| NEWS | R Documentation |
Version 0.8-0 represents a major update of permute, with some backwards-incompatible changes to the main functions. The main addition is the availability of block-level restrictions on the permutations, which are required for whole- and split-plot designs.
how(), a new function to create permutation
designs. This replaces the deprecated function permControl.
permute gains the addition of true blocking structures with which to restrict the permutations. Blocks sit as the outermost layer of the permutations, and can contain plots which in turn contain samples. In contrasts to plots, blocks are never permuted and samples are never shuffled between blocks. Permutation only ever happens within blocks.
To facilitate this, plot-level strata are now specified via
Plots() instead of via the old strata argument of
how(). Blocks are specified via a new argument blocks,
which takes a factor variable.
A new suite of extractor and replacement functions is
provided with which to interact with permutation designs created
by how(). Extractor functions have names getFoo(),
where Foo() is a component of the design. Replacement
functions have names 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.
As a convenience for users, the update() function
will now work with objects of classes "how", "Plots"
or "Within" to allow quick updating of features of the
permutation design. This approach is intended for interactive use
at the top-level and not within functions, where the new
setFoo replacement functions should be used.
shuffleSet() is enhanced in this version. Firstly, the
function now returns a classed object which has a print()
method to allow for compact printing of the design elements used
to generate the set of permutations. Second, shuffleSet()
will sample 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.
allPerms() no longer assumes that samples are in
block and/or plot ordering.
The package vignette is much expanded in this version with new sections on using permute within functions that will be of interest to package authors wishing to use permute in their packages.
permControl is deprecated in favour of how.
permuplot is broken and effectively defunct given the
changes to the way permutation are defined and the addition of
blocks. permuplot is no longer expoerted from the package
namespace.