Overview | Simulated data | Step 1 — Compute fractional occupancy | Step 2 — Test each state | Step 3 — Dwell time pipeline | Step 4 — Markov transition pipeline | Using ptestR for permutation tests | Notes on vars and covariate carriage | Further reading

What is a Markov transition? | Simulated data | Computing transitions | The transition matrix | Removing self-transitions | The tag convention | vars vs groupBy | Further reading

What is a brain state? | Input format | Simulated data | Fractional occupancy with nest_fo() | Dwell time with nest_dwell() | Markov transitions with clusters_markov() | Output structure at a glance | Further reading

The real use case | Simulated dataset | Running across features with grouped_perm_glmm() | Filtering to a term of interest | FDR correction | Handling p.perm = 0 | Plotting the results | Using grouped_perm_glm() instead | Tips for large-scale analyses | Further reading

Why permutation tests? | The three functions | A simple example | Interpreting p.perm | The family argument | Binomial logistic regression | Reproducibility | Multiple comparisons | Further reading

Why lmer doesn't give p-values | When to use grouped_perm_glmm() | A worked example | Comparing to lme4 output directly | Random effects structure | Random slopes | Convergence warnings | Computational cost | Further reading