summary.estimate_infections

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

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 

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", and "samples". "snapshot" return
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.
"samples" similarly returns posterior
samples.</dd>
<dt>date</dt>
<dd>A date in the form "yyyy-mm-dd" to inspect estimates for.</dd>
<dt>params</dt>
<dd>A character vector of parameters to filter for.</dd>
<dt>...</dt>
<dd>Pass additional arguments to <code>report_summary</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", and "samples". "snapshot" return
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.
"samples" similarly returns posterior
samples.</dd>


<dt>date</dt>
<dd>A date in the form "yyyy-mm-dd" to inspect estimates for.</dd>


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


<dt>...</dt>
<dd>Pass additional arguments to <code>report_summary</code></dd>

</dl>

Summary output from estimate_infections

summary.estimate_infections: Summary output from estimate_infections

Description

Usage

Value

Arguments

See Also