UTC (rev 2895)
+++ pkg/vegan/inst/NEWS.Rd 2014-10-09 08:25:19 UTC (rev 2896)
@@ -45,6 +45,20 @@
} % end new functions
\subsection{BUG FIXES}{
+ \itemize{
+
+ \item \code{ordiellipse} can handle points exactly on a line,
+ including only two points.
+
+ \item plotting \code{radfit} results for several species failed if
+ any of the communities had no species or had only one species.
+
+ \item \code{RsquareAdj} for \code{capscale} with negative
+ eigenvalues will now report \code{NA}.
+
+ \item \code{simper} failed when a group had only a single member.
+
+ }% end itemize
} % end bug fixes
\subsection{NEW FEATURES}{
@@ -63,11 +77,20 @@
\code{bioenvdist} can extract the dissimilarities applied in
best model or any other model.
+ \item \code{cascadeKM} of only one group will be \code{NA} instead
+ of a random value.
+
\item \code{MDSrotate} can rotate to multidimensional target.
\item \code{nestednodf} gained new option for defining weighted
nestedness statistic.
+ \item \code{ordiellipse}, \code{ordihull} and \code{ordiellipse}
+ can handle missing values in \code{groups}.
+
+ \item \code{ordispider} can now use spatial medians instead of
+ means.
+
\item \code{rankindex} can use Manhattan, Gower and Mahalanobis
distance in addition to Euclidean.
@@ -76,6 +99,14 @@
\item \code{fitspecaccum} can do weighted analysis.
+ \item \code{tabasco} uses now \code{reorder.hclust} for
+ \code{hclust} for better ordering than previously when it cast
+ trees to \code{dendrogram} objects.
+
+ \item \code{treedive} and \code{treedist} default now to
+ \code{match.force = TRUE} and can be silenced with
+ \code{verbose = FALSE}.
+
\item \code{vegdist} gained Mahalanobis distance.
\item Nomenclature updated in plant community
More information about the Vegan-commits
mailing list