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tsiR: An R package for time-series Susceptible-Infected-Recovered models of epidemics
Alexander D Becker1, Bryan T Grenfell1,2,3
1Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States of America.
Abstract:
tsiR is an open source software package implemented in the R programming language designed to analyze infectious disease time-series data. The software extends a well-studied and widely-applied algorithm, the time-series Susceptible-Infected-Recovered (TSIR) model, to infer parameters from incidence data, such as contact seasonality, and to forward simulate the underlying mechanistic model. The tsiR package aggregates a number of different fitting features previously described in the literature in a user-friendly way, providing support for their broader adoption in infectious disease research. Also included in tsiR are a number of diagnostic tools to assess the fit of the TSIR model. This package should be useful for researchers analyzing incidence data for fully-immunizing infectious diseases.
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