extract_stan_param

<a href="https://lifecycle.r-lib.org/articles/stages.html#stable"><img src="figures/lifecycle-stable.svg?package=EpiNow2&version=1.3.4" alt="[Stable]"></a>
Extracts summarised parameter posteriors from a <code>stanfit</code> object using
<code>rstan::summary</code> in a format consistent with other summary functions in
<code>EpiNow2</code>.

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.

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

Pietro Monticone

Lloyd Chapman

EpiForecasts 

Sebastian Funk

extract_stan_param function

<dl><dt>fit</dt>
<dd>A <code>stanfit</code> objec.</dd>
<dt>params</dt>
<dd>A character vector of parameters to extract. Defaults to all
parameters.</dd>
<dt>CrIs</dt>
<dd>Numeric vector of credible intervals to calculate.</dd>
<dt>var_names</dt>
<dd>Logical defaults to <code>FALSE</code>. Should variables be named.
Automatically set to TRUE if multiple parameters are to be extracted.</dd></dl>

Arguments

Author

<a href='https://lifecycle.r-lib.org/articles/stages.html#stable'><img src='figures/lifecycle-stable.svg' alt='[Stable]' /></a>
Extracts summarised parameter posteriors from a <code>stanfit</code> object using
<code>rstan::summary</code> in a format consistent with other summary functions in
<code>EpiNow2</code>.

Extract a Parameter Summary from a Stan Object — extract_stan_param

<dl>

<dt>fit</dt>
<dd>A <code>stanfit</code> objec.</dd>


<dt>params</dt>
<dd>A character vector of parameters to extract. Defaults to all
parameters.</dd>


<dt>CrIs</dt>
<dd>Numeric vector of credible intervals to calculate.</dd>


<dt>var_names</dt>
<dd>Logical defaults to <code>FALSE</code>. Should variables be named.
Automatically set to TRUE if multiple parameters are to be extracted.</dd>

</dl>

Extract a Parameter Summary from a Stan Object

extract_stan_param: Extract a Parameter Summary from a Stan Object

Description

Usage

Value

Arguments

Author