[Vegan-commits] r2514 - in pkg/permute: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 12 19:41:58 CEST 2013
Author: gsimpson
Date: 2013-06-12 19:41:58 +0200 (Wed, 12 Jun 2013)
New Revision: 2514
Added:
pkg/permute/R/permute-deprecated.R
pkg/permute/R/print.check.R
pkg/permute/R/print.summary.check.R
pkg/permute/R/summary.check.R
pkg/permute/man/permCheck-deprecated.Rd
Removed:
pkg/permute/R/permControl.R
pkg/permute/R/print.permCheck.R
pkg/permute/R/print.permControl.R
pkg/permute/R/print.summary.permCheck.R
pkg/permute/R/summary.permCheck.R
Modified:
pkg/permute/man/check.Rd
Log:
clean up sources following deprecation and follow best practice
Deleted: pkg/permute/R/permControl.R
===================================================================
--- pkg/permute/R/permControl.R 2013-06-12 15:50:07 UTC (rev 2513)
+++ pkg/permute/R/permControl.R 2013-06-12 17:41:58 UTC (rev 2514)
@@ -1,17 +0,0 @@
-`permControl` <- function(within = Within(),
- plots = Plots(),
- blocks = NULL,
- nperm = 199, complete = FALSE,
- maxperm = 9999, minperm = 99,
- all.perms = NULL,
- observed = FALSE)
-{
- .Deprecated("how", package = "permute")
- out <- list(within = within, plots = plots, blocks = blocks,
- nperm = nperm, complete = complete,
- maxperm = maxperm, minperm = minperm,
- all.perms = all.perms, observed = observed,
- blocks.name = deparse(substitute(blocks)))
- class(out) <- "how"
- out
-}
Added: pkg/permute/R/permute-deprecated.R
===================================================================
--- pkg/permute/R/permute-deprecated.R (rev 0)
+++ pkg/permute/R/permute-deprecated.R 2013-06-12 17:41:58 UTC (rev 2514)
@@ -0,0 +1,43 @@
+`permControl` <- function(within = Within(),
+ plots = Plots(),
+ blocks = NULL,
+ nperm = 199, complete = FALSE,
+ maxperm = 9999, minperm = 99,
+ all.perms = NULL,
+ observed = FALSE)
+{
+ .Deprecated("how", package = "permute")
+ out <- list(within = within, plots = plots, blocks = blocks,
+ nperm = nperm, complete = complete,
+ maxperm = maxperm, minperm = minperm,
+ all.perms = all.perms, observed = observed,
+ blocks.name = deparse(substitute(blocks)))
+ class(out) <- "how"
+ out
+}
+
+`print.permControl` <- function(x, ...)
+{
+ .Deprecated("print.how", package = "permute")
+ class(x) <- "how"
+ print(x)
+}
+
+
+`print.permCheck` <- function(x, ...)
+{
+ print(x$n)
+}
+
+`print.summary.permCheck` <- function(x, ...)
+{
+ cat(paste("Number of possible permutations:", x$n, "\n"))
+ print(x$control)
+ invisible(x)
+}
+
+`summary.permCheck` <- function(object, ...)
+{
+ class(object) <- "summary.permCheck"
+ object
+}
Copied: pkg/permute/R/print.check.R (from rev 2496, pkg/permute/R/print.permCheck.R)
===================================================================
--- pkg/permute/R/print.check.R (rev 0)
+++ pkg/permute/R/print.check.R 2013-06-12 17:41:58 UTC (rev 2514)
@@ -0,0 +1,4 @@
+`print.check` <- function(x, ...)
+{
+ print(x$n)
+}
Deleted: pkg/permute/R/print.permCheck.R
===================================================================
--- pkg/permute/R/print.permCheck.R 2013-06-12 15:50:07 UTC (rev 2513)
+++ pkg/permute/R/print.permCheck.R 2013-06-12 17:41:58 UTC (rev 2514)
@@ -1,4 +0,0 @@
-`print.check` <- function(x, ...)
-{
- print(x$n)
-}
Deleted: pkg/permute/R/print.permControl.R
===================================================================
--- pkg/permute/R/print.permControl.R 2013-06-12 15:50:07 UTC (rev 2513)
+++ pkg/permute/R/print.permControl.R 2013-06-12 17:41:58 UTC (rev 2514)
@@ -1,6 +0,0 @@
-`print.permControl` <- function(x, ...)
-{
- .Deprecated("print.how", package = "permute")
- class(x) <- "how"
- print(x)
-}
Copied: pkg/permute/R/print.summary.check.R (from rev 2496, pkg/permute/R/print.summary.permCheck.R)
===================================================================
--- pkg/permute/R/print.summary.check.R (rev 0)
+++ pkg/permute/R/print.summary.check.R 2013-06-12 17:41:58 UTC (rev 2514)
@@ -0,0 +1,6 @@
+`print.summary.check` <- function(x, ...)
+{
+ cat(paste("Number of possible permutations:", x$n, "\n"))
+ print(x$control)
+ invisible(x)
+}
Deleted: pkg/permute/R/print.summary.permCheck.R
===================================================================
--- pkg/permute/R/print.summary.permCheck.R 2013-06-12 15:50:07 UTC (rev 2513)
+++ pkg/permute/R/print.summary.permCheck.R 2013-06-12 17:41:58 UTC (rev 2514)
@@ -1,6 +0,0 @@
-`print.summary.check` <- function(x, ...)
-{
- cat(paste("Number of possible permutations:", x$n, "\n"))
- print(x$control)
- invisible(x)
-}
Copied: pkg/permute/R/summary.check.R (from rev 2496, pkg/permute/R/summary.permCheck.R)
===================================================================
--- pkg/permute/R/summary.check.R (rev 0)
+++ pkg/permute/R/summary.check.R 2013-06-12 17:41:58 UTC (rev 2514)
@@ -0,0 +1,5 @@
+`summary.check` <- function(object, ...)
+{
+ class(object) <- "summary.check"
+ object
+}
Deleted: pkg/permute/R/summary.permCheck.R
===================================================================
--- pkg/permute/R/summary.permCheck.R 2013-06-12 15:50:07 UTC (rev 2513)
+++ pkg/permute/R/summary.permCheck.R 2013-06-12 17:41:58 UTC (rev 2514)
@@ -1,5 +0,0 @@
-`summary.check` <- function(object, ...)
-{
- class(object) <- "summary.check"
- object
-}
Modified: pkg/permute/man/check.Rd
===================================================================
--- pkg/permute/man/check.Rd 2013-06-12 15:50:07 UTC (rev 2513)
+++ pkg/permute/man/check.Rd 2013-06-12 17:41:58 UTC (rev 2514)
@@ -1,7 +1,5 @@
\name{check}
\alias{check}
-\alias{permCheck} % for the deprecated function
-\alias{permCheck-deprecated} % for the deprecated function
\alias{print.check}
\alias{print.summary.check}
\alias{summary.check}
@@ -28,12 +26,11 @@
\item{object}{an R object. See Details for a
complete description, especially for \code{numPerms}. For
\code{\link{summary.check}} an object of class
- \code{"check"}. For \code{\link{summary.allPerms}} an object of
- class \code{"allPerms"}.}
+ \code{"check"}.}
\item{control}{a list of control values describing properties of the
permutation design, as returned by a call to
\code{\link{how}}.}
- \item{make.all}{logical; should \code{check} generate all
+ \item{make.all}{logical; should \code{permCheck} generate all
possible permutations? Useful if want to check permutation design
but not produce the matrix of all permutations.}
\item{n}{the number of observations or an 'object' from which the
@@ -93,16 +90,11 @@
}
\value{
For \code{check} a list containing the maximum number of
- permutations possible and an object of class
- \code{"\link{how}"}.
-
- For \code{permuplot}, a plot on the currently active device.
+ permutations possible and an object of class \code{"\link{how}"}.
}
\author{Gavin L. Simpson}
-\seealso{\code{\link{shuffle}} and \code{\link{how}}.}
+\seealso{\code{\link{shuffle}} and \code{\link{how}}.}\examples{
-\examples{
-
## use example data from ?pyrifos in package vegan
require(vegan)
example(pyrifos)
@@ -137,7 +129,6 @@
control = how(plots = Plots(strata = ditch),
within = Within(type = "series", mirror = TRUE)))
-\dontrun{ % FIXME these fail in allStrata needing 235.5 Gb RAM!!
## time series within strata, no mirroring, same permutation
## within strata
check(pyrifos,
@@ -151,6 +142,7 @@
within = Within(type = "series", mirror = TRUE,
constant = TRUE)))
+\dontrun{ % FIXME these fail in allStrata needing 235.5 Gb RAM!!
## permute strata
check(pyrifos, how(plots = Plots(strata = ditch, type = "free"),
within = Within(type = "none")))
@@ -195,7 +187,8 @@
%% Fixed one, above, but there may still be problems with some of
%% the code below:
\dontrun{
-allPerms(7, how(type = "free", strata = fac))
+allPerms(7, how(within = Within(type = "free"),
+ plots = Plots(strata = fac)))
## series permutations in levels of strata
numPerms(7, how(type = "series", strata = fac))
allPerms(7, how(type = "series", strata = fac))
Added: pkg/permute/man/permCheck-deprecated.Rd
===================================================================
--- pkg/permute/man/permCheck-deprecated.Rd (rev 0)
+++ pkg/permute/man/permCheck-deprecated.Rd 2013-06-12 17:41:58 UTC (rev 2514)
@@ -0,0 +1,69 @@
+\name{permCheck-deprecated}
+\alias{permCheck} % for the deprecated function
+\alias{permCheck-deprecated} % for the deprecated function
+\alias{print.permCheck}
+\alias{print.summary.permCheck}
+\alias{summary.permCheck}
+
+\title{Utility functions for permutation schemes}
+\description{
+ \code{permCheck} provides checking of permutation schemes for
+ validity. \code{permuplot} produces a graphical representation of the
+ selected permutation design.
+}
+\usage{
+permCheck(object, control = how(), make.all = TRUE)
+
+\method{summary}{permCheck}(object, \dots)
+}
+
+\arguments{
+ \item{object}{an R object. See Details for a
+ complete description, especially for \code{numPerms}. For
+ \code{\link{summary.permCheck}} an object of class
+ \code{"permCheck"}.}
+ \item{control}{a list of control values describing properties of the
+ permutation design, as returned by a call to
+ \code{\link{how}}.}
+ \item{make.all}{logical; should \code{permCheck} generate all
+ possible permutations? Useful if want to check permutation design
+ but not produce the matrix of all permutations.}
+ \item{\dots}{arguments to other methods. For \code{permuplot}
+ graphical parameters can be passed to plotting functions, though
+ note that not all parameters will be accepted gracefully at the
+ moment.}
+}
+\details{
+ \code{permCheck} is a utility functions for working
+ with the new permutation schemes available in \code{\link{shuffle}}.
+
+ \code{permCheck} is used to check the current permutation schemes
+ against the object to which it will be applied. It calculates the
+ maximum number of possible permutations for the number of observations
+ in \code{object} and the permutation scheme described by
+ \code{control}. The returned object contains component \code{control},
+ an object of class \code{"how"} suitably modified if
+ \code{permCheck} identifies a problem.
+
+ The main problem is requesting more permutations than possible with
+ the number of observations and the permutation design. In such cases,
+ \code{nperm} is reduced to equal the number of possible permutations,
+ and complete enumeration of all permutations is turned on
+ (\code{control$complete} is set to \code{TRUE}).
+
+ Alternatively, if the number of possible permutations is low, and less
+ than \code{control$minperm}, it is better to enumerate all possible
+ permutations, and as such complete enumeration of all permutations is
+ turned on (\code{control$complete} is set to \code{TRUE}).
+}
+\value{
+ For \code{permCheck} a list containing the maximum number of
+ permutations possible and an object of class
+ \code{"\link{how}"}.
+
+ For \code{permuplot}, a plot on the currently active device.
+}
+\author{Gavin L. Simpson}
+\seealso{\code{\link{shuffle}} and \code{\link{how}}.}
+\keyword{ utilities }
+\keyword{ methods }
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