Reference

Model
outbreak_model()	Run a single instance of the branching process model
outbreak_setup()	Set up initial cases for branching process
outbreak_step()	Move forward one generation in the branching process
Helper functions
Probability distribution manipulation
incubation_to_generation_time()	Samples the generation time for given incubation period samples
Loop wrappers for scenario modelling
parameter_sweep()	Sweep across parameters
scenario_sim()	Run a specified number of simulations with identical parameters
Post-processing
detect_extinct()	Calculate whether outbreaks went extinct or not
extinct_prob()	Calculate proportion of runs that have controlled outbreak