[Vegan-commits] r2899 - in pkg/vegan: . inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Oct 13 10:59:00 CEST 2014
Author: jarioksa
Date: 2014-10-13 10:58:59 +0200 (Mon, 13 Oct 2014)
New Revision: 2899
Added:
pkg/vegan/.gitattributes
pkg/vegan/appveyor.yml
Modified:
pkg/vegan/.Rbuildignore
pkg/vegan/README.md
pkg/vegan/inst/NEWS.Rd
Log:
Squashed commit of the following:
commit 6b293572804d0dc653a53e5a847524b0fcc673ff
Merge: 4d10697 e6fedc7
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Sun Oct 12 19:04:32 2014 +0300
Merge pull request #55 from jarioksa/NEWS
News
commit e6fedc707a3d0d2503d410a31af2579463d204be
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Sun Oct 12 19:01:27 2014 +0300
First draft of complete release NEWS
commit 4d10697b90ada025c36b0d3022a5dad2841dc2e6
Author: Gavin Simpson <ucfagls at gmail.com>
Date: Sat Oct 11 14:00:07 2014 -0600
add appveyor badge to README.md
commit 769d9a145770f7450e5f0cbf05f3c321f25c0388
Author: Gavin Simpson <ucfagls at gmail.com>
Date: Sat Oct 11 13:58:04 2014 -0600
add appveyor CI support
commit f988022a5335011a013f933c688a973b2d717e21
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Sat Oct 11 11:04:37 2014 +0300
more flesh to NEWS
commit 0d019be1a56809519f527ea2a22ef7de3af44240
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Sat Oct 11 08:57:27 2014 +0300
more flesh to the NEWS skeleton
commit 93fd83cc7f7723c78b0b26676608e092cd994901
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Sat Oct 11 08:28:46 2014 +0300
Pick NEWS from diff -U2 vegan_2.0-10/R vegan_2.2-0/R
commit 16d74e39dd745c445cb862aae860ddbc83d25a57
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Tue Oct 7 21:06:02 2014 +0300
skeleton of NEWS about vegan 2.2-0
Modified: pkg/vegan/.Rbuildignore
===================================================================
--- pkg/vegan/.Rbuildignore 2014-10-12 16:07:26 UTC (rev 2898)
+++ pkg/vegan/.Rbuildignore 2014-10-13 08:58:59 UTC (rev 2899)
@@ -1,3 +1,5 @@
LICENSE
^\.travis\.yml$
+^travis-tool\.sh
+^appveyor\.yml$
Added: pkg/vegan/.gitattributes
===================================================================
--- pkg/vegan/.gitattributes (rev 0)
+++ pkg/vegan/.gitattributes 2014-10-13 08:58:59 UTC (rev 2899)
@@ -0,0 +1,5 @@
+* text=auto
+data/* binary
+src/* text=lf
+R/* text=lf
+
Modified: pkg/vegan/README.md
===================================================================
--- pkg/vegan/README.md 2014-10-12 16:07:26 UTC (rev 2898)
+++ pkg/vegan/README.md 2014-10-13 08:58:59 UTC (rev 2899)
@@ -4,4 +4,4 @@
Linux | Windows
------------|------------
-[](https://travis-ci.org/vegandevs/vegan) |
+[](https://travis-ci.org/vegandevs/vegan) | [](https://ci.appveyor.com/project/gavinsimpson/vegan/branch/master)
Added: pkg/vegan/appveyor.yml
===================================================================
--- pkg/vegan/appveyor.yml (rev 0)
+++ pkg/vegan/appveyor.yml 2014-10-13 08:58:59 UTC (rev 2899)
@@ -0,0 +1,44 @@
+# DO NOT CHANGE the "init" and "install" sections below
+
+environment:
+ R_CHECK_ARGS: --no-build-vignettes --no-manual
+
+# Download script file from GitHub
+init:
+ ps: |
+ $ErrorActionPreference = "Stop"
+ Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
+ Import-Module '..\appveyor-tool.ps1'
+
+install:
+ ps: Bootstrap
+
+# Adapt as necessary starting from here
+
+build_script:
+ - travis-tool.sh install_deps
+
+test_script:
+ - travis-tool.sh run_tests
+
+on_failure:
+ - travis-tool.sh dump_logs
+
+artifacts:
+ - path: '*.Rcheck\**\*.log'
+ name: Logs
+
+ - path: '*.Rcheck\**\*.out'
+ name: Logs
+
+ - path: '*.Rcheck\**\*.fail'
+ name: Logs
+
+ - path: '*.Rcheck\**\*.Rout'
+ name: Logs
+
+ - path: '\*_*.tar.gz'
+ name: Bits
+
+ - path: '\*_*.zip'
+ name: Bits
Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd 2014-10-12 16:07:26 UTC (rev 2898)
+++ pkg/vegan/inst/NEWS.Rd 2014-10-13 08:58:59 UTC (rev 2899)
@@ -7,11 +7,70 @@
\subsection{GENERAL}{
\itemize{
- \item Parallel processing
+ \item Several \pkg{vegan} functions can now use parallel
+ processing for slow and repeating calculations. All these
+ functions have argument \code{parallel}. The argument can be an
+ integer giving the number of parallel processes. In unix-alikes
+ (Mac OS, Linux) this will launch \code{"multicore"} processing
+ and in Windows it will set up \code{"snow"} clusters as desribed
+ in the documentation of \pkg{parallel} package. If \code{option}
+ \code{"mc.cores"} is set to an integer > 1, this will be used to
+ automatically start parallel processing. Finally, the argument
+ can also be a previously set up \code{"snow"} cluster which will
+ be used both in Windows and in unix-alikes. \pkg{Vegan} vignette
+ on Design decision explains the implementation (use
+ \code{vegandocs("decission")}, and \pkg{parallel} package has more
+ extensive documentation on parallel processing in \R.
- \item Restricted permutations
+ The following function use parallel processing in analysing
+ permutatin statistics: \code{adonis}, \code{anosim},
+ \code{anova.cca} (and \code{permutest.cca}), \code{mantel} (and
+ \code{mantel.partial}), \code{mrpp}, \code{permutest.betadisper}
+ and \code{simper}. In addition, \code{bioenv} can compare
+ several candidate sets of models in paralle, \code{metaMDS} can
+ launch several random starts in parallel, and \code{oecosimu}
+ can evaluate test statistics for several null models in
+ parallel.
- \item New null models
+ \item All permutation tests are based on the \pkg{permute}
+ package which offers strong tools for restricted
+ permutation. All these functions have argument
+ \code{permutations}. The default usage of simple non-restricted
+ permutations is achieved by giving a single integer number as
+ its argument. Restricted permutations can be defined using the
+ \code{how} function of the \pkg{permute} package. Finally, the
+ argument can be a permutation matrix where rows define
+ permutations. It is possible to use external or user constructed
+ permutations.
+
+ See \code{help(permutations)} for a brief introduction on
+ permutations in \pkg{vegan}, and \pkg{permute} package for the
+ full documention. The vignette of the \pkg{permute} package can
+ be read from \pkg{vegan} with command
+ \code{vegandocs("permutations")}.
+
+ The following functions use the \pkg{permute} package:
+ \code{CCorA}, \code{adonis}, \code{anosim}, \code{anova.cca}
+ (plus associated \code{permutest.cca}, \code{add1.cca},
+ \code{drop1.cca}, \code{ordistep}, \code{ordiR2step}),
+ \code{envfit} (plus associated \code{factorfit} and
+ \code{vectorfit}), \code{mantel} (and \code{mantel.partial}),
+ \code{mrpp}, \code{mso}, \code{permutest.betadisper},
+ \code{protest} and \code{simper}.
+
+ \item Community null model generation has been completely
+ redesigned and rewritten. The communities are constructed with
+ new \code{nullmodel} function and defined in a low level
+ \code{commsim} function. The actual null models are generated
+ with a \code{simulate} function that builds an array of null
+ models. The new null models include a wide array of quantitative
+ models in addition to the old binary models, and users can plug
+ in their own generating functions. The basic tool invoking and
+ analysing null models is \code{oecosimu}. The null models are
+ often used only for the analysis of nestedness, but the
+ implementation in \code{oecosimu} allows analysing any
+ statistic, and null models are better seen as an alternative to
+ permutation tests.
} %end itemize
} % end general
@@ -19,9 +78,14 @@
\subsection{INSTALLATION}{
\itemize{
- \item Changes in NAMESPACE and passes tests
+ \item \pkg{vegan} package dependencies and namespace imports
+ were adapted to changes in \R, and no more trigger warnings and
+ notes in package tests.
- \item Split \pkg{vegan3d}
+ \item Three-dimensional ordination graphics using
+ \pkg{scatterplot3d} for static plots and \pkg{rgl} for dynamic
+ plots were removed from \pkg{vegan} and moved to a companion
+ package \pkg{vegan3d}. The package is available in CRAN.
} %end itemize
} % end installation
@@ -29,17 +93,41 @@
\subsection{NEW FUNCTIONS}{
\itemize{
- \item Dispersion weighting \code{dispweight} plus a new method
- for generalized dispersion weigthing \code{gdispweight}.
+ \item Function \code{dispweight} implements dispersion weighting
+ of Clarke et al. (\emph{Marine Ecology Progress Series}, 320,
+ 11--27). In addition, we implemented a new method for
+ generalized dispersion weighting \code{gdispweight}. Both
+ methods downweight species that are significantly
+ over-dispersed.
- \item \code{hclust} support functions \code{reorder}, \code{rev}
- and \code{scores}.
+ \item New \code{hclust} support functions \code{reorder},
+ \code{rev} and \code{scores}. Functions \code{reorder} and
+ \code{rev} are similar as these functions for \code{dendrogram}
+ objects. However, \code{reorder} can use (and defaults to)
+ weighted mean. In weighted mean the node average is always the
+ mean of member leaves, whereas the \code{dendrogram} uses always
+ the unweighted means of joined branches.
\item \code{permustats} to extract and inspect permutation
results with support functions \code{summary}, \code{density},
- \code{densityplot}, \code{qqnorm} and \code{qqmath}.
+ \code{densityplot}, \code{qqnorm} and \code{qqmath}. The
+ \code{density} and \code{qqnorm} are standard \R{} tools that
+ only work with one statistic, and \code{densityplot} and
+ \code{qqmath} are \pkg{lattice} graphics that work with
+ univariate and multivariate statistics. The results of following
+ functions can be extracted: \code{anosim}, \code{adonis},
+ \code{mantel} (and \code{mantel.partial}), \code{mrpp},
+ \code{oecosimu}, \code{permustest.cca} (but not the
+ corresponding \code{anova} methods),
+ \code{permutest.betadisper}, and \code{protest}.
- \item \code{stressplot} functions.
+ \item \code{stressplot} functions display the ordination
+ distances at given number of dimensions against original
+ distances. These are a generalization of \code{stressplot} for
+ \code{metaMDS}, and always use the inherent distances of each
+ ordination method. The functions are available for the results
+ \code{capscale}, \code{cca}, \code{princomp}, \code{prcomp},
+ \code{rda}, and \code{wcmdscale}.
} % end itemize
} % end new functions
@@ -47,6 +135,9 @@
\subsection{BUG FIXES}{
\itemize{
+ \item \code{cascadeKM} of only one group will be \code{NA} instead
+ of a random value.
+
\item \code{ordiellipse} can handle points exactly on a line,
including only two points.
@@ -54,7 +145,8 @@
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}.
+ eigenvalues will now report \code{NA} instead of using biased
+ method of \code{rda} results.
\item \code{simper} failed when a group had only a single member.
@@ -64,26 +156,39 @@
\subsection{NEW FEATURES}{
\itemize{
- \item \code{anova.cca} functions re-written, and added an option
- of analysing a sequence of models against each other.
+ \item \code{anova.cca} functions were re-written to use the
+ \pkg{permute} package. Old results may not be exactly
+ reproduced, and models with missing data may fail in several
+ cases. There is a new option of analysing a sequence of models
+ against each other.
\item \code{simulate} functions for \code{cca} and \code{rda}
can return several simulations in a \code{nullmodel} compatible
object. The functions can produce simulations with correlated
- errors (also for \code{capscale}).
+ errors (also for \code{capscale}) in parametric simulation with
+ Gaussian error.
\item \code{bioenv} can use Manhattan, Gower and Mahalanobis
- distances in addition to Euclidean. New helper function
- \code{bioenvdist} can extract the dissimilarities applied in
- best model or any other model.
+ distances in addition to the default Euclidean. New helper
+ function \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{metaMDS(..., trace = 2)} will show convergence
+ information with the default \code{monoMDS} engine.
- \item \code{MDSrotate} can rotate to multidimensional target.
+ \item Function \code{MDSrotate} can rotate a \eqn{k}-dimensional
+ ordination to \eqn{k-1} variables. When these variables are
+ correlated (like usually is the case), the vectors can also be
+ correlated to previously rotated dimensions, but will be
+ uncorrelated to all later ones.
- \item \code{nestednodf} gained new option for defining weighted
- nestedness statistic.
+ \item \pkg{vegan} 2.0-10 changed the weighted \code{nestednodf}
+ so that weighted analysis of binary data was equivalent to
+ binary analysis. However, this broke the equivalence to the
+ original method. Now the function has an argument \code{wbinary}
+ to select the method of analysis. The problem was reported and a
+ fix submitted by Vanderlei Debastiani (Universidade Federal do
+ Rio Grande do Sul, Brasil).
\item \code{ordiellipse}, \code{ordihull} and \code{ordiellipse}
can handle missing values in \code{groups}.
@@ -92,37 +197,44 @@
means.
\item \code{rankindex} can use Manhattan, Gower and Mahalanobis
- distance in addition to Euclidean.
+ distance in addition to the default Euclidean.
+ \item User can set colours and line types in unction
+ \code{rarecurve} for plotting rarefaction curves.
+
\item \code{spantree} gained a support function \code{as.hclust}
to change the minimum spannig tree into an \code{hclust} tree.
- \item \code{fitspecaccum} can do weighted analysis.
+ \item \code{fitspecaccum} can do weighted analysis. Gained
+ \code{lines} method.
\item \code{tabasco} uses now \code{reorder.hclust} for
- \code{hclust} for better ordering than previously when it cast
- trees to \code{dendrogram} objects.
+ \code{hclust} object 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{match.force = TRUE} and can be silenced with
\code{verbose = FALSE}.
\item \code{vegdist} gained Mahalanobis distance.
- \item Nomenclature updated in plant community
- data. \code{varespec} and \code{dune} use 8-character names (4
+ \item Nomenclature updated in plant community data with the help
+ of \pkg{Taxonstand} and \pkg{taxize} packages. The taxonomy of
+ the \code{dune} data was adapted to the same sources and APG
+ III. \code{varespec} and \code{dune} use 8-character names (4
from genus + 4 from species epithet). New data set on
- phylogenetic distances for \code{dune}.
+ phylogenetic distances for \code{dune} was extracted from Zanne
+ et al. (\emph{Nature}, 2014).
\item User configurable plots for \code{rarecurve}.
} %end itemize
- } % end new features
+ } % end new featuresq
\subsection{DEPRECATED AND DEFUNCT}{
\itemize{
- \item \code{strata} deprecated in permutations. It is still
+ \item \code{strata} are deprecated in permutations. It is still
accepted but will be phased out in next releases. Use \code{how}
of \pkg{permute} package.
@@ -135,12 +247,9 @@
method))}.
\item \code{density} and \code{densityplot} for permutation
- results: use \code{density(permustats(<permutation-object))}.
+ results: use \code{permustats} with its \code{density} and
+ \code{densityplot} method.
- \item \code{ordirgl} with its support functions, other \pkg{rgl}
- functions and \code{ordiplot3d} were moved to the \pkg{vegan3d}
- package.
-
} %end itemize
} % end deprecated
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