package_skeleton

Describe your model in a logical way in R, then <code>mparse</code>
creates a <code>SimInf_model</code> object with your model
definition that can be installed as an add-on R package.

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>.

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>The <code>model</code> <code>SimInf_model</code>
object with your model to create the package skeleton from.</dd>
<dt>name</dt>
<dd>Character string with the package name. It should
contain only (ASCII) letters, numbers and dot, have at least
two characters and 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 '.'
i.e. the current directory.</dd>
<dt>author</dt>
<dd>Author of the package.</dd>
<dt>email</dt>
<dd>Email of the package maintainer.</dd>
<dt>maintainer</dt>
<dd>Maintainer of the package.</dd>
<dt>license</dt>
<dd>License of the package. Default is 'GPL-3'.</dd></dl>

Arguments

Create a package skeleton from a SimInf_model — package_skeleton

<dl>

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


<dt>name</dt>
<dd>Character string with the package name. It should
contain only (ASCII) letters, numbers and dot, have at least
two characters and 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 '.'
i.e. the current directory.</dd>


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


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


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


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

</dl>

package_skeleton: Create a package skeleton from a `SimInf_model`

Description

Usage

Value

Arguments

References