incidence_to_R

internal

Estimate the effective reproduction number from wastewater
and clinical data sources.

David Champredon

Effective Reproduction Number Estimation

Warsame Yusuf

Irena Papst

incidence_to_R function

<dl><dt>incidence</dt>
<dd>Data frame. Estimated incidence. Must include at least
<code>date</code>, <code>I</code>, and <code>t</code> columns.</dd>
<dt>generation.interval</dt>
<dd>List. Parameters for a single generation interval distribution, as generated by <code>sample_a_dist()</code>.</dd>
<dt>prm.R</dt>
<dd>List. Settings for the ensemble when calculating Rt.
Elements include:<ul>
<li><code>iter</code>: Integer. Number of iterations for the Rt ensemble</li>
<li><code>CI</code>: Numeric between 0 and 1. Confidence interval width for Rt
estimates after sampling uncertain distributions.</li>
<li><code>window</code>: Integer. Number of days defining the window of data used by
<code>EpiEstim</code> to estimate Rt. If <code>NULL</code>, will default to 7.</li>
<li><code>config.EpiEstim</code>: (optional) configuration for <code>EpiEstim</code> defined via
<code>EpiEstim::make_config()</code>. If <code>NULL</code>, will use default config from
<code>EpiEstim</code>.</li>
</ul></dd></dl>

Arguments

Estimate Rt using EpiEstim — incidence_to_R

<dl>

<dt>incidence</dt>
<dd>Data frame. Estimated incidence. Must include at least
<code>date</code>, <code>I</code>, and <code>t</code> columns.</dd>


<dt>generation.interval</dt>
<dd>List. Parameters for a single generation interval distribution, as generated by <code>sample_a_dist()</code>.</dd>


<dt>prm.R</dt>
<dd>List. Settings for the ensemble when calculating Rt.
Elements include:<ul>
<li><code>iter</code>: Integer. Number of iterations for the Rt ensemble</li>
<li><code>CI</code>: Numeric between 0 and 1. Confidence interval width for Rt
estimates after sampling uncertain distributions.</li>
<li><code>window</code>: Integer. Number of days defining the window of data used by
<code>EpiEstim</code> to estimate Rt. If <code>NULL</code>, will default to 7.</li>
<li><code>config.EpiEstim</code>: (optional) configuration for <code>EpiEstim</code> defined via
<code>EpiEstim::make_config()</code>. If <code>NULL</code>, will use default config from
<code>EpiEstim</code>.</li>
</ul></dd>

</dl>

incidence_to_R: Estimate Rt using EpiEstim

Description

Usage

Arguments

See Also