plot.estimate_secondary

<a href="https://lifecycle.r-lib.org/articles/stages.html#experimental"><img src="figures/lifecycle-experimental.svg?package=EpiNow2&version=1.6.1" alt="[Experimental]"></a>
<code>plot</code> method for class "estimate_secondary".

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 

plot.estimate_secondary function

<dl><dt>x</dt>
<dd>A list of output as produced by <code>estimate_secondary</code></dd>
<dt>primary</dt>
<dd>Logical, defaults to <code>FALSE</code>. Should <code>primary</code> reports also
be plot?</dd>
<dt>from</dt>
<dd>Date object indicating when to plot from.</dd>
<dt>to</dt>
<dd>Date object indicating when to plot up to.</dd>
<dt>new_obs</dt>
<dd>A <code>&lt;data.frame&gt;</code> containing the columns <code>date</code> and <code>secondary</code>
which replace the secondary observations stored in the <code>estimate_secondary</code>
output.</dd>
<dt>...</dt>
<dd>Pass additional arguments to plot function. Not currently in use.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#experimental'><img src='figures/lifecycle-experimental.svg' alt='[Experimental]' /></a>
<code>plot</code> method for class "estimate_secondary".

Plot method for estimate_secondary — plot.estimate_secondary

<dl>

<dt>x</dt>
<dd>A list of output as produced by <code>estimate_secondary</code></dd>


<dt>primary</dt>
<dd>Logical, defaults to <code>FALSE</code>. Should <code>primary</code> reports also
be plot?</dd>


<dt>from</dt>
<dd>Date object indicating when to plot from.</dd>


<dt>to</dt>
<dd>Date object indicating when to plot up to.</dd>


<dt>new_obs</dt>
<dd>A <code>&lt;data.frame&gt;</code> containing the columns <code>date</code> and <code>secondary</code>
which replace the secondary observations stored in the <code>estimate_secondary</code>
output.</dd>


<dt>...</dt>
<dd>Pass additional arguments to plot function. Not currently in use.</dd>

</dl>

Plot method for estimate_secondary

plot.estimate_secondary: Plot method for estimate_secondary

Description

Usage

Value

Arguments

See Also