The basic reproduction number (R0) describes the expected number of secondary cases for a primary case in a completely susceptible population and is a key parameter in understanding the growth of cases, the potential impact of intervention, the vaccination rate required to achieve herd immunity, and the potential final size of an epidemic. Additionally, the effective reproduction number (Rt), which is the expected number of secondary cases in a general population, provides context on the impact of intervention, changes in population behaviour, and size of the susceptible population. Both measures depend on a number of underlying modelling, data, and assumptions. This talk will provide an overview of some of the considerations for interpreting R0 and Rt and how to fit to data.

Function factories and lazy evaluation in R talk

Introduction to the method for calculating the reproduction number from a general compartmental model with application to vaccination

A short introduction to version control concepts and the use of git in Rstudio

Slides for CEFI short course 2023