This repository contains code used to analyse the spread of SARS-CoV-2 in Australia. This includes a modelling framework for estim ating the current and potential reproduction number in various states in periods with high, low, and no transmission. These methods are described in the published article:

Nick Golding, David J Price, Gerard Ryan, Jodie McVernon, James M McCaw, Freya M Shearer (2023) A modelling approach to estimate the transmissibility of SARS-CoV-2 during periods of high, low, and zero case incidence eLife 12:e78089.