# permute v0.9-5

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## Functions for Generating Restricted Permutations of Data

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.

## Readme

## Restricted permutations with R

#### Released version

#### Build status

## What is permute?

**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**:

- Free permutation of objects
- Time series or line transect designs, where the temporal or spatial ordering is preserved.
- Spatial grid designs, where the spatial ordering is preserved in both coordinate directions
- Permutation of plots or groups of samples.
- Blocking factors which restrict permutations to within blocks. The preceding designs can be nested within blocks, allowing analysis of hierachical designs (e.g. split plot designs)

### References

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).

## Functions in permute

Name | Description | |

check | Utility functions for permutation schemes | |

shuffle | Unrestricted and restricted permutations | |

shuffleSet | Generate a set of permutations from the specified design. | |

allPerms | Complete enumeration of all possible permutations | |

nobs-methods | Number of observations in a given object | |

numPerms | Number of possible permutations for a given object | |

allUtils | Utility functions for complete enumeration of all possible permutations | |

set-methods | Replacement functions to set components of a permutation design | |

shuffle-utils | Utility functions for unrestricted and restricted permutations | |

how | How to define a permutation design? | |

jackal | Mandible lengths of male and female golden jackals | |

get-methods | Extractor functions to access components of a permutation design | |

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## Vignettes of permute

Name | ||

permutations.Rnw | ||

permute.bib | ||

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## Last month downloads

## Details

Date | 2019-03-10 |

License | GPL-2 |

ByteCompile | true |

URL | https://github.com/gavinsimpson/permute |

BugReports | https://github.com/gavinsimpson/permute/issues |

Copyright | see file COPYRIGHTS |

NeedsCompilation | no |

Packaged | 2019-03-10 22:40:39 UTC; gavin |

Repository | CRAN |

Date/Publication | 2019-03-12 09:40:08 UTC |

suggests | parallel , testthat (>= 0.5) , vegan (>= 2.0-0) |

depends | R (>= 2.14.0) |

imports | stats |

Contributors | Jari Oksanen, R Core team, Douglas M. Bates |

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