An R Package for Mathematical Modeling of Infectious Disease over Networks

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Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel, designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel,designed to facilitate the exploration of novel research questions for advanced modelers.
Keywords: mathematical model, infectious disease, epidemiology, networks, R.
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Section 5 outlines the generalized EpiModel API for extending the disease states and modules
to address new research questions. Extension modules can be written to either
modify the existing functions or to build entirely new processes into the epidemic system.
We show examples of both