Introduction | Simple randomisation | The shuffle() and shuffleSet() functions | Generating restricted permutations | Generating sets of permutations with shuffleSet() | Defining permutation designs | Set the number of permutations | The levels of the permutation hierarchy | Permuting samples at the lowest level | Permuting samples at the Plot level | Specifying blocks; the top of the permute hierarchy | Examples | Using permute in R functions | Accessing and changing permutation designs | Computational details

Installing MRFtools | Setup | Discrete random walks | Creating $\mathbf{S}$ | Creating the data | Fitting the model | Visualising the fitted smooth | Phylogenetic smooth | References

Introduction | A brief overview of coenocliner | Future directions | Appendix

Plotting | Model diagnostics | Want to learn more? | References

Symmetric Co-CA

Introduction | Using analogue | Alternative methods for choosing k | Other features of analogue | Final remarks and future development plans