plot,SimInf_pfilter-method

Diagnostic plot of a particle filter object

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 

plot,SimInf_pfilter-method function

<dl><dt>x</dt>
<dd>The <code>SimInf_pfilter</code> object to plot.</dd>
<dt>y</dt>
<dd>If y is <code>NULL</code> or missing (default), the filtered
trajectory (top) and the effective sample size (bottom) are
displayed. If <code>y</code> is a character vector or a formula, the
plot function for a <code>SimInf_model</code> object is called with
the filtered trajectory, see
<code>plot,SimInf_model-method</code> for more details about
the specification a plot.</dd>
<dt>...</dt>
<dd>Other graphical parameters that are passed on to the
plot function.</dd></dl>

Arguments

Diagnostic plot of a particle filter object — plot,SimInf_pfilter-method

<dl>

<dt>x</dt>
<dd>The <code>SimInf_pfilter</code> object to plot.</dd>


<dt>y</dt>
<dd>If y is <code>NULL</code> or missing (default), the filtered
trajectory (top) and the effective sample size (bottom) are
displayed. If <code>y</code> is a character vector or a formula, the
plot function for a <code>SimInf_model</code> object is called with
the filtered trajectory, see
<code>plot,SimInf_model-method</code> for more details about
the specification a plot.</dd>


<dt>...</dt>
<dd>Other graphical parameters that are passed on to the
plot function.</dd>

</dl>

plot,SimInf_pfilter-method: Diagnostic plot of a particle filter object

Description

Usage

Arguments