[Vegan-commits] r2685 - in pkg/permute: R inst man

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

Author: gsimpson
Date: 2013-11-09 03:02:54 +0100 (Sat, 09 Nov 2013)
New Revision: 2685

Modified:
   pkg/permute/R/how.R
   pkg/permute/inst/ChangeLog
   pkg/permute/man/how.Rd
Log:
how gets a make argument

Modified: pkg/permute/R/how.R
===================================================================
--- pkg/permute/R/how.R	2013-11-09 02:00:19 UTC (rev 2684)
+++ pkg/permute/R/how.R	2013-11-09 02:02:54 UTC (rev 2685)
@@ -6,12 +6,13 @@
                   maxperm = 9999,
                   minperm = 99,
                   all.perms = NULL,
-                  observed = FALSE)
-{
+                  make = TRUE,
+                  observed = FALSE) {
     out <- list(within = within, plots = plots, blocks = blocks,
                 nperm = nperm, complete = complete,
                 maxperm = maxperm, minperm = minperm,
-                all.perms = all.perms, observed = observed,
+                all.perms = all.perms, make = make,
+                observed = observed,
                 blocks.name = deparse(substitute(blocks)),
                 call = match.call())
     class(out) <- "how"

Modified: pkg/permute/inst/ChangeLog
===================================================================
--- pkg/permute/inst/ChangeLog	2013-11-09 02:00:19 UTC (rev 2684)
+++ pkg/permute/inst/ChangeLog	2013-11-09 02:02:54 UTC (rev 2685)
@@ -8,6 +8,10 @@
 	`update()` to update elements of a stored permutation design object.
 	Suggested by Jari Oksanen.
 
+	`how` also gains an argument `make` which is the user-level way
+	to control whether all possible permutations are actually
+	created should the heuristics in `check()` decide they should be.
+
 	The `print` method for class "how" wasn't printing details of
 	mirroring or constant settings for within-plot components.
 

Modified: pkg/permute/man/how.Rd
===================================================================
--- pkg/permute/man/how.Rd	2013-11-09 02:00:19 UTC (rev 2684)
+++ pkg/permute/man/how.Rd	2013-11-09 02:02:54 UTC (rev 2685)
@@ -16,7 +16,8 @@
 \usage{
 how(within = Within(), plots = Plots(), blocks = NULL,
     nperm = 199, complete = FALSE, maxperm = 9999,
-    minperm = 99, all.perms = NULL, observed = FALSE)
+    minperm = 99, all.perms = NULL, make = TRUE,
+    observed = FALSE)
 
 Within(type = c("free","series","grid","none"),
        constant = FALSE, mirror = FALSE,
@@ -47,8 +48,13 @@
     \code{complete} and Details, below.} 
   \item{all.perms}{an object of class \code{allPerms}, the result of a
     call to \code{\link{allPerms}}.}
+  \item{make}{logical; should \code{check} generate all possible
+    permutations? Useful if want to check permutation design but not
+    produce the matrix of all permutations, or to circumvent the
+    heuristics governing when complete enumeration is activated.}
   \item{observed}{logical; should the observed permutation be returned
-    as part of the set of all permutations?}
+    as part of the set of all permutations? Default is \code{FALSE} to
+    facilitate usage in higher level functions.}
   \item{constant}{logical; should the same permutation be used within
     each level of strata? If \code{FALSE} a separate, possibly restricted,
     permutation is produced for each level of \code{strata}.}