Generate A Synthetic Cholera Outbreak Time Series — chlaa_generate_example_outbreak

Convenience wrapper around `chlaa_case_study_setup()` that returns only the synthetic observed case data frame.

Usage

chlaa_generate_example_outbreak_data(
  time = 0:915,
  start_date = as.Date("2022-07-01"),
  trigger_date = as.Date("2022-10-25"),
  declaration_date = as.Date("2022-12-14"),
  late_vax_start_date = as.Date("2023-01-20"),
  seed = 42,
  n_particles = 20,
  dt = 1,
  obs_size = 18,
  vax_total_doses = 280000,
  campaign_days = 150
)

Arguments

time: Numeric vector of simulation times (days).
start_date: Start date corresponding to `time = 0`.
trigger_date: Anticipatory action trigger date.
declaration_date: Outbreak declaration date.
late_vax_start_date: Planned campaign start date for scenarios 1 and 2.
seed: Integer random seed.
n_particles: Number of particles used to generate latent incidence.
dt: Model time step.
obs_size: Observation over-dispersion (Negative Binomial size).
vax_total_doses: Total vaccine doses used in scenario definitions.
campaign_days: Vaccination campaign duration (days).

Value

A data.frame with columns `date`, `time`, `cases`, `mu_cases`, `inc_symptoms_truth`, and `inc_infections_truth`. The generating parameter set is attached as `attr(x, "truth_parameters")`.