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| Authors: | Stefan Widgren, Pavol Bauer, Robin Eriksson, Stefan Engblom | ||||
| Title: | SimInf: An R Package for Data-Driven Stochastic Disease Spread Simulations | ||||
| Abstract: | We present the R package SimInf which 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 divide work over multiple processors ensures high performance when simulating a sample outcome. One of our design goals was to make SimInf extendable and enable usage of the numerical solvers from other R extension packages in order to facilitate complex epidemiological research. In this paper, we provide a technical description of the framework and demonstrate its use on some basic examples. We also discuss how to specify and extend the framework with user-defined models. | ||||
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Page views:: 2815. Submitted: 2017-06-22. Published: 2019-11-12. |
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| Paper: |
SimInf: An R Package for Data-Driven Stochastic Disease Spread Simulations
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| DOI: |
10.18637/jss.v091.i12
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This work is licensed under the licenses Paper: Creative Commons Attribution 3.0 Unported License Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license. |