permute is an R package for generating restricted permutations. Its original intention was for use with the vegan package to analyse multivariate models for ecological data.
permute is an R package that generates permutations from restricted designs, such as permutations within blocks. permute allows the following designs
- Randomisation (free permutation)
- Cyclic shifts for line transects and time series
- Toroidal shifts for spatial grids
These can be nested hierarchically with samples present at 3 levels:
- Block: these are never permuted, only samples within blocks are permuted.
- Plot: Plots lie within Blocks. Plots may further restrict permutation (i.e. the plots are not permuted) or they may be permuted using any of the above 3 permutation types.
- Within-plot: these are the samples at the lowest level, the individual rows of the data. These may be held fixed (within any Plots and/or Blocks) or be permuted following one of the three methods above)
This hierarchy allows for the testing of complex designs, including split-plot experimental designs.
