EpiFire: An open source C++ library and application for contact network epidemiology
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Background: Contact network models have become increasingly common in epidemiology, but we lack a flexible programming framework for the generation and analysis of epidemiological contact networks and for the simulation of disease transmission through such networks. Results: Here we present EpiFire, an applications programming interface and graphical user interface implemented in C++, which includes a fast and efficient library for generating, analyzing and manipulating networks. Network-based percolation and chain-binomial simulations of susceptible-infected-recovered disease transmission, as well as traditional non-network mass-action simulations, can be performed using EpiFire. Conclusions: EpiFire provides an open-source programming interface for the rapid development of network models with a focus in contact network epidemiology. EpiFire also provides a point-and-click interface for generating networks, conducting epidemic simulations, and creating figures. This interface is particularly useful as a pedagogical tool.
Thomas Hladish, Luis Alberto Barrera, and Lauren Ancel Meyers are with the Section of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA. -- Eugene Melamud is with the Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA. -- Luis Alberto Barrera is with Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. -- Alison Galvani is with the Department of Epidemiology and Public Health, Yale University Medical School, New Haven, CT 06520, USA. -- Lauren Ancel Meyers is with the Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA.