dist_spec_plus

This is done via convolution with <code><a href="/link/stats%3A%3Aconvolve()?package=EpiNow2&version=1.4.0" data-mini-rdoc="EpiNow2::stats::convolve()">stats::convolve()</a></code>. Nonparametric delays
that can be combined are processed together, and their cumulative
distribution function is truncated at a specified tolerance level, ensuring
numeric stability.

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

dist_spec_plus function

<dl><dt>e1</dt>
<dd>The first delay distribution (from a call to <code>dist_spec()</code>) to
combine.</dd>
<dt>e2</dt>
<dd>The second delay distribution (from a call to <code>dist_spec()</code>) to
combine.</dd>
<dt>tolerance</dt>
<dd>A numeric value that sets the cumulative probability
to retain when truncating the cumulative distribution function of the
combined nonparametric delays. The default value is 0.001 with this retaining
0.999 of the cumulative probability. Note that using a larger tolerance may
result in a smaller number of points in the combined nonparametric delay but
may also impact the accuracy of the combined delay (i.e., change the mean
and standard deviation).</dd></dl>

Arguments

Author

This is done via convolution with <code><a href='https://rdrr.io/r/stats/convolve.html'>stats::convolve()</a></code>. Nonparametric delays
that can be combined are processed together, and their cumulative
distribution function is truncated at a specified tolerance level, ensuring
numeric stability.

Creates a delay distribution as the sum of two other delay distributions — dist_spec_plus

<dl>

<dt>e1</dt>
<dd>The first delay distribution (from a call to <code>dist_spec()</code>) to
combine.</dd>


<dt>e2</dt>
<dd>The second delay distribution (from a call to <code>dist_spec()</code>) to
combine.</dd>


<dt>tolerance</dt>
<dd>A numeric value that sets the cumulative probability
to retain when truncating the cumulative distribution function of the
combined nonparametric delays. The default value is 0.001 with this retaining
0.999 of the cumulative probability. Note that using a larger tolerance may
result in a smaller number of points in the combined nonparametric delay but
may also impact the accuracy of the combined delay (i.e., change the mean
and standard deviation).</dd>

</dl>

Creates a delay distribution as the sum of two other delay distributions

dist_spec_plus: Creates a delay distribution as the sum of two other delay distributions

Description

Usage

Value

Arguments

Author