create_rt_data

<a href="https://lifecycle.r-lib.org/articles/stages.html#stable"><img src="figures/lifecycle-stable.svg?package=EpiNow2&version=1.4.0" alt="[Stable]"></a>
Takes the output from <code>rt_opts()</code> and converts it into a list understood by
<code>stan</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

James M. Azam

Andrew Johnson

EpiForecasts 

Sebastian Funk

create_rt_data function

<dl><dt>rt</dt>
<dd>A list of options as generated by <code>rt_opts()</code> defining Rt
estimation. Defaults to <code>rt_opts()</code>. Set to <code>NULL</code> to switch to using back
calculation rather than generating infections using Rt.</dd>
<dt>breakpoints</dt>
<dd>An integer vector (binary) indicating the location of
breakpoints.</dd>
<dt>delay</dt>
<dd>Numeric mean delay</dd>
<dt>horizon</dt>
<dd>Numeric, forecast horizon.</dd></dl>

Arguments

Author

<a href='https://lifecycle.r-lib.org/articles/stages.html#stable'><img src='figures/lifecycle-stable.svg' alt='[Stable]' /></a>
Takes the output from <code>rt_opts()</code> and converts it into a list understood by
<code>stan</code>.

Create Time-varying Reproduction Number Data — create_rt_data

<dl>

<dt>rt</dt>
<dd>A list of options as generated by <code>rt_opts()</code> defining Rt
estimation. Defaults to <code>rt_opts()</code>. Set to <code>NULL</code> to switch to using back
calculation rather than generating infections using Rt.</dd>


<dt>breakpoints</dt>
<dd>An integer vector (binary) indicating the location of
breakpoints.</dd>


<dt>delay</dt>
<dd>Numeric mean delay</dd>


<dt>horizon</dt>
<dd>Numeric, forecast horizon.</dd>

</dl>

Create Time-varying Reproduction Number Data

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create_rt_data: Create Time-varying Reproduction Number Data

Description

Usage

Value

Arguments

Author

See Also

Examples