package_skeleton

Generate a source package directory from a
<code>SimInf_model</code> object, allowing the model to be
installed as a standalone add-on R package. This is useful for
distributing custom models or for improving startup performance by
compiling the C code once during package installation rather than
on the first call to <code>run()</code>.

Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models. For more details see the paper by
Widgren, Bauer, Eriksson and Engblom (2019)
<doi:10.18637/jss.v091.i12>. The package also provides
functionality to fit models to time series data using the
Approximate Bayesian Computation Sequential Monte Carlo
('ABC-SMC') algorithm of Toni and others (2009)
<doi:10.1098/rsif.2008.0172> or the Particle Markov Chain Monte
Carlo ('PMCMC') algorithm of 'Andrieu' and others (2010)
<doi:10.1111/j.1467-9868.2009.00736.x>.

Stefan Widgren

SimInf

A Framework for Data-Driven Stochastic Disease Spread
Simulations

Robin Eriksson

Stefan Engblom

Pavol Bauer

Thomas Rosendal

Ivana Rodriguez Ewerlöf

Attractive Chaos 

package_skeleton function

<dl><dt>model</dt>
<dd>A <code>SimInf_model</code> object to create
the package skeleton from.</dd>
<dt>name</dt>
<dd>Character string with the package name. It must
contain only ASCII letters, numbers, and dots; have at least
two characters; start with a letter; and not end in a dot.
The package name is also used for the class name of the model
and the directory name of the package.</dd>
<dt>path</dt>
<dd>Path to put the package directory in. Default is
<code>"."</code> (the current directory).</dd>
<dt>author</dt>
<dd>Author of the package.</dd>
<dt>email</dt>
<dd>Email address of the package maintainer.</dd>
<dt>maintainer</dt>
<dd>Maintainer of the package.</dd>
<dt>license</dt>
<dd>License of the package. Default is <code>"GPL-3"</code>.</dd></dl>

Arguments

Create a package skeleton from a SimInf_model — package_skeleton

<dl>

<dt>model</dt>
<dd>A <code>SimInf_model</code> object to create
the package skeleton from.</dd>


<dt>name</dt>
<dd>Character string with the package name. It must
contain only ASCII letters, numbers, and dots; have at least
two characters; start with a letter; and not end in a dot.
The package name is also used for the class name of the model
and the directory name of the package.</dd>


<dt>path</dt>
<dd>Path to put the package directory in. Default is
<code>"."</code> (the current directory).</dd>


<dt>author</dt>
<dd>Author of the package.</dd>


<dt>email</dt>
<dd>Email address of the package maintainer.</dd>


<dt>maintainer</dt>
<dd>Maintainer of the package.</dd>


<dt>license</dt>
<dd>License of the package. Default is <code>"GPL-3"</code>.</dd>

</dl>

package_skeleton: Create a package skeleton from a `SimInf_model`

Description

Usage

Value

Arguments

Details

References

See Also