Build A Shared Paper-Aligned Cholera Case Study Setup

Constructs a reusable synthetic case study aligned to the outbreak response framing in: https://pmc.ncbi.nlm.nih.gov/articles/PMC12477517/

Usage

chlaa_case_study_setup(
  time = 0:730,
  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 named list with `data`, `pars`, `scenarios`, `dates`, and `time`. `data` includes columns `date`, `time`, `cases`, `mu_cases`, `inc_symptoms_truth`, and `inc_infections_truth`.

Details

The returned object includes: - one synthetic observed case time series (generated from scenario 1 baseline), - calibrated baseline parameters, - scenario definitions used throughout the vignettes.