Set up initial cases for branching process

Usage

outbreak_setup(initial_cases, delays, event_probs)

Arguments

initial_cases: a non-negative integer scalar: number of initial or starting cases which are all assumed to be missed.
delays: a list with class <ringbp_delay_opts>: the delay distribution functions for the ringbp model, returned by delay_opts(). Contains two elements: incubation_period and onset_to_isolation
event_probs: a list with class <ringbp_event_prob_opts>: the event probabilities for the ringbp model, returned by event_prob_opts(). Contains three elements: asymptomatic, presymptomatic_transmission and symptomatic_ascertained

Value

data.table of cases in outbreak so far. data.table columns are:

$exposure: numeric
$asymptomatic: logical
$caseid: integer
$infector: numeric
$missed: logical
$onset: numeric
$new_cases: logical
$isolated_time: numeric
$isolated: logical

Examples

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 = 0.15,
  symptomatic_ascertained = 0
)

# generate initial cases
case_data <- outbreak_setup(
  initial_cases = 5,
  delays = delays,
  event_probs = event_probs
)
case_data
#> Index: <asymptomatic>
#>    exposure asymptomatic caseid infector isolated missed     onset new_cases
#>       <num>       <lgcl>  <int>    <num>   <lgcl> <lgcl>     <num>    <lgcl>
#> 1:        0        FALSE      1        0    FALSE   TRUE  5.327302        NA
#> 2:        0        FALSE      2        0    FALSE   TRUE 10.248073        NA
#> 3:        0        FALSE      3        0    FALSE   TRUE  9.878893        NA
#> 4:        0        FALSE      4        0    FALSE   TRUE  1.781222        NA
#> 5:        0        FALSE      5        0    FALSE   TRUE  5.395534        NA
#>    isolated_time
#>            <num>
#> 1:      7.479154
#> 2:     11.923502
#> 3:     15.219283
#> 4:      4.397555
#> 5:     18.466834