epinow2_cmdstan_model

The function has been adapted from a similar function in the epinowcast
package (Copyright holder: epinowcast authors, under MIT License).

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 

epinow2_cmdstan_model function

<dl><dt>model</dt>
<dd>A character string indicating the model to use. Needs to be
present in <code>dir</code> (with extension <code>.stan</code>). Defaults to "estimate_infections".</dd>
<dt>dir</dt>
<dd>A character string specifying the path to any stan
files to include in the model. If missing the package default is used.</dd>
<dt>verbose</dt>
<dd>Logical, defaults to <code>TRUE</code>. Should verbose
messages be shown.</dd>
<dt>...</dt>
<dd>Additional arguments passed to <code>cmdstanr::cmdstan_model()</code>.</dd></dl>

Arguments

Load and compile an EpiNow2 cmdstanr model — epinow2_cmdstan_model

<dl>

<dt>model</dt>
<dd>A character string indicating the model to use. Needs to be
present in <code>dir</code> (with extension <code>.stan</code>). Defaults to "estimate_infections".</dd>


<dt>dir</dt>
<dd>A character string specifying the path to any stan
files to include in the model. If missing the package default is used.</dd>


<dt>verbose</dt>
<dd>Logical, defaults to <code>TRUE</code>. Should verbose
messages be shown.</dd>


<dt>...</dt>
<dd>Additional arguments passed to <code>cmdstanr::cmdstan_model()</code>.</dd>

</dl>

Load and compile an EpiNow2 cmdstanr model

epinow2_cmdstan_model: Load and compile an EpiNow2 cmdstanr model

Description

Usage

Value

Arguments