check_truncation_length

Checks if the truncation distribution PMF is longer than the
observed time period (excluding seeding time and forecast horizon). The
truncation is applied to the observed time period in the Stan model, so
having a truncation distribution longer than this period means the tail of
the distribution will be used.

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

check_truncation_length function

<dl><dt>stan_args</dt>
<dd>List of stan arguments including the data element with
delay information from <code>create_stan_delays()</code></dd>
<dt>time_points</dt>
<dd>Integer length of the observed time period
(t - seeding_time - horizon)</dd></dl>

Arguments

Check and warn if truncation distribution is longer than observed time — check_truncation_length

<dl>

<dt>stan_args</dt>
<dd>List of stan arguments including the data element with
delay information from <code>create_stan_delays()</code></dd>


<dt>time_points</dt>
<dd>Integer length of the observed time period
(t - seeding_time - horizon)</dd>

</dl>

Check and warn if truncation distribution is longer than observed time

check_truncation_length: Check and warn if truncation distribution is longer than observed time

Description

Usage

Value

Arguments