extract_inits

A function that returns a list of initial conditions (such as
<code>create_initial_conditions()</code>). Only used in <code>exclude_list</code> is specified.

current_inits

A character vector of parameters to not initialise from the fit
object, defaulting to <code>NULL</code>.

exclude_list

Numeric, defaults to 50. Number of posterior samples.

samples

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 <code>estimate_infections()</code>, <code>epinow()</code> and <code>regional_epinow()</code> this option can be
engaged by setting <code>stan_opts(init_fit = &lt;stanfit&gt;)</code>.
This implementation is based on the approach taken in <a href="https://github.com/ImperialCollegeLondon/epidemia/">epidemia</a>
authored by James Scott.

Estimates the time-varying reproduction number, rate of spread,
and doubling time using a range of open-source tools (Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>),
and current best practices (Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>).
It aims to help users avoid some of the limitations of naive implementations in a framework
that is informed by community feedback and is under active development.

Sam Abbott 

EpiNow2

Estimate Real-Time Case Counts and Time-Varying Epidemiological
Parameters

Sam Abbott

Joel Hellewell

Katharine Sherratt

Katelyn Gostic

Joe Hickson

Hamada S. Badr

Michael DeWitt

Robin Thompson

Sophie Meakin

James Munday

Nikos Bosse

Paul Mee

Peter Ellis

EpiForecasts 

Sebastian Funk

extract_inits function

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 <code>estimate_infections()</code>, <code>epinow()</code> and <code>regional_epinow()</code> this option can be
engaged by setting <code>stan_opts(init_fit = &lt;stanfit&gt;)</code>.
This implementation is based on the approach taken in <a href='https://github.com/ImperialCollegeLondon/epidemia/'>epidemia</a>
authored by James Scott.

Generate initial conditions from a Stan fit — extract_inits

Generate initial conditions from a Stan fit

extract_inits: Generate initial conditions from a Stan fit

Description

Usage

Arguments

Value