check_reports_valid

<a href="https://lifecycle.r-lib.org/articles/stages.html#stable"><img src="figures/lifecycle-stable.svg?package=EpiNow2&version=1.7.1" alt="[Stable]"></a>
<code>check_reports_valid()</code> checks that the supplied data is a <code>&lt;data.frame&gt;</code>,
and that it has the right column names and types. In particular, it checks
that the date column is in date format and does not contain NAs, and that
the other columns are numeric.

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 

check_reports_valid function

<dl><dt>data</dt>
<dd>A data frame with either:<ul>
<li>a minimum of two columns: <code>date</code> and <code>confirm</code>, if to be
used by <code>estimate_infections()</code> or <code>estimate_truncation()</code>, or</li>
<li>a minimum of three columns: <code>date</code>, <code>primary</code>, and <code>secondary</code>, if to be
used by <code>estimate_secondary()</code>.</li>
</ul></dd>
<dt>model</dt>
<dd>The EpiNow2 model to be used. Either
"estimate_infections", "estimate_truncation", or "estimate_secondary".
This is used to determine which checks to perform on the data input.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#stable'><img src='figures/lifecycle-stable.svg' alt='[Stable]' /></a>
<code>check_reports_valid()</code> checks that the supplied data is a <code>&lt;data.frame&gt;</code>,
and that it has the right column names and types. In particular, it checks
that the date column is in date format and does not contain NAs, and that
the other columns are numeric.

Validate data input — check_reports_valid

<dl>

<dt>data</dt>
<dd>A data frame with either:<ul>
<li>a minimum of two columns: <code>date</code> and <code>confirm</code>, if to be
used by <code>estimate_infections()</code> or <code>estimate_truncation()</code>, or</li>
<li>a minimum of three columns: <code>date</code>, <code>primary</code>, and <code>secondary</code>, if to be
used by <code>estimate_secondary()</code>.</li>
</ul></dd>


<dt>model</dt>
<dd>The EpiNow2 model to be used. Either
"estimate_infections", "estimate_truncation", or "estimate_secondary".
This is used to determine which checks to perform on the data input.</dd>

</dl>

Validate data input

check_reports_valid: Validate data input

Description

Usage

Value

Arguments