create_clean_reported_cases

A data frame of confirmed cases (confirm) by date (date). confirm must be integer and date must be
in date format.

reported_cases

Numeric, defaults to 7. Number of days into the future to forecast.

horizon

Numeric defaults to 50. Indicates if detected zero cases are meaningful by
using a threshold of 50 cases on average over the last 7 days. If the average is above this thresold
then the zero is replaced with the

zero_threshold

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 under active development.

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

EpiForecasts 

Sebastian Funk

create_clean_reported_cases function

Create Clean Reported Cases — create_clean_reported_cases

Create Clean Reported Cases

create_clean_reported_cases: Create Clean Reported Cases

Description

Usage

Arguments

Value