[Vegan-commits] r1958 - branches branches/2.0 branches/2.0/inst pkg/vegan pkg/vegan/inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Oct 20 11:50:59 CEST 2011
Author: jarioksa
Date: 2011-10-20 11:50:46 +0200 (Thu, 20 Oct 2011)
New Revision: 1958
Modified:
branches/2.0/DESCRIPTION
branches/2.0/inst/ChangeLog
branches/vegan_releases.txt
pkg/vegan/DESCRIPTION
pkg/vegan/inst/ChangeLog
pkg/vegan/inst/NEWS.Rd
Log:
CRAN release of vegan 2.0-1
Modified: branches/2.0/DESCRIPTION
===================================================================
--- branches/2.0/DESCRIPTION 2011-10-20 07:57:54 UTC (rev 1957)
+++ branches/2.0/DESCRIPTION 2011-10-20 09:50:46 UTC (rev 1958)
@@ -1,6 +1,6 @@
Package: vegan
Title: Community Ecology Package
-Version: 2.0-1
+Version: 2.0-2
Date: October 20, 2011
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog 2011-10-20 07:57:54 UTC (rev 1957)
+++ branches/2.0/inst/ChangeLog 2011-10-20 09:50:46 UTC (rev 1958)
@@ -2,6 +2,8 @@
VEGAN RELEASE VERSIONS at http://cran.r-project.org/
+Version 2.0-2 (opened October 20, 2011)
+
Version 2.0-1 (released October 20, 2011)
* merge r1945: add plot & lines for as.preston & as.fisher.
Modified: branches/vegan_releases.txt
===================================================================
--- branches/vegan_releases.txt 2011-10-20 07:57:54 UTC (rev 1957)
+++ branches/vegan_releases.txt 2011-10-20 09:50:46 UTC (rev 1958)
@@ -13,6 +13,7 @@
vegan release: revision (date) directory at vegan-forge
+2.0-1: r1957 (Thu, 20 Oct 2011) branches/2.0
2.0-0: r1801 (Wed, 07 Sep 2011) branches/2.0
1.17-12: r1725 (Wed, 17 Aug 2011) branches/1.17
1.17-11: r1634 (Tue, 14 Jun 2011) branches/1.17
Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION 2011-10-20 07:57:54 UTC (rev 1957)
+++ pkg/vegan/DESCRIPTION 2011-10-20 09:50:46 UTC (rev 1958)
@@ -1,7 +1,7 @@
Package: vegan
Title: Community Ecology Package
-Version: 2.1-4
-Date: October 16, 2011
+Version: 2.1-5
+Date: October 20, 2011
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 2011-10-20 07:57:54 UTC (rev 1957)
+++ pkg/vegan/inst/ChangeLog 2011-10-20 09:50:46 UTC (rev 1958)
@@ -2,8 +2,13 @@
VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
-Version 2.1-4 (opened October 16, 2011)
+Version 2.1-5 (opened October 20, 2011)
+ * opened a new version with the release of vegan 2.0-1 on Oct 20,
+ 2011.
+
+Version 2.1-4 (opened October 20, 2011)
+
* adonis, anosim, CCorA, envfit (factorfit, vectorfit), mantel,
mantel.partial, mrpp, protest: user interface changed and
'permutations' can now be a matrix where each row gives permuted
Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd 2011-10-20 07:57:54 UTC (rev 1957)
+++ pkg/vegan/inst/NEWS.Rd 2011-10-20 09:50:46 UTC (rev 1958)
@@ -7,17 +7,17 @@
\itemize{
\item \code{clamtest}: new function to classify species as
- generalists and specialists in two distinct habitats (CLAM test
- of Chazdon et al., \emph{Ecology} 92, 1332--1343; 2011). The
- test is based on multinomial distribution of individuals in two
- habitat types or sampling units, and is applicable only to count
- data with no over-dispersion.
+ generalists and specialists in two distinct habitats (CLAM test of
+ Chazdon et al., \emph{Ecology} 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.
- \item \code{as.preston} gained \code{plot} and \code{lines}, and
- \code{as.fisher} gained \code{plot} method (which also can add
- items to existing plots). These are similar as \code{plot} and
- \code{lines} for \code{prestonfit} and \code{fisherfit}, but
- display only data without the fitted model.
+ \item \code{as.preston} gained \code{plot} and \code{lines}
+ methods, and \code{as.fisher} gained \code{plot} method (which
+ also can add items to existing plots). These are similar as
+ \code{plot} and \code{lines} for \code{prestonfit} and
+ \code{fisherfit}, but display only data without the fitted lines.
\item \code{raupcrick}: new function to implement Raup-Crick
dissimilarity as a probability of number of co-occurring species
@@ -36,7 +36,7 @@
\subsection{BUG FIXES}{
\itemize{
- \item Function \code{meandist} can scramble items and confusing
+ \item Function \code{meandist} can scramble items and give wrong
results, especially when the \code{grouping} was numerical. The
problem was reported by Dr Miguel Alvarez (Univ. Bonn).
@@ -52,13 +52,13 @@
\code{update}d because of a \file{NAMESPACE} issue.
\item \R 2.14.0 changed so that it does not accept using
- \code{sd()} function for matrices, and several \pkg{vegan}
- functions were changed to adapt to these changes (\code{rda},
- \code{capscale}, \code{simulate} methods for \code{rda},
- \code{cca} and \code{capscale}). The change in \R 2.14.0 does
- not change the results but causes a lot of annoying warnings in
- \code{rda} and related functions, and you probably wish to
- upgrade \pkg{vegan}.
+ \code{sd()} function for matrices (which was the behaviour at
+ least since \R 1.0-0), and several \pkg{vegan} functions were
+ changed to adapt to this change (\code{rda}, \code{capscale},
+ \code{simulate} methods for \code{rda}, \code{cca} and
+ \code{capscale}). The change in \R 2.14.0 does not influence the
+ results but you probably wish to upgrade \pkg{vegan} to avoid
+ annoying warnings.
}
} % end BUG FIXES
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