Calculate whether outbreaks went extinct or not
detect_extinct(outbreak_df_week = NULL, cap_cases = NULL, week_range = 12:16)
a data.table
: weekly cases produced by the
outbreak model
a positive integer
scalar: number of cumulative cases at
which the branching process (simulation) was terminated
a positive integer
vector: giving the (zero indexed)
week range to test for whether an extinction occurred.
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.
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
)
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 0
#> 6: 6 1
#> 7: 7 1
#> 8: 8 1
#> 9: 9 1
#> 10: 10 1