[Vegan-commits] r2650 - in pkg/vegan: . R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 5 16:12:11 CET 2013
Author: jarioksa
Date: 2013-11-05 16:12:11 +0100 (Tue, 05 Nov 2013)
New Revision: 2650
Modified:
pkg/vegan/DESCRIPTION
pkg/vegan/R/permutest.cca.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/anova.cca.Rd
Log:
permutest.cca uses permute package
Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION 2013-11-05 04:48:34 UTC (rev 2649)
+++ pkg/vegan/DESCRIPTION 2013-11-05 15:12:11 UTC (rev 2650)
@@ -1,12 +1,12 @@
Package: vegan
Title: Community Ecology Package
-Version: 2.1-37
-Date: October 14, 2013
+Version: 2.1-38
+Date: November 5, 2013
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
Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>
-Depends: permute (>= 0.7-4), lattice, R (>= 2.14.0)
+Depends: permute (>= 0.7-5), lattice, R (>= 2.14.0)
Suggests: MASS, mgcv, cluster, parallel, scatterplot3d, rgl, tcltk
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Modified: pkg/vegan/R/permutest.cca.R
===================================================================
--- pkg/vegan/R/permutest.cca.R 2013-11-05 04:48:34 UTC (rev 2649)
+++ pkg/vegan/R/permutest.cca.R 2013-11-05 15:12:11 UTC (rev 2650)
@@ -5,7 +5,7 @@
stop("No default permutation test defined")
`permutest.cca` <-
- function (x, permutations = 99,
+ function (x, permutations = how(nperm=99),
model = c("reduced", "direct", "full"), first = FALSE,
strata = NULL, parallel = getOption("mc.cores") , ...)
{
@@ -113,15 +113,23 @@
if (!exists(".Random.seed", envir = .GlobalEnv, inherits = FALSE))
runif(1)
seed <- get(".Random.seed", envir = .GlobalEnv, inherits = FALSE)
- ## permutations
+ ## permutations is either a single number, a how() structure or a
+ ## permutation matrix
if (length(permutations) == 1) {
- if (is.null(strata))
- permutations <- shuffleSet(N, permutations)
- else
- permutations <-
- t(sapply(1:permutations,
- function(x) permuted.index(N, strata=strata)))
+ nperm <- permutations
+ permutations <- how(nperm = nperm)
}
+ if (!is.null(strata)) {
+ if (!inherits(permutations, "how"))
+ stop("'strata' can be used only with simple permutation or with 'how()'")
+ if (!is.null(permutations$block))
+ stop("'strata' cannot be applied when 'blocks' are defined in 'how()'")
+ permutations <- update(permutations, blocks = strata)
+ }
+ ## now permutations is either a how() structure or a permutation
+ ## matrix. Make it to a matrix if it is "how"
+ if (inherits(permutations, "how"))
+ permutations <- shuffleSet(N, control = permutations)
nperm <- nrow(permutations)
## Parallel processing (similar as in oecosimu)
if (is.null(parallel) || getRversion() < "2.14.0")
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2013-11-05 04:48:34 UTC (rev 2649)
+++ pkg/vegan/inst/ChangeLog 2013-11-05 15:12:11 UTC (rev 2650)
@@ -2,8 +2,20 @@
VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
-Version 2.1-37 (opened October 14, 2013)
+Version 2.1-38 (opened November 5, 2013)
+ * DESCRIPTION: depends on permute >= 0.7-5.
+
+ * permutest.cca: permutation test uses 'permute' package. The old
+ interface was retained, and 'permutations' can be a single number
+ or a permutation matrix (as previously), but now it can also be a
+ how() object of the 'permute' package. The argument 'strata' was
+ also retained, but it is planned to be deprecated in the future,
+ and it is recommended that users switch to defining 'blocks' in
+ how().
+
+Version 2.1-37 (closed November 5, 2013)
+
* anova.cca: added new function anova.ccalist() to compare a
sequence of models. The function is still experimental ("proof of
the concept") and unexported. If this stays in vegan, it should
Modified: pkg/vegan/man/anova.cca.Rd
===================================================================
--- pkg/vegan/man/anova.cca.Rd 2013-11-05 04:48:34 UTC (rev 2649)
+++ pkg/vegan/man/anova.cca.Rd 2013-11-05 15:12:11 UTC (rev 2650)
@@ -23,7 +23,7 @@
permutest(x, ...)
-\method{permutest}{cca}(x, permutations = 99,
+\method{permutest}{cca}(x, permutations = how(nperm=99),
model = c("reduced", "direct", "full"),
first = FALSE, strata = NULL,
parallel = getOption("mc.cores") , ...)
@@ -46,14 +46,23 @@
\code{permutest.cca}. In \code{anova} with \code{by = "axis"} you
can use argument \code{cutoff} (defaults \code{1}) which stops
permutations after exceeding the given level. }
- \item{permutations}{Number of permutations for assessing significance
- of constraints.}
+
+ \item{permutations}{Either a \code{\link[permute]{how}} result
+ defining permutations, or a permutation matrix with each row giving
+ the permutation indices, or the number of permutations for simple
+ permutations. See \code{\link{permutations}} for details.}
+
\item{model}{Permutation model (partial match).}
\item{first}{Assess only the significance of the first constrained
eigenvalue; will be passed from \code{anova.cca}. }
+
\item{strata}{An integer vector or factor specifying the strata for
permutation. If supplied, observations are permuted only within the
- specified strata.}
+ specified strata. It is an error to use this when
+ \code{permutations} is a matrix, or a \code{\link[permute]{how}}
+ defines \code{blocks}. This is a legacy argument that will be
+ deprecated in the future: use \code{permutations = how(\dots, blocks)}
+ instead. }
\item{parallel}{Number of parallel processes or a predefined socket
cluster. With \code{parallel = 1} uses ordinary, non-parallel
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