sd_prior_checks {readsdr}

Prior predictive checks

Description

Prior predictive checks

Usage

sd_prior_checks(
  filepath,
  meas_mdl,
  estimated_params,
  n_draws,
  start_time = NULL,
  stop_time = NULL,
  timestep = NULL,
  integ_method = "euler"
)

Arguments

filepath

A string that indicates a path to a file with extension .stmx or .xmile. Vensim files (.mdl) are not xmile files. They must be exported from Vensim with extension .xmile

meas_mdl

A list of strings. Each string corresponds to a sampling statement written in Stan language.

estimated_params

A list of lists. Each sublist describes each parameter that will be estimated in the inference stage. To construct this description, the user can avail of the function 'sd_prior'.

n_draws

An integer that indicates how many time-series will be returned.

start_time

A number indicating the time at which the simulation begins.

stop_time

A number indicating the time at which the simulation ends.

timestep

A number indicating the time interval for the simulation. Also known as dt.

integ_method

A string indicating the integration method. It can be either "euler" or "rk4"

Value

A list of two data frames.

Examples

  filepath <- system.file("models/", "SEIR.stmx", package = "readsdr")
  meas_mdl   <- list("y ~ neg_binomial_2(net_flow(C), phi)")
  estimated_params <- list(
    sd_prior("par_beta", "lognormal", c(0, 1)),
    sd_prior("par_rho", "beta", c(2, 2)),
    sd_prior("I0", "lognormal", c(0, 1), "init"))
  sd_prior_checks(filepath, meas_mdl, estimated_params, n_draws = 2,
   start_time = 0, stop_time = 5,
   integ_method = "rk4", timestep = 1/32)