jrcpulliam/reinfections

SARS-CoV-2 reinfection trends in South Africa: analysis of routine surveillance data (Pulliam et al. 2021) # SARS-CoV-2 reinfection trends in South Africa: analysis of routine surveillance data This repository provides code and data for the analyses presented in: > Pulliam, JRC, C van Schalkwyk, N Govender, A von Gottberg, C Cohen, MJ Groome, J Dushoff, K Mlisana, and H Moultrie. (2022) _Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa_. _Science_ DOI: 10.1126/science.abn4947 **The materials in this repository are made available under a CC-BY-NC 4.0 International License. See the LICENSE file for additional information.** Note: An early release this repository (v1.0) contained a large simulation output file (>50 MB), which caused it to take a long time to download / clone when using a slow internet connection. This and another moderately large file have been removed from the repository but can be downloaded from elsewhere (see the **Output files** section for more details) or recreated using the code provided. If you have questions or comments, please contact the repository maintainer, Juliet Pulliam, at . ## Software requirements - R - a statistical programming language (download links for Windows, Linux, and MacOS) - R Studio (recommended)- a user interface for R (download link) The following R packages are required to run the code in this repository (version numbers indicate the versions used for manuscript preparation): - coda (0.19-4) - colorspace (2.0-1) - data.table (1.14.0) - ggplot2 (3.3.4) - hexbin (1.28.2) - jsonlite (1.7.2) - lme4 (1.1-27.1) - Matrix (1.3-4) - patchwork (1.1.1) - uniformly (0.1.0) ## Pipeline files The files listed below are located in the main directory: - `Makefile` - full pipeline via GNU Make (requires use of Unix-like command line); see for more information - `pub.json` - configuration file used for manuscript preparation - `test.json` - test configuration file (useful to see how the code works without requiring intensive computation) - `reinfections_pub.Rproj` - R project file, …