create_clean_reported_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>
Cleans a data frame of reported cases by replacing missing dates with 0
cases and applies an optional threshold at which point 0 cases are replaced
with a moving average of observed cases. See <code>zero_threshold</code> for details.

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_clean_reported_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>horizon</dt>
<dd>Numeric, defaults to 7. Number of days into the future to
forecast.</dd>
<dt>filter_leading_zeros</dt>
<dd>Logical, defaults to TRUE. Should zeros at the
start of the time series be filtered out.</dd>
<dt>zero_threshold</dt>
<dd><a href="https://lifecycle.r-lib.org/articles/stages.html#experimental"><img src="figures/lifecycle-experimental.svg?package=EpiNow2&version=1.4.0" alt="[Experimental]"></a> Numeric defaults
to Inf. Indicates if detected zero cases are meaningful by using a threshold
number of cases based on the 7 day average. If the average is above this
threshold then the zero is replaced with the backwards looking rolling
average. If set to infinity then no changes are made.</dd></dl>

Arguments

Author

<a href='https://lifecycle.r-lib.org/articles/stages.html#stable'><img src='figures/lifecycle-stable.svg' alt='[Stable]' /></a>
Cleans a data frame of reported cases by replacing missing dates with 0
cases and applies an optional threshold at which point 0 cases are replaced
with a moving average of observed cases. See <code>zero_threshold</code> for details.

Create Clean Reported Cases — create_clean_reported_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>horizon</dt>
<dd>Numeric, defaults to 7. Number of days into the future to
forecast.</dd>


<dt>filter_leading_zeros</dt>
<dd>Logical, defaults to TRUE. Should zeros at the
start of the time series be filtered out.</dd>


<dt>zero_threshold</dt>
<dd><a href='https://lifecycle.r-lib.org/articles/stages.html#experimental'><img src='figures/lifecycle-experimental.svg' alt='[Experimental]' /></a> Numeric defaults
to Inf. Indicates if detected zero cases are meaningful by using a threshold
number of cases based on the 7 day average. If the average is above this
threshold then the zero is replaced with the backwards looking rolling
average. If set to infinity then no changes are made.</dd>

</dl>

Create Clean Reported Cases

create_clean_reported_cases: Create Clean Reported Cases

Description

Usage

Value

Arguments

Author