[Vegan-commits] r2781 - in pkg/permute: inst man

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

Author: gsimpson
Date: 2013-11-30 23:08:36 +0100 (Sat, 30 Nov 2013)
New Revision: 2781

Modified:
   pkg/permute/inst/NEWS.Rd
   pkg/permute/man/allPerms.Rd
Log:
Remove warning about requiring that samples be in plot/block order; document this as a user-level new feature

Modified: pkg/permute/inst/NEWS.Rd
===================================================================
--- pkg/permute/inst/NEWS.Rd	2013-11-30 22:05:56 UTC (rev 2780)
+++ pkg/permute/inst/NEWS.Rd	2013-11-30 22:08:36 UTC (rev 2781)
@@ -29,19 +29,19 @@
       permuted and samples are never shuffled between
       blocks. Permutation only ever happens within blocks.
 
-      To facilitate this, plot-level strata are no specified via
-      \code{Plots} instead of via the old strata argument of
-      \code{how}. Blocks are specified via a new argument \code{blocks},
+      To facilitate this, plot-level strata are now specified via
+      \code{Plots()} instead of via the old strata argument of
+      \code{how()}. Blocks are specified via a new argument \code{blocks},
       which takes a factor variable.
 
       \item A new suite of extractor and replacement functions is
       provided with which to interact with permutation designs created
-      by \code{how}. Extractor functions have names \code{getFoo}, where
-      \code{Foo} is a component of the design. Replacement functions
-      have names \code{setFoo}. The replacement function are especially
-      for use by package authors wishing to alter permutation within
-      their functions. The extractor functions are recommened for all
-      users wishing to extract features of the permutation design.
+      by \code{how()}. Extractor functions have names \code{getFoo()},
+      where \code{Foo()} is a component of the design. Replacement
+      functions have names \code{setFoo}. The replacement function are
+      especially for use by package authors wishing to alter permutation
+      within their functions. The extractor functions are recommened for
+      all users wishing to extract features of the permutation design. 
 
       \item As a convenience for users, the \code{update()} function
       will now work with objects of classes \code{"how"}, \code{"Plots"}
@@ -50,16 +50,19 @@
       at the top-level and not within functions, where the new
       \code{setFoo} replacement functions should be used.
 
-      \item \code{shuffleSet} is enhanced in this version. Firstly, the
-      function now returns a classed object which has a \code{print}
+      \item \code{shuffleSet()} is enhanced in this version. Firstly, the
+      function now returns a classed object which has a \code{print()}
       method to allow for compact printing of the design elements used
-      to generate the set of permutations. Second, \code{shuffleSet}
+      to generate the set of permutations. Second, \code{shuffleSet()}
       will sample \code{nset} permutations from the entire set of
       permutations should a small number of possible permutations
       trigger generation of the entire set. This avoids the generation
       of a set of non-unique permutations. Finally the random seed that
       generated the set is stored as an attribute.
 
+      \item \code{allPerms()} no longer assumes that samples are in
+      block and/or plot ordering.
+
       \item The package vignette is much expanded in this version with
       new sections on using \pkg{permute} within functions that will be
       of interest to package authors wishing to use \pkg{permute} in

Modified: pkg/permute/man/allPerms.Rd
===================================================================
--- pkg/permute/man/allPerms.Rd	2013-11-30 22:05:56 UTC (rev 2780)
+++ pkg/permute/man/allPerms.Rd	2013-11-30 22:08:36 UTC (rev 2781)
@@ -54,10 +54,6 @@
   \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.