tests/testthat/testdata/README.md

In simulist: Simulate Disease Outbreak Line List and Contacts Data

Instructions for updating test data

The {simulist} R package contains test data files in order to test internal functions. The intermediate output required to test the internals of the simulation functions cannot be produced by running a function (hence intermediate). The test data files contain in progress mock line lists at different stages of the simulation. Each test data file contains a single R object (stored as .rds), and is named according to where in the simulation the data object is saved from. The names are:

• "pre_date_contact"
• "pre_hospitalisation"
• "pre_outcome"
• "pre_names"
• "pre_ct"

Each of the scenarios are created by taking a snapshot (i.e copy) of the line list <data.frame> are each stage of the simulation (sim_linelist()) after setting the seed to 1 (set.seed(1)). The scenarios are before each function call, for example, "pre_date_contact" is the state of the line list prior to calling .add_date_contact(), and "pre_names" is the state of the line list prior to calling .add_names().

Breakpoints (browser()) need to be placed before each function call to stop the simulation and snapshot the intermediate <data.frame>.

The script to reproduce the data is:

# load data required to simulate line list
contact_distribution <- function(x) stats::dpois(x = x, lambda = 2)
infectious_period <- function(x) stats::rgamma(n = x, shape = 1, scale = 1)
onset_to_hosp <- function(x) {
  stats::rlnorm(n = x, meanlog = 0.947, sdlog = 1.628)
}
onset_to_death <- function(x) {
  stats::rlnorm(n = x, meanlog = 2.863, sdlog = 0.534)
}

set.seed(1)

linelist <- sim_linelist(
  contact_distribution = contact_distribution,
  infectious_period = infectious_period,
  prob_infection = 0.5,
  onset_to_hosp = onset_to_hosp,
  onset_to_death = onset_to_death,
  hosp_risk = 0.5
)

Files can be saved using saveRDS(). Ensure the working directory is at the root of the R package (working directory can be queried with getwd() and set with setwd()). For example:

saveRDS(pre_ct, file = "tests/testthat/testdata/pre_ct.rds")

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