Estimating transmission parameters from stochastic epidemic models using survival analysis techniques

Compartmental models based on ordinary differential equations quantifying the interactions between susceptible, infectious and recovered individuals within a population have played an important role in infectious disease modelling. The aim of the present paper is to explain the link between stochastic epidemic models based on the susceptible-infectious-recovered (SIR) model and methods from survival analysis. We illustrate how standard software for survival analysis in the statistical language R can be used to estimate pivotal parameters in the stochastic SIR model in the very much idealized situation where the epidemic is completely observed. Extensions incorporating interventions, age structure and heterogeneity are explored and illustrated.