Overview | Data | Setting up the inputs | Onset times | Generation time | Offspring distribution | Simulation controls | Modelling assumptions | Running the simulations | Post-processing | Visualization | References

Transmission chains likelihoods | Use case | What we have | What we assume | likelihood() | Joint and individual log-likelihoods | Observation probability | How likelihood() works | Transmission chain simulation | simulate_chains() | simulate_chain_stats() | S3 Methods | Summarising | Aggregating | Plotting | Some notes about interoperability between and objects | References

Reducing the strength of transmission | Population-wide control | Individual-level control. | Preventing superspreading events | Truncating the generation interval | References

Branching processes | Simulation | Summary statistics | Inference | Size and length distributions for some offspring distributions | Negative binomial and special cases | Size distributions | Length distributions | Gamma-Borel mixture | Numerical approximations of chain size and length distributions | References

Scope | Design decisions | Simulation functions | likelihood estimation | Naming and documentation style | Dependencies | Development journey

Bibliography