Calculate whether outbreaks went extinct or not

detect_extinct(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 data.table, with two columns sim and extinct, for a binary classification of whether the outbreak went extinct in each simulation replicate. 1 is an outbreak that went extinct, 0 if not.

Details

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

Author

Joel Hellewell

Examples

res <- scenario_sim(
  n = 10,
  initial_cases = 1,
  prop_asymptomatic = 0,
  prop_ascertain = 0.2,
  cap_cases = 4500,
  cap_max_days = 350,
  r0_isolated = 0.5,
  r0_community = 2.5,
  disp_community = 0.16,
  disp_isolated = 1,
  onset_to_isolation = \(x) rweibull(n = x, shape = 1.65, scale = 4.28),
  incubation_period = \(x) rweibull(n = x, shape = 2.322737, scale = 6.492272),
  prop_presymptomatic = 0.5,
  quarantine = FALSE
)
detect_extinct(outbreak_df_week = res, cap_cases = 4500)
#>       sim extinct
#>     <int>   <num>
#>  1:     1       1
#>  2:     2       1
#>  3:     3       1
#>  4:     4       1
#>  5:     5       1
#>  6:     6       1
#>  7:     7       1
#>  8:     8       1
#>  9:     9       1
#> 10:    10       0