/usr/lib/R/site-library/permute/NEWS.Rd is in r-cran-permute 0.8-3-1.
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\title{permute News}
\encoding{UTF-8}
\section{Changes in version 0.8-0}{
\subsection{GENERAL}{
\itemize{
\item Version 0.8-0 represents a major update of \pkg{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.
}
} % general
\subsection{NEW FEATURES}{
\itemize{
\item \code{how()}, a new function to create permutation
designs. This replaces the deprecated function \code{permControl}.
\item \pkg{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
\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.
\item As a convenience for users, the \code{update()} function
will now work with objects of classes \code{"how"}, \code{"Plots"}
or \code{"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
\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()}
method to allow for compact printing of the design elements used
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
their packages.
}
} % new features
\subsection{DEPRECATED}{
\itemize{
\item \code{permControl} is deprecated in favour of \code{how}.
\item \code{permuplot} is broken and effectively defunct given the
changes to the way permutation are defined and the addition of
blocks. \code{permuplot} is no longer expoerted from the package
namespace.
}
} % deprecated
}
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