ALL-IN-META-BCG-CORONA R code to reproduce analysis and figures

Abstract

This R code reproduces all figures and tables in the manuscript: Ter Schure et al. (2022) Bacillus Calmette-Guérin vaccine to reduce COVID-19 infections and hospitalisations in healthcare workers – a living systematic review and prospective ALL-IN meta-analysis of individual participant data from randomised controlled trials* All analyses are based on summary statistics, since the ALL-IN-META-BCG results are based on two-stage analyses. The summary statistics are included as .csv-files in the Data zip file. The code that produces the summary statistics is also available, with synthetic data added in the DataSynthetic zip file to try it out. *Unfortunately, Figure 4 (Exact logrank e-values for COVID-19 infections and hospitalisations) and Figure 7 (Sequences of anytime-valid confidence intervals for the trials and the meta-analysis) in the MedRxiv manuscript of December 19 2022 are based on outdated results for the SA trial. Fortunately, the abstract and discussion section show the up-to-date trial results, as well as all other figures and tables in the manuscript. The updated Figure 4 and Figure 7 are qualitatively similar to the figures in the manuscript, and included in the Data zip file attached.