[Vegan-commits] r1677 - in pkg/permute: . R inst man

[noreply at r-forge.r-project.org]

Author: gsimpson
Date: 2011-07-05 10:22:30 +0200 (Tue, 05 Jul 2011)
New Revision: 1677

Added:
   pkg/permute/R/shuffleSet.R
   pkg/permute/man/shuffleSet.Rd
Modified:
   pkg/permute/DESCRIPTION
   pkg/permute/NAMESPACE
   pkg/permute/inst/ChangeLog
Log:
add shuffleSet for simple cases without strata

Modified: pkg/permute/DESCRIPTION
===================================================================
--- pkg/permute/DESCRIPTION	2011-07-05 06:07:23 UTC (rev 1676)
+++ pkg/permute/DESCRIPTION	2011-07-05 08:22:30 UTC (rev 1677)
@@ -1,6 +1,6 @@
 Package: permute
 Title: Functions for generating restricted permutations of data
-Version: 0.5-1
+Version: 0.5-2
 Date: $Date$
 Author: Gavin L. Simpson
 Maintainer: Gavin L. Simpson <gavin.simpson at ucl.ac.uk>

Modified: pkg/permute/NAMESPACE
===================================================================
--- pkg/permute/NAMESPACE	2011-07-05 06:07:23 UTC (rev 1676)
+++ pkg/permute/NAMESPACE	2011-07-05 08:22:30 UTC (rev 1677)
@@ -2,7 +2,8 @@
 export(`allPerms`, `Blocks`, `numPerms`, `permCheck`,
        `permControl`, `permute`, `shuffle`, `Within`,
        `shuffleFree`, `shuffleSeries`, `shuffleGrid`, `shuffleStrata`,
-       `getBlocks`, `getWithin`, `getStrata`)
+       `getBlocks`, `getWithin`, `getStrata`,
+       `shuffleSet`)
 
 ### Imports
 importFrom(`stats`, `nobs`)

Added: pkg/permute/R/shuffleSet.R
===================================================================
--- pkg/permute/R/shuffleSet.R	                        (rev 0)
+++ pkg/permute/R/shuffleSet.R	2011-07-05 08:22:30 UTC (rev 1677)
@@ -0,0 +1,26 @@
+`shuffleSet` <- function(n, nset = 1, control = permControl()) {
+    Set <- matrix(nrow = nset, ncol = n)
+    ## If no strata then permute all samples using stated scheme
+    WI <- getWithin(control)
+    if(is.null(getStrata(control))) {
+        Args <- switch(WI$type,
+                       "free" = list(x = n, size = n),
+                       "series" = list(x = seq_len(n), mirror = WI$mirror),
+                       "grid" = list(nrow = WI$nrow, ncol = WI$ncol,
+                       mirror = WI$mirror))
+        FUN <- switch(WI$type,
+                      "free" = shuffleFree,
+                      "series" = shuffleSeries,
+                      "grid" = shuffleGrid)
+        if(WI$type == "none") {
+            Set <- rep(seq_len(n), each = nset)
+        } else {
+            for(i in seq_len(nset)) {
+                Set[i,] <- do.call(FUN, Args)
+            }
+        }
+    } else {
+        .NotYetImplemented()
+    }
+    Set
+}

Modified: pkg/permute/inst/ChangeLog
===================================================================
--- pkg/permute/inst/ChangeLog	2011-07-05 06:07:23 UTC (rev 1676)
+++ pkg/permute/inst/ChangeLog	2011-07-05 08:22:30 UTC (rev 1677)
@@ -2,8 +2,15 @@
 
 permute ChangeLog
 
-Version 0.5-1 (opened June 28, 2011)
+Version 0.5-2 (opened 5, 2011)
 
+	* shuffelSet: new function to generate a set of `n`
+	permutations without the overhead of `n` repeated calls to
+	`shuffle()`. Currently only for designs without
+	strata/blocks.
+
+Version 0.5-1 (closed July 5, 2011)
+
 	* shuffle: now returns seq_len(n) for no permutation within
 	blocks or of blocks.
 

Added: pkg/permute/man/shuffleSet.Rd
===================================================================
--- pkg/permute/man/shuffleSet.Rd	                        (rev 0)
+++ pkg/permute/man/shuffleSet.Rd	2011-07-05 08:22:30 UTC (rev 1677)
@@ -0,0 +1,68 @@
+\name{shuffleSet}
+\alias{shuffleSet}
+
+\title{
+  Generate a set of permutations from the specified design.
+}
+\description{
+  \code{shuffleSet} returns a set of \code{nset} permutations from the
+  specified design. The main purpose of the function is to circumvent
+  the overhead of repeatedly calling \code{\link{shuffle}} to generate a
+  set of permutations.
+}
+\usage{
+shuffleSet(n, nset = 1, control = permControl())
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{n}{
+    numeric; the number of observations in the sample set.
+  }
+  \item{nset}{
+    numeric; the number of permutations to generate for the set
+  }
+  \item{control}{
+    an object of class \code{"permControl"} describing a valid
+    permutation design.
+  }
+}
+\details{
+  Currently, only the simple case of permutations not in the presence of
+  blocks (strata) is implemented.
+}
+\value{
+  Returns a matrix of permutations, where each row is a separate
+  permutation. As such, the returned matrix has \code{nset} rows and
+  \code{n} columns.
+}
+\author{
+  Gavin L. Simpson
+}
+
+%\note{
+%%  ~~further notes~~
+%}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+  See \code{\link{shuffle}} for generating a single permutation, and
+  \code{\link{permControl}} for setting up permutation designs.
+}
+\examples{
+## simple random permutations, 5 permutations in set
+shuffleSet(n = 10, nset = 10)
+
+## series random permutations, 10 permutations in set
+shuffleSet(10, 10, permControl(within = Within(type = "series")))
+
+## series random permutations, 10 permutations in set,
+## with possible mirroring
+CTRL <- permControl(within = Within(type = "series", mirror = TRUE))
+shuffleSet(10, 10, CTRL)
+
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ htest }
+\keyword{ design }% __ONLY ONE__ keyword per line