Fit the reporting delay function

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

Sample from the serial interval distribution

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

Run the branching process

Functions used to run the branching process

run_sim()

Negative binomial branching process model

Run scenario analysis

Functions that facilitate running the scenario analysis

run_scenario_grid()

Run the scenario analysis grid.

scenario_analysis()

Run a scenario analyis

Condition on data

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

Evaluate output

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