Choices and trade-offs in inference with infectious disease models
Sebastian Funk1, Aaron A King2
1Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK.
None:
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.
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