ABSTRACT
Infectious disease dynamics mathematical models have a long history, dating back over a century. Simple mathematical formulations describing individuals' transition in a population between “compartments” that capture their infection status yield surprisingly significant insight. Their elegance and simplicity make it simple to expand to more complexities by adding compartments. This chapter presents some classical compartment models, such as the SIR and SEIR models, and their characteristics are also discussed. It demonstrates how to use compartment models in the R environment to predict the course of an epidemic by calculating associated parameters between compartments, such as the rate of infection or recovery. The chapter introduces the concept of the basic reproduction number, the effective reproduction number, and herd immunity. The simplicity of the SIS model makes it easy to compute and understand the trajectory of the disease.
