create_stan_args: Create a List of Stan Arguments

In epiforecasts/EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

Create a List of Stan Arguments

Description

Generates a list of arguments as required by the stan sampling functions by combining the required options with data, and type of initialisation. Initialisation defaults to random but it is expected that create_initial_conditions() will be used.

Usage

create_stan_args(
  stan = stan_opts(),
  data = NULL,
  init = "random",
  model = "estimate_infections",
  fixed_param = FALSE,
  verbose = FALSE
)

Arguments

stan	A list of stan options as generated by stan_opts(). Defaults to stan_opts(). Can be used to override data, init, and verbose settings if desired.
data	A list of stan data as created by create_stan_data()
init	Initial conditions passed to {rstan}. Defaults to "random" (initial values randomly drawn between -2 and 2) but can also be a function (as supplied by create_initial_conditions()).
model	Character, name of the model for which arguments are to be created.
fixed_param	Logical, defaults to FALSE. Should arguments be created to sample from fixed parameters (used by simulation functions).
verbose	Logical, defaults to FALSE. Should verbose progress messages be returned.

Value

A list of stan arguments

Examples

# default settings
create_stan_args()

# increasing warmup
create_stan_args(stan = stan_opts(warmup = 1000))

epiforecasts/EpiNow2 documentation built on April 27, 2024, 9:15 p.m.