create_shifted_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, mean delay shift to apply.

shift

Numeric, the rolling average smoothing window
to apply. Must be odd in order to be defined as a centred average.

smoothing_window

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

horizon

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 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_shifted_cases function

Create Delay Shifted Cases — create_shifted_cases

Create Delay Shifted Cases

create_shifted_cases: Create Delay Shifted Cases

Description

Usage

Arguments

Value

Examples