extract_inits: Generate initial conditions from a Stan fit

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

Generate initial conditions from a Stan fit

Description

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.

Usage

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.

Value

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

Author(s)

Sam Abbott

EpiNow2 documentation built on Sept. 26, 2023, 5:11 p.m.