summary.estimate_infections

<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>
<code>summary</code> method for class "estimate_infections".

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

summary.estimate_infections function

<dl><dt>object</dt>
<dd>A list of output as produced by "estimate_infections".</dd>
<dt>type</dt>
<dd>A character vector of data types to return. Defaults to
"snapshot" but also supports "parameters". "snapshot" returns a summary at
a given date (by default the latest date informed by data). "parameters"
returns summarised parameter estimates that can be further filtered using
<code>params</code> to show just the parameters of interest and date.
Note: <code>type = "samples"</code> is deprecated. Use <code>get_samples()</code> instead.</dd>
<dt>target_date</dt>
<dd>Date, defaults to maximum found in the data if not
specified.</dd>
<dt>params</dt>
<dd>A character vector of parameters to filter for.</dd>
<dt>CrIs</dt>
<dd>Numeric vector of credible intervals to calculate.</dd>
<dt>...</dt>
<dd>Pass additional arguments to <code>report_summary</code> when
<code>type = "snapshot"</code>.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#stable'><img src='figures/lifecycle-stable.svg' alt='[Stable]' /></a>
<code>summary</code> method for class "estimate_infections".

Summary output from estimate_infections — summary.estimate_infections

<dl>

<dt>object</dt>
<dd>A list of output as produced by "estimate_infections".</dd>


<dt>type</dt>
<dd>A character vector of data types to return. Defaults to
"snapshot" but also supports "parameters". "snapshot" returns a summary at
a given date (by default the latest date informed by data). "parameters"
returns summarised parameter estimates that can be further filtered using
<code>params</code> to show just the parameters of interest and date.
Note: <code>type = "samples"</code> is deprecated. Use <code>get_samples()</code> instead.</dd>


<dt>target_date</dt>
<dd>Date, defaults to maximum found in the data if not
specified.</dd>


<dt>params</dt>
<dd>A character vector of parameters to filter for.</dd>


<dt>CrIs</dt>
<dd>Numeric vector of credible intervals to calculate.</dd>


<dt>...</dt>
<dd>Pass additional arguments to <code>report_summary</code> when
<code>type = "snapshot"</code>.</dd>

</dl>

Summary output from estimate_infections

summary.estimate_infections: Summary output from estimate_infections

Description

Usage

Value

Arguments

See Also