create_stan_data

<a href="https://lifecycle.r-lib.org/articles/stages.html#stable"><img src="figures/lifecycle-stable.svg?package=EpiNow2&version=1.4.0" alt="[Stable]"></a>
Takes the output of <code>stan_opts()</code> and converts it into a list understood by
<code>stan</code>. Internally calls the other <code>create_</code> family of functions to
construct a single list for input into stan with all data required present.

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.

Sam Abbott 

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

Robin Thompson

Sophie Meakin

James Munday

Nikos Bosse

Paul Mee

Peter Ellis

Pietro Monticone

Lloyd Chapman

James M. Azam

Andrew Johnson

EpiForecasts 

Sebastian Funk

create_stan_data function

<dl><dt>reported_cases</dt>
<dd>A data frame of confirmed cases (confirm) by date
(date). confirm must be integer and date must be in date format.</dd>
<dt>seeding_time</dt>
<dd>Integer; seeding time, usually obtained using
<code>get_seeding_time()</code></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>. Set to <code>NULL</code> to switch to using back
calculation rather than generating infections using Rt.</dd>
<dt>gp</dt>
<dd>A list of options as generated by <code>gp_opts()</code> to define the
Gaussian process. Defaults to <code>gp_opts()</code>.Set to NULL to disable the
Gaussian process.</dd>
<dt>obs</dt>
<dd>A list of options as generated by <code>obs_opts()</code> defining the
observation model. Defaults to <code>obs_opts()</code>.</dd>
<dt>horizon</dt>
<dd>Numeric, forecast horizon.</dd>
<dt>backcalc</dt>
<dd>A list of options as generated by <code>backcalc_opts()</code> to
define the back calculation. Defaults to <code>backcalc_opts()</code>.</dd>
<dt>shifted_cases</dt>
<dd>A dataframe of delay shifted cases</dd></dl>

Arguments

Author

<a href='https://lifecycle.r-lib.org/articles/stages.html#stable'><img src='figures/lifecycle-stable.svg' alt='[Stable]' /></a>
Takes the output of <code>stan_opts()</code> and converts it into a list understood by
<code>stan</code>. Internally calls the other <code>create_</code> family of functions to
construct a single list for input into stan with all data required present.

Create Stan Data Required for estimate_infections — create_stan_data

<dl>

<dt>reported_cases</dt>
<dd>A data frame of confirmed cases (confirm) by date
(date). confirm must be integer and date must be in date format.</dd>


<dt>seeding_time</dt>
<dd>Integer; seeding time, usually obtained using
<code>get_seeding_time()</code></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>. Set to <code>NULL</code> to switch to using back
calculation rather than generating infections using Rt.</dd>


<dt>gp</dt>
<dd>A list of options as generated by <code>gp_opts()</code> to define the
Gaussian process. Defaults to <code>gp_opts()</code>.Set to NULL to disable the
Gaussian process.</dd>


<dt>obs</dt>
<dd>A list of options as generated by <code>obs_opts()</code> defining the
observation model. Defaults to <code>obs_opts()</code>.</dd>


<dt>horizon</dt>
<dd>Numeric, forecast horizon.</dd>


<dt>backcalc</dt>
<dd>A list of options as generated by <code>backcalc_opts()</code> to
define the back calculation. Defaults to <code>backcalc_opts()</code>.</dd>


<dt>shifted_cases</dt>
<dd>A dataframe of delay shifted cases</dd>

</dl>

Create Stan Data Required for estimate_infections

Data Engineering and BI courses are free this week!

create_stan_data: Create Stan Data Required for estimate_infections

Description

Usage

Value

Arguments

Author