Predictors and Microbiology of Co-Infection in Patients with COVID-19: Living Rapid Review Update and Meta-Regression
This repository contains all code and data necessary to reproduce the analyses presented in the manuscript "Predictors and microbiology of respiratory and bloodstream bacterial infection in patients with COVID-19: living rapid review update and meta-regression" by Langford et al (doi: 10.1016/j.cmi.2021.11.008). This includes every table and figure except for figure 1, figure 4, supplementary table 3 and supplementary table 4. Supplementary table 1 comprises a subset of the complete dataset found in the directory data. Note that the included scripts may produce figures and tables beyond what are directly presented in the manuscript.
For more details on the methodological approach used in this meta-analysis, please see the manuscript Meta-analysis of Proportions Using Generalized Linear Mixed Models by Lin & Chu (2020) and the sample code they provide.
All code is written in the programming language R. It is mostly easily run using the IDE RStudio. An .Rproj file is included with this repository for your convenience.
The R packages required to reproduce the tables and figures at listed at the top of their respective scripts. They must be installed using install.packages prior to running the script.
Run tables.R.
Run figures.R.