Create A Sample Line List — create_sample_linelist • SeverityEstimate

Generates a sample line list that can be used as an example data set for analysis with this package.

Usage

create_sample_linelist(
  strata,
  times,
  active_detection,
  passive_asymptomatic_detection,
  passive_symptomatic_detection,
  force_of_infection = NULL,
  force_of_infection_mean = -5,
  seed = 1L
)

Arguments

strata: A data.frame like object with the columns 'population', 'sir', and 'ifr'. Any additional columns are treated as descriptions for the strata. If strata only contains the columns 'population', 'sir', 'ifr' it's assumed that the sample data set contains no strata.
times: A vector denoting time steps for the sample data set. Must be provided in order.
active_detection: The probability of detecting a case through active detection.
passive_asymptomatic_detection: The probability of detecting a case presenting asymptomatically through passive surveillance.
passive_symptomatic_detection: The probability of detecting a case presenting symptomatically through passive surveillance.
force_of_infection: A matrix representing the force of infection where the row dimension corresponds to the times given and the column dimension corresponds to the strata given or NULL to generate a random one.
force_of_infection_mean: The mean of the initial force of infection to use. Only used when force_of_infection is NULL.
seed: The random seed to use for generating the data set.

Value

A data.frame with the columns 'patient', 'time', 'detection', 'outcome' along with the strata columns provided in strata.