Abstract

The COVID-19 pandemic has illustrated both the utility and limitation of using epidemic models for understanding and forecasting disease spread. One of the many difficulties in modelling epidemic spread is that caused by behavioural change in the underlying population. This can be a major issue in public health since, as we have seen during the COVID-19 pandemic, behaviour in the population can change drastically as infection levels vary, both due to government mandates and personal decisions. Such changes in the underlying population result in major changes in transmission dynamics of the disease, making the modelling challenges. However, these issues arise in agriculture and public health, as changes in farming practice are also often observed as disease prevalence changes. We propose a model formulation where time-varying transmission is captured by the level of alarm in the population and specified as a function of the past epidemic trajectory. The model is set in a data-augmented Bayesian framework as epidemic data are often only partially observed, and we can utilize prior information to help with parameter identifiability. We investigate the estimability of the population alarm across a wide range of scenarios, using both parametric functions and non-parametric Gaussian process and splines. The benefit and utility of the proposed approach is illustrated through an application to COVID-19 data from New York City.