A flexible and efficient framework for data-driven stochastic disease spread simulations

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SimInf

The 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.

Installation

You can install the released version of SimInf from CRAN

install.packages("SimInf")

or use the remotes package to install the development version from GitHub

library(remotes)
install_github("stewid/SimInf")

We refer to section 3.1 in the vignette for detailed installation instructions.

Authors

In alphabetical order: Pavol Bauer ORCID iD, Robin Eriksson ORCID iD, Stefan Engblom ORCID iD, and Stefan Widgren ORCID iD (Maintainer)

Any suggestions, bug reports, forks and pull requests are appreciated. Get in touch.

Acknowledgments

This work was financially supported by the Swedish Research Council within the UPMARC Linnaeus centre of Excellence (Pavol Bauer, Robin Eriksson and Stefan Engblom), the Swedish Research Council Formas (Stefan Engblom and Stefan Widgren), the Swedish Board of Agriculture (Stefan Widgren), and by the Swedish strategic research program eSSENCE (Stefan Widgren).

License

The SimInf package is licensed under the GPLv3.