This repository contains all data and code necessary to reproduce the analyses presented in the manuscript "Antimicrobial resistance in patients with COVID-19: a systematic review and meta-analysis" by Langford et al. (doi: 10.1016/j.cmi.2022.12.006). This includes every table and figure except for figure 1, supplementary table 1 and supplementary table 3. Supplementary table 1 is a subset of the dataset found in the file data.csv. Supplementary table 3 is also calculated from this dataset. Note that the included scripts produces additional figures beyond those 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). Sample code is also provided.
All code is written in the programming language R. The easiest way to run it is to use the RStudio IDE. An .Rproj file is included with this repository for ease of use with RStudio. The scripts should run with any modern version of R.
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 or similar functionality within RStudio prior to running the script.
Run analysis.R to create the output tables and figures.