fit_model_with_nuts

<a href="https://lifecycle.r-lib.org/articles/stages.html#maturing"><img src="figures/lifecycle-maturing.svg?package=EpiNow2&version=1.6.1" alt="[Maturing]"></a>
Fits a stan model using <code>rstan::sampling()</code>. Provides the optional ability to
run chains using <code>future</code> with error catching, timeouts and merging of
completed chains.

internal

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 

fit_model_with_nuts function

<dl><dt>args</dt>
<dd>List of stan arguments.</dd>
<dt>future</dt>
<dd>Logical, defaults to <code>FALSE</code>. Should <code>future</code> be used to run
stan chains in parallel.</dd>
<dt>max_execution_time</dt>
<dd>Numeric, defaults to Inf. What is the maximum
execution time per chain in seconds. Results will still be returned as long
as at least 2 chains complete successfully within the timelimit.</dd>
<dt>id</dt>
<dd>A character string used to assign logging information on error.
Used by <code>regional_epinow()</code> to assign errors to regions. Alter the default to
run with error catching.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#maturing'><img src='figures/lifecycle-maturing.svg' alt='[Maturing]' /></a>
Fits a stan model using <code>rstan::sampling()</code>. Provides the optional ability to
run chains using <code>future</code> with error catching, timeouts and merging of
completed chains.

Fit a Stan Model using the NUTs sampler — fit_model_with_nuts

<dl>

<dt>args</dt>
<dd>List of stan arguments.</dd>


<dt>future</dt>
<dd>Logical, defaults to <code>FALSE</code>. Should <code>future</code> be used to run
stan chains in parallel.</dd>


<dt>max_execution_time</dt>
<dd>Numeric, defaults to Inf. What is the maximum
execution time per chain in seconds. Results will still be returned as long
as at least 2 chains complete successfully within the timelimit.</dd>


<dt>id</dt>
<dd>A character string used to assign logging information on error.
Used by <code>regional_epinow()</code> to assign errors to regions. Alter the default to
run with error catching.</dd>

</dl>

Fit a Stan Model using the NUTs sampler

fit_model_with_nuts: Fit a Stan Model using the NUTs sampler

Description

Usage

Value

Arguments