Data for SARS­-CoV-­2 Reinfection Trends in South Africa: Monthly Report (2022-10-04)

This version contains a single file, with time series data for the most recent monthly report on SARS­-CoV-­2 Reinfection Trends in South Africa: <code>ts_data.csv</code> - national daily time series of newly detected putative primary infections (<code>cnt</code>), suspected second infections (<code>reinf</code>), suspected third infections (<code>third</code>), and suspected fourth infections (<code>fourth</code>) by specimen receipt date (<code>date</code>) Note: There may be some inconsistencies with the numbers of infections through time in earlier versions of this data set due to back-filling of late-arriving data. Note: Earlier versions of this data set included data files for Pulliam, JRC, C van Schalkwyk, B Lombard, N Govender, A von Gottberg, C Cohen, MJ Groome, J Dushoff, K Mlisana, and H Moultrie. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. DOI: 0.1126/science.abn4947 For code and more details see: https://github.com/jrcpulliam/reinfections/releases/tag/v3.0 or 10.5281/zenodo.6108448 The version of this data set associated with the publication (available via the links above) included the following files: <code>ts_data.csv</code> - national daily time series of newly detected putative primary infections (<code>cnt</code>), suspected second infections (<code>reinf</code>), suspected third infections (<code>third</code>), and suspected fourth infections (<code>fourth</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) <code>emp_haz_sens_an.RDS</code> - output of sensitivity analysis of relative empirical hazard estimation to assumed observation probabilities (as used in the manuscript)