simulist (version 0.7.0)

create_config: Create a list of configuration settings for some details of sim_linelist()

Description

Create a list of configuration settings for some details of sim_linelist()

Usage

create_config(...)

Value

A list of settings for sim_linelist().

Arguments

...

<dynamic-dots> Named elements to replace default settings. Only if names match exactly are elements replaced, otherwise the function errors.

Accepted arguments and their defaults are:

last_contact_distribution

A function to generate the time for last contact. Default parameterisation is a Poisson distribution with a \(\lambda\) of 3.

first_contact_distribution

A function to generate the time for the first contact. Default parameterisation is a Poisson distribution with a \(\lambda\) of 3.

ct_distribution

A function to generate Ct values for each confirmed case. Default parameterisation is a Normal distribution with a mean (\(\mu\)) of 25 and a standard deviation (\(\sigma\)) of 2.

network

A character string, either "adjusted" (default) or "unadjusted".

time_varying_death_risk

By default is NULL, but can also accept a function with two arguments, risk and time, to apply a time varying death risk of hospitalised and non-hospitalised cases in the outbreak simulation. See vignette("time-varying-cfr", package = "simulist").

prob_male

By default is 0.5, so there is a equal probability of each case or contact being male or female. The value must be non-negative and less than or equal to 1. Smaller values will result in a higher probability of female contacts and cases (1 - prob_male).

Details

The config argument in sim_linelist() controls the small details around time windows around infections (time of first contact and last contact with infector), and the distribution of the Cycle threshold (Ct) value from a Real-time PCR or quantitative PCR (qPCR) for confirmed cases, the network effect in the simulation, and if there is a time-varying death risk, as well as the probability of a case or contact being male/female.

These parameters do not warrant their own arguments in sim_linelist() as they rarely need to be changed from their default setting. Therefore it is not worth increasing the number of sim_linelist() arguments to accommodate these and the config argument keeps the function signature simpler and more readable.

The last_contact_distribution and first_contact_distribution can accept any function that generates positive integers (e.g. discrete probability distribution, rpois() or rgeom()). The ct_distribution can accept any function that generates real numbers (e.g. continuous or discrete probability distribution, rnorm(), rlnorm()).

The network option controls whether to sample contacts from a adjusted or unadjusted contact distribution. Adjusted (default) sampling uses \(q(n) \sim (n + 1)p(n + 1)\) where \(p(n)\) is the probability density function of a distribution, e.g., Poisson or Negative binomial. Unadjusted (network = "unadjusted") instead samples contacts directly from a probability distribution \(p(n)\).

Examples

# example with default configuration
create_config()

# example with customised Ct distribution
create_config(
  ct_distribution = function(n) rlnorm(n = n, meanlog = 2, sdlog = 1)
)