extract_samples

If the <code>object</code> argument is a <code>&lt;stanfit&gt;</code> object, it simply returns the
result of <code>rstan::extract()</code>. If it is a <code>&lt;CmdStanMCMC&gt;</code> it returns samples
in the same format as <code>rstan::extract()</code> does for <code>&lt;stanfit&gt;</code> objects.

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_samples function

<dl><dt>stan_fit</dt>
<dd>A <code>&lt;stanfit&gt;</code> or <code>&lt;CmdStanMCMC&gt;</code> object as returned by
<code>fit_model()</code>.</dd>
<dt>pars</dt>
<dd>Any selection of parameters to extract</dd>
<dt>include</dt>
<dd>whether the parameters specified in <code>pars</code> should be included
(<code>TRUE</code>, the default) or excluded (<code>FALSE</code>)</dd></dl>

Arguments

Extract all samples from a stan fit — extract_samples

<dl>

<dt>stan_fit</dt>
<dd>A <code>&lt;stanfit&gt;</code> or <code>&lt;CmdStanMCMC&gt;</code> object as returned by
<code>fit_model()</code>.</dd>


<dt>pars</dt>
<dd>Any selection of parameters to extract</dd>


<dt>include</dt>
<dd>whether the parameters specified in <code>pars</code> should be included
(<code>TRUE</code>, the default) or excluded (<code>FALSE</code>)</dd>

</dl>

Extract all samples from a stan fit

extract_samples: Extract all samples from a stan fit

Description

Usage

Value

Arguments