SimInf_indiv_events-class

Class <code>"SimInf_indiv_events"</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>.

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 

SimInf_indiv_events-class function

<dl>
<dt><code>id</code></dt>
<dd>an integer or character identifier of the individual.</dd></dl>
<dt><code>event</code></dt>
<dd>four event types are supported: exit,
enter, internal transfer, and external
transfer. When assigning the events, they can either be
coded as a numerical value or a character string: exit;
<code>0</code> or <code>'exit'</code>, enter; <code>1</code> or
<code>'enter'</code>, internal transfer; <code>2</code> or
<code>'intTrans'</code>, and external transfer; <code>3</code> or
<code>'extTrans'</code>.</dd>
<dt><code>time</code></dt>
<dd>an integer, character, or date (of class <code>Date</code>)
for when the event occured. If it's a character it must be
able to coerce to <code>Date</code>.</dd>
<dt><code>node</code></dt>
<dd>an integer or character identifier of the source node.</dd>
<dt><code>dest</code></dt>
<dd>an integer or character identifier of the destination
node.</dd>

Slots

Class "SimInf_indiv_events" — SimInf_indiv_events-class

<dl>
<dt><code>id</code></dt>
<dd>an integer or character identifier of the individual.</dd>


<dt><code>event</code></dt>
<dd>four event types are supported: exit,
enter, internal transfer, and external
transfer. When assigning the events, they can either be
coded as a numerical value or a character string: exit;
<code>0</code> or <code>'exit'</code>, enter; <code>1</code> or
<code>'enter'</code>, internal transfer; <code>2</code> or
<code>'intTrans'</code>, and external transfer; <code>3</code> or
<code>'extTrans'</code>.</dd>


<dt><code>time</code></dt>
<dd>an integer, character, or date (of class <code>Date</code>)
for when the event occured. If it's a character it must be
able to coerce to <code>Date</code>.</dd>


<dt><code>node</code></dt>
<dd>an integer or character identifier of the source node.</dd>


<dt><code>dest</code></dt>
<dd>an integer or character identifier of the destination
node.</dd>


</dl>

SimInf_indiv_events-class: Class `"SimInf_indiv_events"`

Description

Arguments

Slots