Functions that allow the use of a fitted reporting delay function
get_linelist()
Get the latest compiled linelist
get_rep_sample_fun()
Get a sampling function for reporting delays
fitted_delay_sample_func
Fitted delay sampling function
Functions that parameterise distributions based on a mean and standard deviation
rgamma_with_mean_sd()
Mean and standard deviation parameterised gamma sampling function
rweibull_with_mean_sd()
Mean and standard deviation parameterised Weibull sampling function
Functions used to run the branching process
run_sim()
Negative binomial branching process model
Functions that facilitate running the scenario analysis
run_scenario_grid()
Run the scenario analysis grid.
scenario_analysis()
Run a scenario analyis
Functions that allow model simulations to be conditioned on observed data.
condition_and_report_on_cases()
Condition on cases and return accepted sample size by scenario
condition_on_known()
Condition on known cases
proportion_allowed_by_condition()
Proportion of samples per scenario allowed by condition
restrict_by_condition()
Restrict scenarios based on allowed scenarios
Functions that facilitate evaluating the output of the analysis.
summarise_end_r0()
Summarise R0 estimates across samples
make_duration_size_table()
Make seeding event duration vs event size table
plot_R0_density()
Plot density plots of the basic reproduction number
plot_per_accepted_tile()
Plot a heat map of accepted samples by scenario