[Vegan-commits] r2700 - in pkg/permute: R inst man

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

Author: gsimpson
Date: 2013-11-12 21:17:26 +0100 (Tue, 12 Nov 2013)
New Revision: 2700

Modified:
   pkg/permute/R/shuffleSet2.R
   pkg/permute/inst/ChangeLog
   pkg/permute/man/shuffleSet.Rd
Log:
a better way of handling small permutation sets; generate all of them, and then sample nset of them.

Modified: pkg/permute/R/shuffleSet2.R
===================================================================
--- pkg/permute/R/shuffleSet2.R	2013-11-11 18:30:52 UTC (rev 2699)
+++ pkg/permute/R/shuffleSet2.R	2013-11-12 20:17:26 UTC (rev 2700)
@@ -7,6 +7,8 @@
             nset <- 1
         else
             nset <- np
+    } else {
+        control <- update(control, nperm = nset)
     }
 
     sn <- seq_len(n) ## sequence of samples in order of input
@@ -50,6 +52,16 @@
         ## Use that instead of a ranodm set
         out <- control$all.perms
     }
+
+    ## Because all.perms might have been generated, we have the
+    ## possibility that nrow(out) != nset. In that case, also no random
+    ## numbers have been generated. Hence we can sample nset rows from
+    ## out and return that. This has the nice side-effect of not
+    ## generating any non-unique permutations. Suggested by Jari.
+    if ((nr <- nrow(out)) > nset) {
+        out <- out[sample.int(nr, nset), ]
+    }
+
     out
 }
 

Modified: pkg/permute/inst/ChangeLog
===================================================================
--- pkg/permute/inst/ChangeLog	2013-11-11 18:30:52 UTC (rev 2699)
+++ pkg/permute/inst/ChangeLog	2013-11-12 20:17:26 UTC (rev 2700)
@@ -2,6 +2,21 @@
 
 permute ChangeLog
 
+Version 0.7-7
+
+	* shuffleSet: Implemented an idea of Jari's to allow `check()` and
+	`allPerms()` to do their thing and possibly generate the set of all
+	permutations, rather than turn off checking. If that now results in
+	more than `nset` permutations, `shuffleSet` randomly takes `nset` of
+	these. This is a nice suggestion as it avoids the problem that with
+	small numbers of possible permutations, you can randomly draw the
+	same permutation more than once.
+
+	As I have added this feature, I reverted some earlier changes to the
+	documentation that used the `check = FALSE` in their call to
+	`shuffleSet()`. The `check` argument is retained though, as a way for
+	function writers to skip that part of the permute workflow if desired.
+
 Version 0.7-6
 
 	* summary.allPerms: Was printing two slightly different subtitles.

Modified: pkg/permute/man/shuffleSet.Rd
===================================================================
--- pkg/permute/man/shuffleSet.Rd	2013-11-11 18:30:52 UTC (rev 2699)
+++ pkg/permute/man/shuffleSet.Rd	2013-11-12 20:17:26 UTC (rev 2700)
@@ -126,7 +126,7 @@
 ## as above, but  with same permutation for each Plot-level stratum
 CTRL <- how(plots = plotStrata,
             within = Within(type = "series", constant = TRUE))
-shuffleSet(20, 10, CTRL, check = FALSE)
+shuffleSet(20, 10, CTRL)
 }
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.