create_shifted_cases

<a href="https://lifecycle.r-lib.org/articles/stages.html#stable"><img src="figures/lifecycle-stable.svg?package=EpiNow2&version=1.4.0" alt="[Stable]"></a>
This functions creates a data frame of reported cases that has been smoothed
using a centred partial rolling average (with a period set by
<code>smoothing_window</code>) and shifted back in time by some delay. It is used by
<code>estimate_infections</code> to generate the mean shifted prior on which the back
calculation method (see <code>backcalc_opts()</code>) is based.

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.

Sam Abbott 

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

Robin Thompson

Sophie Meakin

James Munday

Nikos Bosse

Paul Mee

Peter Ellis

Pietro Monticone

Lloyd Chapman

James M. Azam

Andrew Johnson

EpiForecasts 

Sebastian Funk

create_shifted_cases function

<dl><dt>reported_cases</dt>
<dd>A data frame of confirmed cases (confirm) by date
(date). confirm must be integer and date must be in date format.</dd>
<dt>shift</dt>
<dd>Numeric, mean delay shift to apply.</dd>
<dt>smoothing_window</dt>
<dd>Numeric, the rolling average smoothing window
to apply. Must be odd in order to be defined as a centred average.</dd>
<dt>horizon</dt>
<dd>Numeric, defaults to 7. Number of days into the future to
forecast.</dd></dl>

Arguments

Author

<a href='https://lifecycle.r-lib.org/articles/stages.html#stable'><img src='figures/lifecycle-stable.svg' alt='[Stable]' /></a>
This functions creates a data frame of reported cases that has been smoothed
using a centred partial rolling average (with a period set by
<code>smoothing_window</code>) and shifted back in time by some delay. It is used by
<code>estimate_infections</code> to generate the mean shifted prior on which the back
calculation method (see <code>backcalc_opts()</code>) is based.

Create Delay Shifted Cases — create_shifted_cases

<dl>

<dt>reported_cases</dt>
<dd>A data frame of confirmed cases (confirm) by date
(date). confirm must be integer and date must be in date format.</dd>


<dt>shift</dt>
<dd>Numeric, mean delay shift to apply.</dd>


<dt>smoothing_window</dt>
<dd>Numeric, the rolling average smoothing window
to apply. Must be odd in order to be defined as a centred average.</dd>


<dt>horizon</dt>
<dd>Numeric, defaults to 7. Number of days into the future to
forecast.</dd>

</dl>

Create Delay Shifted Cases

create_shifted_cases: Create Delay Shifted Cases

Description

Usage

Value

Arguments

Author

Examples