New version of permute on CRAN
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After some time brewing on my machines, I’m happy to have released a new version of my permute package for R. This release took quite a while to polish and get right as there was a lot of backandforth between vegan and permute as I tried to get the latter working nicely for both useRs and developers, whilst Jari worked on using the new permute API within vegan itself. All these changes were prompted by Cajo ter Braak taking me to task (nicely of course) over the use in previous versions of permute of the term “blocks” for what were not true blocking factors. Cajo challenged me to add true blocking factors (these restrict permutations within their levels and are never permuted, unlike plots), and the new version of permute is the result of my attempting to meet that challenge.
The changes to the design of permutations meant that I had to break code that used previous versions of permute and wasn’t something I did lightly. But it did need to be done. I took that opportunity to make the package easier to use too and decided I didn’t like typing permControl()
each time I wanted to define a permutation design, resulting in the new how()
.
Version 0.80 represents a major update to permute, the salient details of which are given below, cropped from the new NEWS.Rd
file. You can get the new version of permute now from CRAN.
General
Version 0.80 represents a major update of permute, with some backwardsincompatible changes to the main functions. The main addition is the availability of blocklevel restrictions on the permutations, which are required for whole and splitplot designs.
New Features

how()
, a new function to create permutation designs. This replaces the deprecated functionpermControl()
. 
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, plotlevel strata are now specified via
Plots()
instead of via the oldstrata
argument ofhow()
. Blocks are specified via a new argumentblocks
, 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 namesgetFoo()
, whereFoo
is a component of the design. Replacement functions have namessetFoo
. 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
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 toplevel and not within functions, where the newsetFoo
replacement functions should be used. 
shuffleSet()
is enhanced in this version. Firstly, the function now returns a classed object which has aprint()
method to allow for compact printing of the design elements used to generate the set of permutations. Second,shuffleSet()
will samplenset
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 nonunique 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.
Deprecated

permControl()
is deprecated in favour ofhow()
. 
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.
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