## 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).