extract_parameter_samples

<a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated"><img src="figures/lifecycle-deprecated.svg?package=EpiNow2&version=1.8.0" alt="[Deprecated]"></a>
This function has been deprecated. Use <code>format_simulation_output()</code> for
simulation outputs or <code>get_samples()</code> for estimation outputs instead.

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_parameter_samples function

<dl><dt>stan_fit</dt>
<dd>A <code>&lt;stanfit&gt;</code> or <code>&lt;CmdStanMCMC&gt;</code> object as returned by
<code>fit_model()</code>.</dd>
<dt>data</dt>
<dd>A list of the data supplied to the simulation.</dd>
<dt>reported_dates</dt>
<dd>A vector of dates to report estimates for.</dd>
<dt>imputed_dates</dt>
<dd>A vector of dates to report imputed reports for.</dd>
<dt>reported_inf_dates</dt>
<dd>A vector of dates to report infection estimates
for.</dd>
<dt>drop_length_1</dt>
<dd>Logical; drop dimensions of length 1 in arrays extracted
from the stan fit. Used in simulations where there's only 1 realization.</dd>
<dt>merge</dt>
<dd>if TRUE, merge samples into a single data.table using
rbindlist. If FALSE returns a list of samples by parameter.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#deprecated'><img src='figures/lifecycle-deprecated.svg' alt='[Deprecated]' /></a>
This function has been deprecated. Use <code>format_simulation_output()</code> for
simulation outputs or <code>get_samples()</code> for estimation outputs instead.

Extract parameter samples from a Stan model — extract_parameter_samples

<dl>

<dt>stan_fit</dt>
<dd>A <code>&lt;stanfit&gt;</code> or <code>&lt;CmdStanMCMC&gt;</code> object as returned by
<code>fit_model()</code>.</dd>


<dt>data</dt>
<dd>A list of the data supplied to the simulation.</dd>


<dt>reported_dates</dt>
<dd>A vector of dates to report estimates for.</dd>


<dt>imputed_dates</dt>
<dd>A vector of dates to report imputed reports for.</dd>


<dt>reported_inf_dates</dt>
<dd>A vector of dates to report infection estimates
for.</dd>


<dt>drop_length_1</dt>
<dd>Logical; drop dimensions of length 1 in arrays extracted
from the stan fit. Used in simulations where there's only 1 realization.</dd>


<dt>merge</dt>
<dd>if TRUE, merge samples into a single data.table using
rbindlist. If FALSE returns a list of samples by parameter.</dd>

</dl>

Extract parameter samples from a Stan model

extract_parameter_samples: Extract parameter samples from a Stan model

Description

Usage

Value

Arguments