Simulate a line list for testing and examples

Draws onset dates over a window, marks each case fatal with probability cfr, and gives fatal cases an onset-to-death delay drawn from delay. Pass a recovery delay to also simulate onset-to-recovery times for the non-fatal cases and add a recovery_date column. Delays are distspec distributions with fixed parameters, matching what fit_cfr() takes; you can specify them by mean and sd (e.g. LogNormal(mean = 12.75, sd = 7)). Returns a line list with onset_date, death_date (NA for non-fatal cases) and, when recovery is given, recovery_date (NA for fatal cases). The full, untruncated outcomes are simulated; pass the result to prepare_cfr_data() with an obs_time to induce the real-time truncation.

Usage

simulate_linelist(
  n = 200,
  cfr = 0.5,
  delay,
  recovery = NULL,
  onset_start = as.Date("2026-01-01"),
  onset_days = 60
)

Arguments

n

Number of cases.

cfr

True case fatality ratio.

delay

Onset-to-death delay: a distspec distribution (distspec::LogNormal() or distspec::Gamma()) with fixed parameters.

recovery

Optional onset-to-recovery delay (same form as delay); when given, non-fatal cases get a recovery_date.

onset_start

First possible onset date.

onset_days

Width of the onset window (days); onsets are uniform over it.

Value

A data frame with onset_date, death_date and, if recovery is given, recovery_date.

Details

Data are generated to match the model's daily interval-censoring: each case's true onset falls uniformly within its recorded day, and the event day is the floor of the continuous onset-plus-delay time. So the recorded day-level delays are exactly a doubly-interval-censored draw, which makes the simulator suitable for checking calibration, not only rough recovery.

Examples

simulate_linelist(
  n = 5, cfr = 0.6,
  delay = LogNormal(mean = 12.75, sd = 7)
)
#>   onset_date death_date
#> 1 2026-01-02       <NA>
#> 2 2026-01-09 2026-01-23
#> 3 2026-02-26 2026-03-03
#> 4 2026-02-12 2026-03-01
#> 5 2026-02-02 2026-02-14