extract_latent_state

<a href="https://lifecycle.r-lib.org/articles/stages.html#stable"><img src="figures/lifecycle-stable.svg?package=EpiNow2&version=1.8.0" alt="[Stable]"></a>
Extracts a time-varying latent state from a list of stan output and returns
it as a <code>&lt;data.table&gt;</code>.

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_latent_state function

<dl><dt>param</dt>
<dd>Character string indicating the latent state to extract</dd>
<dt>samples</dt>
<dd>Extracted stan model (using <code>rstan::extract()</code>)</dd>
<dt>dates</dt>
<dd>A vector identifying the dimensionality of the latent state to
extract. Generally this will be a date.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#stable'><img src='figures/lifecycle-stable.svg' alt='[Stable]' /></a>
Extracts a time-varying latent state from a list of stan output and returns
it as a <code>&lt;data.table&gt;</code>.

Extract samples for a latent state from a Stan model — extract_latent_state

<dl>

<dt>param</dt>
<dd>Character string indicating the latent state to extract</dd>


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


<dt>dates</dt>
<dd>A vector identifying the dimensionality of the latent state to
extract. Generally this will be a date.</dd>

</dl>

Extract samples for a latent state from a Stan model

extract_latent_state: Extract samples for a latent state from a Stan model

Description

Usage

Value

Arguments