Data for SARS­-CoV-­2 Reinfection Trends in South Africa: Monthly Report (2022-12-07)

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:

ts_data.csv - national daily time series of newly detected putative primary infections (cnt), suspected second infections (reinf), suspected third infections (third), and suspected fourth infections (fourth) by specimen receipt date (date)

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:

ts_data.csv - national daily time series of newly detected putative primary infections (cnt), suspected second infections (reinf), suspected third infections (third), and suspected fourth infections (fourth) by specimen receipt date (date)

demog_data.csv - counts of individuals eligible for reinfection (total), who have 0 suspected reinfections (no_reinf) or >0 suspected reinfections (reinf) by province (province), age group (5-year bands, agegrp5), and sex (M = Male, F = Female, U = Unknown, sex)

posterior_90_null.RData - posterior samples from the MCMC fitting procedure (as used in the manuscript)

sim_90_null.RDS - simulation results (as used in the manuscript)

emp_haz_sens_an.RDS - output of sensitivity analysis of relative empirical hazard estimation to assumed observation probabilities (as used in the manuscript)