A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.
permute generates permutations from a range of restricted permutation designs.
Permute provides an R implementation of the permutation schemes developed by Cajo ter Braak and made available in the Canoco software, version 3.1 (ter Braak, 1990). These permutation schemes draw upon ideas from an earlier paper by Besag & Clifford (1989).
Several types of permutation are available in permute:
Besag, J. and Clifford, P. (1989) Generalized Monte Carlo significance tests. Biometrika 76; 633–642.
ter Braak, C. J. F. (1990). Update notes: CANOCO version 3.1. Wageningen: Agricultural Mathematics Group. (UR).
The example in ?check
was made to suppress package startup messages from vegan.
This release fixed some non-canonical-form CRAN URLs.
This release was purely to avoid issues with CRAN as a new release of vegan had been released and the example reference material hadn't been updated to match.
A minor bug fix release to address a single problem.
shuffleSet()
wasn't returning a matrix if nset = 1
and allPerms
was invoked because of a low set of possible permutations. GitHub Issue #19This is small update to permute, focused mainly on ensuring the many combinations of restrictions on permutations allowed by the package work. An extensive test suite has been written which covers ~87% of the package's codebase at the time of release.
Permutation matrices produced by shuffleSet()
are now printed in a
more compact form.
Better heuristics in check()
allow for more reliable permutations
(i.e. fewer duplicate permutations) when the set is small. This has
increased the minperms
setting. Consequently we generate all possible
permutations up to ~500,000 more often as we now randomly sample from
the entirely generated set rather than randomly generate permutations.
This provides a small performance hit in some rare cases.
shuffleSet()
has a new argument quietly = FALSE
which is passed
on to check()
.
A number of bugs were fixed. See the Changelog and the Bug reports on github for details.
permControl()
and permuplot()
are defunct and have been removed
from the package.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
recommended for all users wishing to extract features of the permutation
design.
As a convenience for users, the \code{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 exported from the package namespace.