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

Source: R/create_config.R
create_config.Rd

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

Usage

create_config(...)

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").

Value

A list of settings for sim_linelist()

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.

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()
#> $last_contact_distribution
#> function (x) 
#> stats::rpois(n = x, lambda = 3)
#> <bytecode: 0x56382fc27538>
#> <environment: 0x56382fc26d90>
#> 
#> $first_contact_distribution
#> function (x) 
#> stats::rpois(n = x, lambda = 3)
#> <bytecode: 0x56382fc27538>
#> <environment: 0x56382fc26d90>
#> 
#> $ct_distribution
#> function (x) 
#> stats::rnorm(n = x, mean = 25, sd = 2)
#> <bytecode: 0x56382fc272d0>
#> <environment: 0x56382fc26d90>
#> 
#> $network
#> [1] "adjusted"
#> 
#> $time_varying_death_risk
#> NULL
#> 

# example with customised Ct distribution
create_config(
  ct_distribution = function(x) rlnorm(n = x, meanlog = 2, sdlog = 1)
)
#> $last_contact_distribution
#> function (x) 
#> stats::rpois(n = x, lambda = 3)
#> <bytecode: 0x56382fc27538>
#> <environment: 0x56382ef3aa40>
#> 
#> $first_contact_distribution
#> function (x) 
#> stats::rpois(n = x, lambda = 3)
#> <bytecode: 0x56382fc27538>
#> <environment: 0x56382ef3aa40>
#> 
#> $ct_distribution
#> function (x) 
#> rlnorm(n = x, meanlog = 2, sdlog = 1)
#> <environment: 0x563830b9bdc0>
#> 
#> $network
#> [1] "adjusted"
#> 
#> $time_varying_death_risk
#> NULL
#>