Aaron A. King, Ph.D.

Nelson G. Hairston Collegiate Professor of Ecology, Evolutionary Biology,
Complex Systems, and Mathematics, University of Michigan
External Professor, Santa Fe Institute
Fellow of the American Association for the Advancement of Science

Choices and trade-offs in inference with infectious disease models

S. Funk and A. A. King
Epidemics 30:  100383, 2020.

Inference using mathematical models of infectious disease dynamics can be an invaluable tool for the interpretation and analysis of epidemiological data. However, researchers wishing to use this tool are faced with a choice of models and model types, simulation methods, inference methods and software packages. Given the multitude of options, it can be challenging to decide on the best approach. Here, we delineate the choices and trade-offs involved in deciding on an approach for inference, and discuss aspects that might inform this decision. We provide examples of inference with a dataset of influenza cases using the R packages pomp and rbi.

The official version of the paper is here.   Please contact Prof. King if you'd like a reprint.

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