Format Simulation Output from Stan

Formats simulation output from Stan models into structured data.tables with dates. This is an internal function used by simulate_infections() and forecast_infections() to process simulation results.

This differs from get_samples() in that it's designed for simulation outputs which have different array structures (especially with drop_length_1 = TRUE) and need different date ranges for different parameters.

Usage

format_simulation_output(
  stan_fit,
  data,
  reported_dates,
  imputed_dates,
  reported_inf_dates,
  drop_length_1 = FALSE,
  merge = FALSE
)

Arguments

stan_fit

A <stanfit> or <CmdStanMCMC> object as returned by fit_model().

data

A list of the data supplied to the simulation.

reported_dates

A vector of dates to report estimates for.

imputed_dates

A vector of dates to report imputed reports for.

reported_inf_dates

A vector of dates to report infection estimates for.

drop_length_1

Logical; drop dimensions of length 1 in arrays extracted from the stan fit. Used in simulations where there's only 1 realization.

merge

if TRUE, merge samples into a single data.table using rbindlist. If FALSE returns a list of samples by parameter.

Value

A list of <data.frame>'s each containing the simulated trajectories of each parameter, or a single merged data.table if merge = TRUE.