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

scenario_sim()

Run a specified number of simulations with identical parameters

Model parameters and control options

delay_opts()

Create a list of delay distributions to run the ringbp model

event_prob_opts()

Create a list of event probabilities to run the ringbp model

intervention_opts()

Create a list of intervention settings to run the ringbp model

offspring_opts()

Create a list of offspring distributions to run the ringbp model

sim_opts()

Create a list of simulation control options for the ringbp model

Post-processing

detect_extinct()

Calculate whether outbreaks went extinct or not

extinct_prob()

Calculate proportion of runs that have controlled outbreak