extract_inits function

Generate initial conditions from a Stan fit

Extracts posterior samples to use to initialise a full model fit. This may be useful for certain data sets where the sampler gets stuck or cannot easily be initialised. In estimate_infections(), epinow() and regional_epinow() this option can be engaged by setting stan_opts(init_fit = <stanfit>).

This implementation is based on the approach taken in epidemia authored by James Scott.

extract_inits(fit, current_inits, exclude_list = NULL, samples = 50)

Arguments

• fit: A <stanfit> object.
• current_inits: A function that returns a list of initial conditions (such as create_initial_conditions()). Only used in exclude_list is specified.
• exclude_list: A character vector of parameters to not initialise from the fit object, defaulting to NULL.
• samples: Numeric, defaults to 50. Number of posterior samples.

Returns

A function that when called returns a set of initial conditions as a named list.