[Vegan-commits] r2701 - in pkg/permute: R inst man

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

Author: gsimpson
Date: 2013-11-12 21:22:28 +0100 (Tue, 12 Nov 2013)
New Revision: 2701

Modified:
   pkg/permute/R/allPerms.R
   pkg/permute/inst/ChangeLog
   pkg/permute/man/allPerms.Rd
Log:
add argument 'check'; turn on some messages

Modified: pkg/permute/R/allPerms.R
===================================================================
--- pkg/permute/R/allPerms.R	2013-11-12 20:17:26 UTC (rev 2700)
+++ pkg/permute/R/allPerms.R	2013-11-12 20:22:28 UTC (rev 2701)
@@ -1,4 +1,4 @@
-`allPerms` <- function(n, control = how()) {
+`allPerms` <- function(n, control = how(), check = TRUE) {
     ## start
     v <- n
     ## expand n if a numeric or integer vector of length 1
@@ -8,7 +8,8 @@
     n <- nobs(v)
     ## check permutation scheme and update control
     make <- getMake(control)
-    pcheck <- check(v, control = update(control, make = FALSE))
+    if (check)
+        pcheck <- check(v, control = update(control, make = FALSE))
     ## ctrl <- pcheck$control
     ## if we do copy the new updated control, we need to update to
     ## reset make

Modified: pkg/permute/inst/ChangeLog
===================================================================
--- pkg/permute/inst/ChangeLog	2013-11-12 20:17:26 UTC (rev 2700)
+++ pkg/permute/inst/ChangeLog	2013-11-12 20:22:28 UTC (rev 2701)
@@ -17,6 +17,18 @@
 	`shuffleSet()`. The `check` argument is retained though, as a way for
 	function writers to skip that part of the permute workflow if desired.
 
+	* allPerms: gains an argument `check`, which defaults to `TRUE`. This
+	is used to turn off checking within `allPerms` if desired. A use-case
+	for this is in `check()`, which might end up caling `allPerms()` to
+	generate the set of all permutations. In that case `allPerms()` used
+	to recheck the design. Now this doesn't happen.
+
+	Turned on some `message()`s when the user asks for too many permutations
+	(more than the set of possible permutations) and when the set of
+	possible permutations is smaller than the `minperm` value stored in the
+	`"how"` object. The latter notifies the user that the entire set of
+	permutations is being generated.
+
 Version 0.7-6
 
 	* summary.allPerms: Was printing two slightly different subtitles.

Modified: pkg/permute/man/allPerms.Rd
===================================================================
--- pkg/permute/man/allPerms.Rd	2013-11-12 20:17:26 UTC (rev 2700)
+++ pkg/permute/man/allPerms.Rd	2013-11-12 20:22:28 UTC (rev 2701)
@@ -10,7 +10,7 @@
   permutations for a given R object and a specified permutation design.
 }
 \usage{
-allPerms(n, control = how())
+allPerms(n, control = how(), check = TRUE)
 
 \method{summary}{allPerms}(object, \dots)
 }
@@ -20,6 +20,9 @@
   \item{control}{a list of control values describing properties of the
     permutation design, as returned by a call to
     \code{\link{how}}.}
+  \item{check}{logical; should \code{allPerms} check the design? The
+    default is to check, but this can be skipped, for example if a
+    function checked the design earlier.}
   \item{object}{an object of class \code{"allPerms"}.}
   \item{\dots}{arguments to other methods.}
 }