smooth_cl

Smooth realizations from estimating daily reports

internal

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

David Champredon

Effective Reproduction Number Estimation

Warsame Yusuf

Irena Papst

smooth_cl function

<dl><dt>cl.daily</dt>
<dd>Data frame. Output of <code>agg_to_daily()</code>.</dd>
<dt>prm.smooth</dt>
<dd>List. list of smoothing parameters. Parameters should be
specified as followed:<ul>
<li><code>method</code>: smoothing method, either <code>'rollmean'</code> (rolling mean) or <code>'loess'</code> (LOESS smoothing via <code><a href="/link/stats%3A%3Aloess()?package=ern&version=2.1.2" data-mini-rdoc="ern::stats::loess()">stats::loess()</a></code>)</li>
<li><code>window</code>: for <code>method = 'rollmean</code> only; width of smoothing window in days</li>
<li><code>align</code>: for <code>method = 'rollmean</code> only; smoothing alignment, either <code>'center'</code>, <code>'left'</code>, <code>'right'</code></li>
<li><code>span</code>: for <code>method = 'loess'</code> only; smoothing span (see the documentation for <code><a href="/link/stats%3A%3Aloess()?package=ern&version=2.1.2" data-mini-rdoc="ern::stats::loess()">stats::loess()</a></code> for details)</li>
<li><code>floor</code>: optional call for wastewater concentration smoothing with <code>method = 'loess'</code> only; user defined minimum smoothing concentration</li>
</ul>Set this entire list to <code>NULL</code> to turn off smoothing</dd></dl>

Arguments

Smooth realizations from estimating daily reports — smooth_cl

<dl>

<dt>cl.daily</dt>
<dd>Data frame. Output of <code>agg_to_daily()</code>.</dd>


<dt>prm.smooth</dt>
<dd>List. list of smoothing parameters. Parameters should be
specified as followed:<ul>
<li><code>method</code>: smoothing method, either <code>'rollmean'</code> (rolling mean) or <code>'loess'</code> (LOESS smoothing via <code><a href='https://rdrr.io/r/stats/loess.html'>stats::loess()</a></code>)</li>
<li><code>window</code>: for <code>method = 'rollmean</code> only; width of smoothing window in days</li>
<li><code>align</code>: for <code>method = 'rollmean</code> only; smoothing alignment, either <code>'center'</code>, <code>'left'</code>, <code>'right'</code></li>
<li><code>span</code>: for <code>method = 'loess'</code> only; smoothing span (see the documentation for <code><a href='https://rdrr.io/r/stats/loess.html'>stats::loess()</a></code> for details)</li>
<li><code>floor</code>: optional call for wastewater concentration smoothing with <code>method = 'loess'</code> only; user defined minimum smoothing concentration</li>
</ul>Set this entire list to <code>NULL</code> to turn off smoothing</dd>

</dl>

smooth_cl: Smooth realizations from estimating daily reports

Description

Usage

Value

Arguments