[Vegan-commits] r1793 - in pkg/permute: . inst man

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

Author: gsimpson
Date: 2011-09-05 23:31:41 +0200 (Mon, 05 Sep 2011)
New Revision: 1793

Modified:
   pkg/permute/DESCRIPTION
   pkg/permute/inst/ChangeLog
   pkg/permute/man/allPerms.Rd
Log:
prepare release for CRAN

Modified: pkg/permute/DESCRIPTION
===================================================================
--- pkg/permute/DESCRIPTION	2011-09-05 19:19:50 UTC (rev 1792)
+++ pkg/permute/DESCRIPTION	2011-09-05 21:31:41 UTC (rev 1793)
@@ -1,6 +1,6 @@
 Package: permute
 Title: Functions for generating restricted permutations of data
-Version: 0.5-4
+Version: 0.6-0
 Date: $Date$
 Author: Gavin L. Simpson
 Maintainer: Gavin L. Simpson <gavin.simpson at ucl.ac.uk>
@@ -8,4 +8,3 @@
 Description: The 'permute' package implements a set of restricted permutation designsfor freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples). 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeble or one of the restricted designs.
 License: GPL-2 
 URL: http://vegan.r-forge.r-project.org/
-

Modified: pkg/permute/inst/ChangeLog
===================================================================
--- pkg/permute/inst/ChangeLog	2011-09-05 19:19:50 UTC (rev 1792)
+++ pkg/permute/inst/ChangeLog	2011-09-05 21:31:41 UTC (rev 1793)
@@ -2,6 +2,13 @@
 
 permute ChangeLog
 
+Version 0.6-0 (opened September 5, 2011)
+
+	* allPerms: added warning regarding current need for samples
+	to be arranged in order of any strata.
+
+	* Release: Pushed to CRAN. First beta release.
+
 Version 0.5-4 (opened August 31, 2011)
 
 	* permCheck: deprecate `permCheck()` in favour of `check()`.

Modified: pkg/permute/man/allPerms.Rd
===================================================================
--- pkg/permute/man/allPerms.Rd	2011-09-05 19:19:50 UTC (rev 1792)
+++ pkg/permute/man/allPerms.Rd	2011-09-05 21:31:41 UTC (rev 1793)
@@ -56,6 +56,15 @@
   \code{control} (possibly updated via \code{check}). Attribute 
   \code{observed} contains argument \code{observed}.
 }
+\section{Warning}{
+  This function currently assumes that any strata are represented by
+  contiguous blocks in the order of the levels of \code{strata}. This is
+  unlike \code{\link{shuffle}} and \code{\link{shuffleSet}}.
+
+  If permuting the strata themselves, a balanced design is required (the
+  same number of observations in each level of \code{strata}. This is
+  common to all functions in the package.
+}
 \author{Gavin Simpson}
 \examples{
 ## allPerms can work with a vector
@@ -86,7 +95,7 @@
 ## well as the matrix of permutations
 % FIXME: uncomment the two lines below when we remove old permute
 % code from vegan and have vegan depend on permute
-##summary(tmp3)
-##summary(tmp4)
+summary(tmp3)
+summary(tmp4)
 %}
 }