Calculate proportion of runs that have controlled outbreak — extinct_prob • ringbp

Calculate proportion of runs that have controlled outbreak

extinct_prob(outbreak_df_week = NULL, cap_cases = NULL, 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.

Value

a single numeric with the probability of extinction

Author

Joel Hellewell

Examples

res <- scenario_sim(
  n.sim = 10,
  num.initial.cases = 1,
  prop.asym = 0,
  prop.ascertain = 0.2,
  cap_cases = 4500,
  cap_max_days = 350,
  r0isolated = 0.5,
  r0community = 2.5,
  disp.com = 0.16,
  disp.iso = 1,
  delay_shape = 1.65,
  delay_scale = 4.28,
  k = 0,
  quarantine = FALSE
)
extinct_prob(res, cap_cases = 4500)
#> [1] 0.4