[Vegan-commits] r1795 - in pkg/vegan: . inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Sep 7 09:13:12 CEST 2011
Author: jarioksa
Date: 2011-09-07 09:13:12 +0200 (Wed, 07 Sep 2011)
New Revision: 1795
Modified:
pkg/vegan/DESCRIPTION
pkg/vegan/inst/ChangeLog
pkg/vegan/inst/NEWS.Rd
Log:
polishing vegan for release 2.0-0
Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION 2011-09-07 07:06:14 UTC (rev 1794)
+++ pkg/vegan/DESCRIPTION 2011-09-07 07:13:12 UTC (rev 1795)
@@ -1,7 +1,7 @@
Package: vegan
Title: Community Ecology Package
Version: 2.0-0
-Date: September 3, 2011
+Date: September 7, 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 2011-09-07 07:06:14 UTC (rev 1794)
+++ pkg/vegan/inst/ChangeLog 2011-09-07 07:13:12 UTC (rev 1795)
@@ -2,9 +2,10 @@
VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
-Version 2.0-0 (opened September 3, 2011)
+Version 2.0-0 (released September 7, 2011)
- * opened the release candidate ov vegan_2.0-0.
+ * opened the release candidate ov vegan_2.0-0 on September 3,
+ 2011.
* some old functions used attributes(x)$which instead of more
correct attr(x, "which"), and in addition postMDS() used
Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd 2011-09-07 07:06:14 UTC (rev 1794)
+++ pkg/vegan/inst/NEWS.Rd 2011-09-07 07:13:12 UTC (rev 1795)
@@ -2,8 +2,7 @@
\title{vegan News}
\encoding{UTF-8}
-\section{Changes in version 2.0-beta}{
-
+\section{Changes in version 2.0-0}{
\subsection{GENERAL}{
\itemize{
@@ -12,9 +11,9 @@
\item \pkg{vegan} implements standard \R \code{NAMESPACE}. In
general, \code{S3} methods are not exported which means that you
cannot directly use or see contents of functions like
- \code{cca.default}, \code{plot.cca} or \code{anova.cca}. To use
- these functions you should rely on \R delegation and simply use
- \code{cca} and for its result objects use \code{plot} and
+ \code{cca.default}, \code{plot.cca} or \code{anova.ccabyterm}. To
+ use these functions you should rely on \R delegation and simply
+ use \code{cca} and for its result objects use \code{plot} and
\code{anova} without suffix \code{.cca}. To see the contents of
the function you can use \code{:::}, such as
\code{vegan:::cca.default}. This change may break packages,
@@ -36,29 +35,29 @@
multidimensional scaling (NMDS). This function replaces
\code{MASS::isoMDS} as the default method in
\code{metaMDS}. Major advantages of \code{monoMDS} are that it
- has \sQuote{primary} or \sQuote{weak} tie treatment which means
+ has \sQuote{weak} (\sQuote{primary}) tie treatment which means
that it can split tied observed dissimilarities. \sQuote{Weak}
tie treatment improves ordination of heterogeneous data sets,
because maximum dissimilarities of \eqn{1} can be split. In
addition to global NMDS, \code{monoMDS} can perform local and
hybrid NMDS and metric MDS. It can also handle missing and zero
dissimilarities. Moreover, \code{monoMDS} is faster than
- previous alternatives.
+ previous alternatives. The function uses \code{Fortran} code
+ written by Peter Minchin.
\item \code{MDSrotate} a new function to replace
- \code{metaMDSrotate}. This function can rotate both
- \code{metaMDS} and \code{monoMDS} results so that the first axis
- is parallel to an environmental vector.
+ \code{metaMDSrotate}. This function can rotate both \code{metaMDS}
+ and \code{monoMDS} results so that the first axis is parallel to
+ an environmental vector.
\item \code{eventstar} 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. (Ecography 31, 450-456; 2008). The code was
- contributed by Eduardo Ribeira Cunha and Heloisa Beatriz
- Antoniazi Evangelista and adapted to \pkg{vegan} by Peter
- Solymos.
+ Mendes et al. (\emph{Ecography} 31, 450-456; 2008). The code was
+ contributed by Eduardo Ribeira Cunha and Heloisa Beatriz Antoniazi
+ Evangelista and adapted to \pkg{vegan} by Peter Solymos.
- \item \code{fitspecaccum} to fit non-linear regression models to
+ \item \code{fitspecaccum} fits non-linear regression models to
the species accumulation results from \code{specaccum}. The
function can use new self-starting species accumulation models
in \pkg{vegan} or other self-starting non-linear regression
@@ -70,14 +69,21 @@
\item Self-starting non-linear species accumulation models
\code{SSarrhenius}, \code{SSgleason}, \code{SSgitay} and
\code{SSlomolino}. These can be used with \code{fitspecaccum} or
- directly in non-linear regression with \code{nls}.
+ directly in non-linear regression with \code{nls}. These functions
+ were implemented because they were found good for species-area
+ models by Dengler (\emph{J. Biogeogr.} 36, 728-744; 2009).
}
} % end NEW FUNCTIONS
\subsection{NEW FEATURES}{
-
\itemize{
+
+ \item \code{adonis}, \code{anosim}, \code{meandist} and
+ \code{mrpp} warn on negative dissimilarities, and
+ \code{betadisper} refuses to analyse them. All these functions
+ expect dissimilarities, and giving something else (like
+ correlations) probably is a user error.
\item \code{betadisper} uses restricted permutation of the
\pkg{permute} package.
@@ -87,13 +93,14 @@
to alternatively select \code{MASS::isoMDS}. The default is not
to use \code{stepacross} with \code{monoMDS} because its
\sQuote{weak} tie treatment can cope with tied maximum
- dissimilarities of one. However, \code{stepacross} is always used
+ dissimilarities of one. However, \code{stepacross} is the default
with \code{isoMDS} because it cannot handle adequately these tied
- maximum dissimilarities.
+ maximum dissimilarities.
\item \code{specaccum} gained \code{predict} method which uses
- either linear or spline interpolation. Extrapolation is possible
- with spline interpolation, but may make little sense.
+ either linear or spline interpolation for data between observed
+ points. Extrapolation is possible with spline interpolation, but
+ may make little sense.
\item \code{specpool} can handle missing values or empty factor
levels in the grouping factor \code{pool}. Now also checks that
@@ -103,12 +110,17 @@
}
} % end NEW FEATURES
- \subsection{DEPRECATED}{
+ \subsection{DEPRECATED AND DEFUNCT}{
\itemize{
\item \code{metaMDSrotate} was replaced with \code{MDSrotate}
that can also handle the results of \code{monoMDS}.
+ \item \code{permuted.index2} and other \dQuote{new} permutation
+ code was removed in favour of the \pkg{permute} package. This code
+ was not intended for normal use, but packages depending on that
+ code in \pkg{vegan} should instead depend on \pkg{permute}.
+
}
} % end DEPRECATED
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