Calculate proportion of runs that have controlled outbreak

extinct_prob(outbreak_df_week, cap_cases, week_range = 12:16)

Arguments

outbreak_df_week: a data.table: weekly cases produced by the outbreak model
cap_cases: a positive integer scalar: number of cumulative cases at which the branching process (simulation) was terminated
week_range: a positive integer vector: giving the (zero indexed) week range to test for whether an extinction occurred. Default is 12:16.

Value

a single numeric with the probability of extinction

Details

The cap_cases argument should be equal to the value supplied to outbreak_model() (possibly passed from scenario_sim()).

Author

Joel Hellewell

Examples

res <- scenario_sim(
  n = 10,
  initial_cases = 1,
  offspring = offspring_opts(
    community = \(n) rnbinom(n = n, mu = 2.5, size = 0.16),
    isolated = \(n) rnbinom(n = n, mu = 0.5, size = 1)
  ),
  delays = delay_opts(
    incubation_period = \(n) rweibull(n = n, shape = 2.32, scale = 6.49),
    onset_to_isolation = \(n) rweibull(n = n, shape = 1.65, scale = 4.28)
  ),
  event_probs = event_prob_opts(
    asymptomatic = 0,
    presymptomatic_transmission = 0.5,
    symptomatic_ascertained = 0.2
  ),
  interventions = intervention_opts(quarantine = FALSE),
  sim = sim_opts(cap_max_days = 350, cap_cases = 4500)
)
extinct_prob(res, cap_cases = 4500)
#> [1] 0.6