format_fit

<a href="https://lifecycle.r-lib.org/articles/stages.html#stable"><img src="figures/lifecycle-stable.svg?package=EpiNow2&version=1.6.1" alt="[Stable]"></a>
Summaries posterior samples and adds additional custom variables.

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 

format_fit function

<dl><dt>posterior_samples</dt>
<dd>A list of posterior samples as returned by
<code>extract_parameter_samples()</code>.</dd>
<dt>horizon</dt>
<dd>Numeric, forecast horizon.</dd>
<dt>shift</dt>
<dd>Numeric, the shift to apply to estimates.</dd>
<dt>burn_in</dt>
<dd>Numeric, number of days to discard estimates for.</dd>
<dt>start_date</dt>
<dd>Date, earliest date with data.</dd>
<dt>CrIs</dt>
<dd>Numeric vector of credible intervals to calculate.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#stable'><img src='figures/lifecycle-stable.svg' alt='[Stable]' /></a>
Summaries posterior samples and adds additional custom variables.

Format Posterior Samples — format_fit

<dl>

<dt>posterior_samples</dt>
<dd>A list of posterior samples as returned by
<code>extract_parameter_samples()</code>.</dd>


<dt>horizon</dt>
<dd>Numeric, forecast horizon.</dd>


<dt>shift</dt>
<dd>Numeric, the shift to apply to estimates.</dd>


<dt>burn_in</dt>
<dd>Numeric, number of days to discard estimates for.</dd>


<dt>start_date</dt>
<dd>Date, earliest date with data.</dd>


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

</dl>

Format Posterior Samples

format_fit: Format Posterior Samples

Description

Usage

Value

Arguments