smooth_ww

Smooth wastewater data (using pre-processed wastewater)

internal

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

David Champredon

Effective Reproduction Number Estimation

Warsame Yusuf

Irena Papst

smooth_ww function

<dl><dt>ww.conc</dt>
<dd>Data frame. Must have variables:<ul>
<li><code>date</code>: calendar date of wastewater collection</li>
<li><code>value</code>: pathogen concentration</li>
</ul></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>
<dt>silent</dt>
<dd>Logical. Flag to suppress all output messages, warnings, and progress bars.</dd></dl>

Arguments

Smooth wastewater data (using pre-processed wastewater) — smooth_ww

<dl>

<dt>ww.conc</dt>
<dd>Data frame. Must have variables:<ul>
<li><code>date</code>: calendar date of wastewater collection</li>
<li><code>value</code>: pathogen concentration</li>
</ul></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>


<dt>silent</dt>
<dd>Logical. Flag to suppress all output messages, warnings, and progress bars.</dd>

</dl>

smooth_ww: Smooth wastewater data (using pre-processed wastewater)

Description

Usage

Value

Arguments