add_breakpoints

Add breakpoints to certain dates in a data set.

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 

add_breakpoints function

<dl><dt>data</dt>
<dd>A <code>&lt;data.frame&gt;</code> of disease reports (confirm) by date (date).
<code>confirm</code> must be numeric and <code>date</code> must be in date format. Optionally
this can also have a logical <code>accumulate</code> column which indicates whether
data should be added to the next data point. This is useful when modelling
e.g. weekly incidence data. See also the <code>fill_missing()</code> function which
helps add the <code>accumulate</code> column with the desired properties when dealing
with non-daily data. If any accumulation is done this happens after
truncation as specified by the <code>truncation</code> argument.</dd>
<dt>dates</dt>
<dd>A vector of dates to use as breakpoints.</dd></dl>

Arguments

Add breakpoints to certain dates in a data set. — add_breakpoints

<dl>

<dt>data</dt>
<dd>A <code>&lt;data.frame&gt;</code> of disease reports (confirm) by date (date).
<code>confirm</code> must be numeric and <code>date</code> must be in date format. Optionally
this can also have a logical <code>accumulate</code> column which indicates whether
data should be added to the next data point. This is useful when modelling
e.g. weekly incidence data. See also the <code>fill_missing()</code> function which
helps add the <code>accumulate</code> column with the desired properties when dealing
with non-daily data. If any accumulation is done this happens after
truncation as specified by the <code>truncation</code> argument.</dd>


<dt>dates</dt>
<dd>A vector of dates to use as breakpoints.</dd>

</dl>

Add breakpoints to certain dates in a data set.

add_breakpoints: Add breakpoints to certain dates in a data set.

Description

Usage

Value

Arguments

Examples