plot_CrIs

<a href="https://lifecycle.r-lib.org/articles/stages.html#stable"><img src="figures/lifecycle-stable.svg?package=EpiNow2&version=1.8.0" alt="[Stable]"></a>
Adds credible intervals to a plot, either as ribbons or error bars.

Estimates the time-varying reproduction number, rate of
spread, and doubling time using a renewal equation approach combined
with Bayesian inference via Stan. Supports Gaussian process and
random walk priors for modelling changes in
transmission over time. Accounts for delays between infection and
observation (incubation period, reporting delays), right-truncation
in recent data, day-of-week effects, and observation overdispersion.
Can estimate relationships between primary and secondary outcomes
(e.g., cases to hospitalisations or deaths) and forecast both. Runs
across multiple regions in parallel. Based on
Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1> and
Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>.

Sebastian Funk

EpiNow2

Estimate and Forecast Real-Time Infection Dynamics

Sam Abbott

Joel Hellewell

Katharine Sherratt

Katelyn Gostic

Joe Hickson

Hamada S. Badr

Michael DeWitt

James M. Azam

Adrian Lison

Robin Thompson

Sophie Meakin

James Munday

Nikos Bosse

Paul Mee

Peter Ellis

Pietro Monticone

Lloyd Chapman

Andrew Johnson

Kaitlyn Johnson

Adam Howes

plot_CrIs function

<dl><dt>plot</dt>
<dd>A <code>{ggplot2}</code> plot</dd>
<dt>CrIs</dt>
<dd>Numeric list of credible intervals present in the data. As
produced by <code>extract_CrIs()</code>.</dd>
<dt>alpha</dt>
<dd>Numeric, overall alpha of the target line range.</dd>
<dt>linewidth</dt>
<dd>Numeric, line width of the default line range.</dd>
<dt>style</dt>
<dd>Character string indicating the plot style. Options are
"ribbon" (default) for shaded ribbon plots or "linerange" for error bars.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#stable'><img src='figures/lifecycle-stable.svg' alt='[Stable]' /></a>
Adds credible intervals to a plot, either as ribbons or error bars.

Plot EpiNow2 Credible Intervals — plot_CrIs

<dl>

<dt>plot</dt>
<dd>A <code>{ggplot2}</code> plot</dd>


<dt>CrIs</dt>
<dd>Numeric list of credible intervals present in the data. As
produced by <code>extract_CrIs()</code>.</dd>


<dt>alpha</dt>
<dd>Numeric, overall alpha of the target line range.</dd>


<dt>linewidth</dt>
<dd>Numeric, line width of the default line range.</dd>


<dt>style</dt>
<dd>Character string indicating the plot style. Options are
"ribbon" (default) for shaded ribbon plots or "linerange" for error bars.</dd>

</dl>

Plot EpiNow2 Credible Intervals

plot_CrIs: Plot EpiNow2 Credible Intervals

Description

Usage

Value

Arguments