Create a list of delay distributions to run the ringbp model

Usage

delay_opts(
  incubation_period,
  onset_to_isolation,
  latent_period = 0,
  onset_to_self_isolation = function(n) rep(Inf, n)
)

Arguments

incubation_period

a function: a random number generating function that samples from incubation period distribution, the function accepts a single integer argument specifying the number of times to sample the incubation period (i.e. length of the function output).

onset_to_isolation

a function: a random number generating function that accepts a single integer argument specifying the length of the function output.

latent_period

a non-negative numeric scalar: the minimum time between an individual being exposed and becoming infectious. It is a population-wide parameter, with no variability between individuals. It sets the minimum generation time in the model. Default is 0 (i.e. an individual becomes immediately infectious after being infected).

If latent_period is positive then generation times are sampled conditional on gt >= latent_period (i.e. left-truncated at latent_period). This may reduce the realised proportion of presymptomatic transmission, depending on the incubation_period distribution and presymptomatic_transmission (in event_prob_opts()).

onset_to_self_isolation

a function: a random number generating function that samples from the onset-to-self-isolation distribution, the function accepts a single integer argument specifying the length of the function output.

By default onset_to_self_isolation is a function that generates Inf (i.e. individuals never self-isolate). A different onset-to-self-isolation function only needs to be specified if a non-zero value is specified to symptomatic_self_isolate in event_prob_opts() (which by default is 0). If onset_to_self_isolation is specified but symptomatic_self_isolate is zero, a warning will be thrown and the onset_to_self_isolation will be ignored; if symptomatic_self_isolate is non-zero and onset_to_self_isolation is an Inf generating function, scenario_sim() will error.

Value

A list with class <ringbp_delay_opts>.

Examples

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)
)
#> $incubation_period
#> function (n) 
#> rweibull(n = n, shape = 2.32, scale = 6.49)
#> <environment: 0x558fe1e97ad0>
#> 
#> $onset_to_isolation
#> function (n) 
#> rweibull(n = n, shape = 1.65, scale = 4.28)
#> <environment: 0x558fe1e97ad0>
#> 
#> $latent_period
#> [1] 0
#> 
#> $onset_to_self_isolation
#> function (n) 
#> rep(Inf, n)
#> <environment: 0x558fe15e37e0>
#> 
#> attr(,"class")
#> [1] "ringbp_delay_opts"