get_seeding_time

The seeding time is set to the mean of the specified delays, constrained
to be at least the maximum generation time

internal

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 

get_seeding_time function

<dl><dt>delays</dt>
<dd>A call to <code>delay_opts()</code> defining delay distributions and
options. See the documentation of <code>delay_opts()</code> and the examples below for
details.</dd>
<dt>generation_time</dt>
<dd>A call to <code>gt_opts()</code> (or its alias
<code>generation_time_opts()</code>) defining the generation time distribution used.
For backwards compatibility a list of summary parameters can also be passed.</dd>
<dt>rt</dt>
<dd>A list of options as generated by <code>rt_opts()</code> defining Rt
estimation. Defaults to <code>rt_opts()</code>. To generate new infections using
the non-mechanistic model instead of the renewal equation model, use
<code>rt = NULL</code>. The non-mechanistic model internally uses the setting
<code>rt = rt_opts(use_rt = FALSE, future = "project", gp_on = "R0")</code>.</dd></dl>

Arguments

Estimate seeding time from delays and generation time — get_seeding_time

<dl>

<dt>delays</dt>
<dd>A call to <code>delay_opts()</code> defining delay distributions and
options. See the documentation of <code>delay_opts()</code> and the examples below for
details.</dd>


<dt>generation_time</dt>
<dd>A call to <code>gt_opts()</code> (or its alias
<code>generation_time_opts()</code>) defining the generation time distribution used.
For backwards compatibility a list of summary parameters can also be passed.</dd>


<dt>rt</dt>
<dd>A list of options as generated by <code>rt_opts()</code> defining Rt
estimation. Defaults to <code>rt_opts()</code>. To generate new infections using
the non-mechanistic model instead of the renewal equation model, use
<code>rt = NULL</code>. The non-mechanistic model internally uses the setting
<code>rt = rt_opts(use_rt = FALSE, future = "project", gp_on = "R0")</code>.</dd>

</dl>

Estimate seeding time from delays and generation time

get_seeding_time: Estimate seeding time from delays and generation time

Description

Usage

Value

Arguments