readsdr (version 0.3.0)

sd_posterior_fun: Posterior function

Description

Posterior function

Usage

sd_posterior_fun(
  filepath,
  meas_data_mdl,
  estimated_params,
  start_time = NULL,
  stop_time = NULL,
  timestep = NULL,
  integ_method = "euler",
  const_list = NULL
)

Value

A function

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_data_mdl

A list of lists. Each second-level list corresponds to a sampling statement along with its measurements. Here is an example:
list(formula = "y ~ neg_binomial_2(net_flow(C), phi)", measurements = 1:10))

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`.

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"

const_list

A list in which each element's name is the name of the constant to override and the element's value correspond to the new value.

Examples

filepath         <- system.file("models/", "SEIR.stmx", package = "readsdr")
meas_data_mdl <- list(list(formula      = "y ~ neg_binomial_2(net_flow(C), phi)",
                            measurements = 1:10))
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"))
fun <- sd_posterior_fun(filepath, meas_data_mdl, estimated_params)