extract_delays

Extracts samples from all delay parameters using the delay ID lookup system.
Similar to extract_parameters(), this extracts all delay distribution
parameters and uses the *_id variables (e.g., delay_id, trunc_id) to assign
meaningful names.

internal

Estimates the time-varying reproduction number, rate of
spread, and doubling time using a renewal equation approach combined
with Bayesian inference via Stan. Supports Gaussian process and
random walk priors for modelling changes in
transmission over time. Accounts for delays between infection and
observation (incubation period, reporting delays), right-truncation
in recent data, day-of-week effects, and observation overdispersion.
Can estimate relationships between primary and secondary outcomes
(e.g., cases to hospitalisations or deaths) and forecast both. Runs
across multiple regions in parallel. Based on
Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1> and
Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>.

Sebastian Funk

EpiNow2

Estimate and Forecast Real-Time Infection Dynamics

Sam Abbott

Joel Hellewell

Katharine Sherratt

Katelyn Gostic

Joe Hickson

Hamada S. Badr

Michael DeWitt

James M. Azam

Adrian Lison

Robin Thompson

Sophie Meakin

James Munday

Nikos Bosse

Paul Mee

Peter Ellis

Pietro Monticone

Lloyd Chapman

Andrew Johnson

Kaitlyn Johnson

Adam Howes

extract_delays function

<dl><dt>samples</dt>
<dd>Extracted stan model (using <code>rstan::extract()</code>)</dd>
<dt>args</dt>
<dd>Stan data list with delay_id_* and related lookup variables.</dd></dl>

Arguments

Extract samples from all delay parameters — extract_delays

<dl>

<dt>samples</dt>
<dd>Extracted stan model (using <code>rstan::extract()</code>)</dd>


<dt>args</dt>
<dd>Stan data list with delay_id_* and related lookup variables.</dd>

</dl>

Extract samples from all delay parameters

extract_delays: Extract samples from all delay parameters

Description

Usage

Value

Arguments