View source: R/create_config.R
create_config | R Documentation |
sim_linelist()
Create a list of configuration settings for some details of sim_linelist()
create_config(...)
... |
< Accepted arguments and their defaults are:
|
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)
.
A list of settings for sim_linelist()
# example with default configuration
create_config()
# example with customised Ct distribution
create_config(
ct_distribution = function(x) rlnorm(n = x, meanlog = 2, sdlog = 1)
)
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