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Restricted permutations with R

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).

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install.packages('permute')

Monthly Downloads

74,751

Version

0.9-7

License

GPL-2

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Last Published

January 27th, 2022

Functions in permute (0.9-7)

jackal

Mandible lengths of male and female golden jackals
numPerms

Number of possible permutations for a given object
allUtils

Utility functions for complete enumeration of all possible permutations
nobs-methods

Number of observations in a given object
allPerms

Complete enumeration of all possible permutations
how

How to define a permutation design?
shuffle-utils

Utility functions for unrestricted and restricted permutations
check

Utility functions for permutation schemes
set-methods

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

Extractor functions to access components of a permutation design
shuffle

Unrestricted and restricted permutations
shuffleSet

Generate a set of permutations from the specified design.