dot-cross_check_sim_input: Cross check the onset-to-hospitalisation or -death arguments...

In simulist: Simulate Disease Outbreak Line List and Contacts Data

Cross check the onset-to-hospitalisation or -death arguments are compatible with hospitalisation and death risks

Description

There are two types of cross-checking:

1. If the onset-to-event distribution is specified but the corresponding risk is not specified (i.e. NULL) the function will error (stop()).

2. If the onset-to-event distribution is not specified (i.e. NULL) but the corresponding risk is specified the function will throw a warning (warning()).

The difference in condition handling is because in the case that the onset-to-event is NULL the simulation can safely ignore the corresponding risk, while throwing a warning, as there are no events. In other words, if the onset-to-hospitalisation is not specified, no infected individuals will go to hospital and the date_admission column in the line list will all be NAs. However, if the onset-to-event is specified and the corresponding risk is NULL then the proportion of individuals infected that are hospitalised or die cannot be calculated and therefore the simulation cannot run. It is in this latter case that the cross-checking throws an error.

Usage

.cross_check_sim_input(
  onset_to_hosp,
  onset_to_death,
  hosp_risk,
  hosp_death_risk,
  non_hosp_death_risk
)

Arguments

onset_to_hosp	A function or an ⁠<epiparameter>⁠ object for the onset-to-hospitalisation delay distribution. onset_to_hosp can also be set to NULL to not simulate hospitalisation (admission) dates. The function can be defined or anonymous. The function must return a vector of numerics for the length of the onset-to-hospitalisation delay. The function must have a single argument. An ⁠<epiparameter>⁠ can be provided. This will be converted into a random number generator internally. The default is an anonymous function with a lognormal distribution random number generator (rlnorm()) with meanlog = 1.5 and sdlog = 0.5. If onset_to_hosp is set to NULL then hosp_risk and hosp_death_risk will be automatically set to NULL if not manually specified.
onset_to_death	A function or an ⁠<epiparameter>⁠ object for the onset-to-death delay distribution. onset_to_death can also be set to NULL to not simulate dates for individuals that died. The function can be defined or anonymous. The function must return a vector of numerics for the length of the onset-to-death delay. The function must have a single argument. An ⁠<epiparameter>⁠ can be provided. This will be converted into a random number generator internally. The default is an anonymous function with a lognormal distribution random number generator (rlnorm()) with meanlog = 2.5 and sdlog = 0.5. If onset_to_death is set to NULL then non_hosp_death_risk and hosp_death_risk will be automatically set to NULL if not manually specified. For hospitalised cases, the function ensures the onset-to-death time is greater than the onset-to-hospitalisation time. After many (1000) attempts, if an onset-to-death time (from onset_to_death) cannot be sampled that is greater than a onset-to-hospitalisation time (from onset_to_hosp) then the function will error. Due to this conditional sampling, the onset-to-death times in the line list may not resemble the distributional form input into the function.
hosp_risk	Either a single numeric for the hospitalisation risk of everyone in the population, or a ⁠<data.frame>⁠ with age specific hospitalisation risks. Default is 20% hospitalisation (0.2) for the entire population. If the onset_to_hosp argument is set to NULL this argument will automatically be set to NULL if not specified or can be manually set to NULL. See details and examples for more information.
hosp_death_risk	Either a single numeric for the death risk for hospitalised individuals across the population, or a ⁠<data.frame>⁠ with age specific hospitalised death risks Default is 50% death risk in hospitals (0.5) for the entire population. If the onset_to_death argument is set to NULL this argument will automatically be set to NULL if not specified or can be manually set to NULL. See details and examples for more information. The hosp_death_risk can vary through time if specified in the time_varying_death_risk element of config, see vignette("time-varying-cfr", package = "simulist") for more information.
non_hosp_death_risk	Either a single numeric for the death risk for outside of hospitals across the population, or a ⁠<data.frame>⁠ with age specific death risks outside of hospitals. Default is 5% death risk outside of hospitals (0.05) for the entire population. If the onset_to_death argument is set to NULL this argument will automatically be set to NULL if not specified or can be manually set to NULL. See details and examples for more information. The non_hosp_death_risk can vary through time if specified in the time_varying_death_risk element of config, see vignette("time-varying-cfr", package = "simulist") for more information.

Value

Invisibly return the onset_to_hosp argument. The function is called for its side-effects, which will error or warn if the input is invalid.

simulist documentation built on April 12, 2025, 1:34 a.m.