format_simulation_output: Format Simulation Output from Stan
In EpiNow2: Estimate and Forecast Real-Time Infection Dynamics

format_simulation_output

R Documentation

Format Simulation Output from Stan

Description

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.