[R-sig-eco] [pkg] *permute* an R package for restricted permutations

[Sarah Goslee]

That sounds very useful (and means I can cross it off my own list). Thank
you for your hard work.

Sarah

On Thu, Sep 8, 2011 at 4:56 AM, Gavin Simpson <gavin.simpson at ucl.ac.uk> wrote:
> Dear List,
>
> Yesterday, I rolled up the first public release of the *permute* package
> and submitted it to CRAN. This represents the first beta release of
> *permute* and presages significant changes to the way permutation tests
> are performed, and to the sorts of permutation available, in *vegan*.
>
> *permute* allows the following permutation designs:
>
>      * free permutation (randomisation)
>      * permutation of spatial transect or time series data via cyclic
>        wrapping
>      * permutation of spatial grids via toroidal wrapping
>
> Each of these can be used at one or both of the block level and the
> within-block level. Blocks of samples are defined by the argument
> `strata` as has been used in *vegan* for many years. As such, *permute*
> allows for testing of split-plot designs. For spatial data (transect or
> grid), the cyclic or toroidal wrapping can be performed forwards or
> backwards in either spatial dimension, and the same permutation can be
> used for the samples in each block (for example, in the case of time
> series data where the samples in each block have been "exposed" to the
> same "time process").
>
> An major aim in writing *permute* has been to provide functionality
> found in the widely-used, commercial application Canoco.
>
> The main functions in *permute* are the `shuffle()` and `shuffleSet()`
> functions which generate a single permutation or a set of many
> permutations for a stated design. Permutation designs are defined using
> function `permControl()`. Function `allPerms()` can be used to generate
> the entire set of permutations for a given design, which is useful if
> there are only a small number of permutations possible for the
> combination of permutation design and number of observations and/or
> complete enumeration (an exact test) is required.
>
> With the release of *permute*, the older functions in *vegan* that
> implemented a previous version of these restricted permutations have
> been made defunct. Old code that utilised these functions should be
> ported to use the new functions in *permute*; help is available upon
> request. These changes are in *vegan* from version 2.0-0, which has also
> been released to CRAN.
>
> The main reason for splitting the permutation code out from *vegan* was
> that by doing so we might make this code available to other package
> authors without having to depend on the entirety of *vegan*.
>
> A nascent Vignette is provided with the package which aims to document
> the new functions and will, by version 0.8, include a section on using
> *permute* within functions for package authors wishing to make use of
> the functionality in *permute*.
>
> If you have questions about or comments on the package, contact me or
> post a message in the Forums section of the R-forge website[1] for the
> *vegan* stable of packages.
>
> Gavin Simpson
>
> [1] https://r-forge.r-project.org/forum/?group_id=68
> --
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>  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
>  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
>  Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
>  Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
>  UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
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>


-- 
Sarah Goslee
http://www.functionaldiversity.org