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Restricted permutations with R

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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)


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).