Data set for Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa

Data files for Pulliam, JRC, C van Schalkwyk, N Govender, A von Gottberg, C Cohen, MJ Groome, J Dushoff, K Mlisana, and H Moultrie. (2021) Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa. <em>medRxiv</em> DOI: 10.1101/2021.11.11.21266068 For code and more details see: https://github.com/jrcpulliam/reinfections <code>ts_data.csv</code> - national daily time series of newly detected putative primary infections (<code>inc_1</code>) and suspected reinfections (<code>inc_2</code>) by specimen receipt date (<code>date</code>) <code>demog_data.csv</code> - counts of individuals eligible for reinfection (<code>total</code>), who have 0 suspected reinfections (<code>no_reinf</code>) or &gt;0 suspected reinfections (<code>reinf</code>) by province (<code>province</code>), age group (5-year bands, <code>agegrp5</code>), and sex (M = Male, F = Female, U = Unknown, <code>sex</code>) <code>posterior_90_null.RData</code> - posterior samples from the MCMC fitting procedure (as used in the manuscript) <code>sim_90_null.RDS</code> - simulation results (as used in the manuscript)