This function runs the epidemiological model using different parameter sets sampled from the MCMC posterior.
Usage
run_mcmc_simulations(
model,
param_inputs,
param_samples,
start_date,
end_date,
prewarm_years = 2,
days_per_year = 360
)Arguments
- model
A function representing the epidemiological model, typically compiled via
odin.dust.- param_inputs
A list of default model parameters to be updated with sampled values.
- param_samples
A matrix or data frame of parameter sets sampled from the MCMC posterior. Each row is a distinct sample.
- start_date
Character string or Date object indicating the simulation start date (e.g., "2014-01-01").
- end_date
Character string or Date object indicating the simulation end date (e.g., "2022-12-31").
- prewarm_years
Number of years for model prewarming to reach equilibrium before the start date (default: 2).
- days_per_year
Number of simulation time steps per year (default: 360).
Value
A list of data frames, each containing the simulated compartment outputs for one parameter set.
Examples
if (FALSE) { # \dontrun{
# Assume model is loaded via `load_model()` and priors are defined
model <- load_model("model_det_1")
# Get default parameter inputs and samples from MCMC
param_inputs <- return_default_param_inputs()
param_samples <- matrix(
c(0, 0, 2, 5, 3, 0, 1, 0.5, 0.8, 1), # Example parameter set (one row)
nrow = 1,
byrow = TRUE
)
colnames(param_samples) <- c("lag_R", "lag_T", "alpha", "sigma_LT", "sigma_RT",
"R_opt", "k1", "eff_SMC", "s", "b") # Adjust as needed
# Run simulation
simulations <- run_mcmc_simulations(
model,
param_inputs,
param_samples,
start_date = "2014-01-01",
end_date = "2022-12-31",
prewarm_years = 2,
days_per_year = 360
)
# View first simulation output
head(simulations[[1]])
} # }