extract_inits

<a href="https://lifecycle.r-lib.org/articles/stages.html#experimental"><img src="figures/lifecycle-experimental.svg?package=EpiNow2&version=1.6.1" alt="[Experimental]"></a>
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 actively supported.

Sebastian Funk

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

James M. Azam

Robin Thompson

Sophie Meakin

James Munday

Nikos Bosse

Paul Mee

Peter Ellis

Pietro Monticone

Lloyd Chapman

Andrew Johnson

Kaitlyn Johnson

EpiForecasts 

extract_inits function

<dl><dt>fit</dt>
<dd>A <code>&lt;stanfit&gt;</code> object.</dd>
<dt>current_inits</dt>
<dd>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.</dd>
<dt>exclude_list</dt>
<dd>A character vector of parameters to not initialise from
the fit object, defaulting to <code>NULL</code>.</dd>
<dt>samples</dt>
<dd>Numeric, defaults to 50. Number of posterior samples.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#experimental'><img src='figures/lifecycle-experimental.svg' alt='[Experimental]' /></a>
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

<dl>

<dt>fit</dt>
<dd>A <code>&lt;stanfit&gt;</code> object.</dd>


<dt>current_inits</dt>
<dd>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.</dd>


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


<dt>samples</dt>
<dd>Numeric, defaults to 50. Number of posterior samples.</dd>

</dl>

Generate initial conditions from a Stan fit

extract_inits: Generate initial conditions from a Stan fit

Description

Usage

Value

Arguments