[Vegan-commits] r2713 - in pkg/vegan: R inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 19 15:40:45 CET 2013
Author: jarioksa
Date: 2013-11-19 15:40:44 +0100 (Tue, 19 Nov 2013)
New Revision: 2713
Modified:
pkg/vegan/R/adonis.R
pkg/vegan/R/anosim.R
pkg/vegan/R/bioenv.default.R
pkg/vegan/R/mantel.R
pkg/vegan/R/mantel.partial.R
pkg/vegan/R/metaMDSiter.R
pkg/vegan/R/mrpp.R
pkg/vegan/R/oecosimu.R
pkg/vegan/R/permutest.cca.R
pkg/vegan/R/simper.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/nobs.adonis.Rd
pkg/vegan/man/screeplot.cca.Rd
pkg/vegan/vignettes/decision-vegan.Rnw
Log:
vegan depends on R>=2.14.0 and now remove unnecessary tests and references to older veersions
Modified: pkg/vegan/R/adonis.R
===================================================================
--- pkg/vegan/R/adonis.R 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/R/adonis.R 2013-11-19 14:40:44 UTC (rev 2713)
@@ -107,7 +107,7 @@
## Apply permutations for each term
## This is the new f.test (2011-06-15) that uses fewer arguments
## Set first parallel processing for all terms
- if (is.null(parallel) || getRversion() < "2.14.0")
+ if (is.null(parallel))
parallel <- 1
hasClus <- inherits(parallel, "cluster")
isParal <- (hasClus || parallel > 1) && require(parallel)
Modified: pkg/vegan/R/anosim.R
===================================================================
--- pkg/vegan/R/anosim.R 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/R/anosim.R 2013-11-19 14:40:44 UTC (rev 2713)
@@ -48,7 +48,7 @@
permutations <- nrow(permat)
}
## Parallel processing
- if (is.null(parallel) || getRversion() < "2.14.0")
+ if (is.null(parallel))
parallel <- 1
hasClus <- inherits(parallel, "cluster")
if ((hasClus || parallel > 1) && require(parallel)) {
Modified: pkg/vegan/R/bioenv.default.R
===================================================================
--- pkg/vegan/R/bioenv.default.R 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/R/bioenv.default.R 2013-11-19 14:40:44 UTC (rev 2713)
@@ -71,7 +71,7 @@
comdis <- vegdist(comm, method = index)
}
## Prepare for parallel processing
- if (is.null(parallel) || getRversion() < "2.14.0")
+ if (is.null(parallel))
parallel <- 1
hasClus <- inherits(parallel, "cluster")
isParal <- (hasClus || parallel > 1) && require(parallel)
Modified: pkg/vegan/R/mantel.R
===================================================================
--- pkg/vegan/R/mantel.R 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/R/mantel.R 2013-11-19 14:40:44 UTC (rev 2713)
@@ -41,7 +41,7 @@
drop(cor(permvec, ydis, method = method, use = use))
}
## Parallel processing
- if (is.null(parallel) || getRversion() < "2.14.0")
+ if (is.null(parallel))
parallel <- 1
hasClus <- inherits(parallel, "cluster")
if ((hasClus || parallel > 1) && require(parallel)) {
Modified: pkg/vegan/R/mantel.partial.R
===================================================================
--- pkg/vegan/R/mantel.partial.R 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/R/mantel.partial.R 2013-11-19 14:40:44 UTC (rev 2713)
@@ -49,7 +49,7 @@
part.cor(rxy, rxz, ryz)
}
## parallel processing
- if (is.null(parallel) || getRversion() < "2.14.0")
+ if (is.null(parallel))
parallel <- 1
hasClus <- inherits(parallel, "cluster")
if ((hasClus || parallel > 1) && require(parallel)) {
Modified: pkg/vegan/R/metaMDSiter.R
===================================================================
--- pkg/vegan/R/metaMDSiter.R 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/R/metaMDSiter.R 2013-11-19 14:40:44 UTC (rev 2713)
@@ -73,7 +73,7 @@
monostop(s0)
tries <- 0
## Prepare for parallel processing
- if (is.null(parallel) || getRversion() < "2.14.0")
+ if (is.null(parallel))
parallel <- 1
hasClus <- inherits(parallel, "cluster")
isParal <- (hasClus || parallel > 1) && require(parallel)
Modified: pkg/vegan/R/mrpp.R
===================================================================
--- pkg/vegan/R/mrpp.R 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/R/mrpp.R 2013-11-19 14:40:44 UTC (rev 2713)
@@ -50,7 +50,7 @@
ncol(perms), N))
}
## Parallel processing
- if (is.null(parallel) || getRversion() < "2.14.0")
+ if (is.null(parallel))
parallel <- 1
hasClus <- inherits(parallel, "cluster")
if ((hasClus || parallel > 1) && require(parallel)) {
Modified: pkg/vegan/R/oecosimu.R
===================================================================
--- pkg/vegan/R/oecosimu.R 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/R/oecosimu.R 2013-11-19 14:40:44 UTC (rev 2713)
@@ -87,7 +87,7 @@
simind <- NULL
## Go to parallel processing if 'parallel > 1' or 'parallel' could
## be a pre-defined socket cluster or 'parallel = NULL'.
- if (is.null(parallel) || getRversion() < "2.14.0")
+ if (is.null(parallel))
parallel <- 1
hasClus <- inherits(parallel, "cluster")
if ((hasClus || parallel > 1) && require(parallel)) {
Modified: pkg/vegan/R/permutest.cca.R
===================================================================
--- pkg/vegan/R/permutest.cca.R 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/R/permutest.cca.R 2013-11-19 14:40:44 UTC (rev 2713)
@@ -132,7 +132,7 @@
permutations <- shuffleSet(N, control = permutations)
nperm <- nrow(permutations)
## Parallel processing (similar as in oecosimu)
- if (is.null(parallel) || getRversion() < "2.14.0")
+ if (is.null(parallel))
parallel <- 1
hasClus <- inherits(parallel, "cluster")
if ((hasClus || parallel > 1) && require(parallel)) {
Modified: pkg/vegan/R/simper.R
===================================================================
--- pkg/vegan/R/simper.R 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/R/simper.R 2013-11-19 14:40:44 UTC (rev 2713)
@@ -38,7 +38,7 @@
if (nperm > 0)
perm.contr <- matrix(nrow=P, ncol=nperm)
## Parallel processing ?
- if (is.null(parallel) || getRversion() < "2.14.0")
+ if (is.null(parallel))
parallel <- 1
hasClus <- inherits(parallel, "cluster")
isParal <- (hasClus || parallel > 1) && require(parallel)
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/inst/ChangeLog 2013-11-19 14:40:44 UTC (rev 2713)
@@ -31,6 +31,13 @@
permutations, constrained ordination, in particular in capscale()
and rounding of output. We have also introduced some changes in
output that were not yet synced.
+
+ * janitorial: vegan has been dependent on R >= 2.14.0 since
+ version 2.1-34 (r2597 Wed 28-Aug-2013). Now superfluous references
+ and tests for the older R version were removed in R code and
+ documentation. FIXME: cca() returns residuals.zombie item that was
+ supposed to be needed in R < 2.13.0. This was not yet removed: we
+ must first check that this can be safely done.
Version 2.1-38 (closed November 10, 2013)
Modified: pkg/vegan/man/nobs.adonis.Rd
===================================================================
--- pkg/vegan/man/nobs.adonis.Rd 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/man/nobs.adonis.Rd 2013-11-19 14:40:44 UTC (rev 2713)
@@ -31,14 +31,15 @@
}
}
-\details{ Function \code{nobs} is generic in \R version 2.13.0, and
+\details{ Function \code{nobs} is generic in \R, and
\pkg{vegan} provides methods for objects from \code{\link{adonis}},
\code{\link{betadisper}}, \code{\link{cca}} and other related
methods, \code{\link{CCorA}}, \code{\link{decorana}},
\code{\link{isomap}}, \code{\link{metaMDS}}, \code{\link{pcnm}},
\code{\link{procrustes}}, \code{\link{radfit}},
- \code{\link{varpart}} and \code{\link{wcmdscale}}. } \value{ A
- single number, normally an integer, giving the number of
+ \code{\link{varpart}} and \code{\link{wcmdscale}}. }
+
+\value{ A single number, normally an integer, giving the number of
observations. }
\author{
Modified: pkg/vegan/man/screeplot.cca.Rd
===================================================================
--- pkg/vegan/man/screeplot.cca.Rd 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/man/screeplot.cca.Rd 2013-11-19 14:40:44 UTC (rev 2713)
@@ -116,10 +116,7 @@
Legendre, P. and Legendre, L. (2012) \emph{Numerical Ecology}. 3rd English
ed. Elsevier.
}
-\note{Function \code{screeplot} is generic from \code{R} version
- 2.5.0. In these versions you can use plain \code{screeplot} command
- without suffices \code{cca}, \code{prcomp} etc.
- }
+
\author{Gavin L. Simpson}
\seealso{
\code{\link{cca}}, \code{\link{decorana}}, \code{\link{princomp}} and
Modified: pkg/vegan/vignettes/decision-vegan.Rnw
===================================================================
--- pkg/vegan/vignettes/decision-vegan.Rnw 2013-11-18 19:52:40 UTC (rev 2712)
+++ pkg/vegan/vignettes/decision-vegan.Rnw 2013-11-19 14:40:44 UTC (rev 2713)
@@ -38,8 +38,8 @@
\section{Parallel processing}
Several \pkg{vegan} functions can perform parallel processing using
-the standard \R{} package \pkg{parallel}.\footnote{Available since
- \R{} version 2.14.0.} The \pkg{parallel} package in \R{} implements
+the standard \R{} package \pkg{parallel}.
+The \pkg{parallel} package in \R{} implements
the functionality of earlier contributed packages \pkg{multicore} and
\pkg{snow}. The \pkg{multicore} functionality forks the analysis to
multiple cores, and \pkg{snow} functionality sets up a socket cluster
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