This repository contains all data and code necessary to reproduce the analyses presented in the manuscript "Antibiotic resistance associated with the COVID-19 pandemic: a systematic review and meta-analysis" by Langford et al (doi: 10.1016/j.cmi.2022.12.006). This includes every figure and table except for figure 1 and table 1. Table 1 is a subset of the dataset found in the file data/amr.csv. Note that the analysis script produces additional figures beyond those directly presented in the manuscript.
All code is written in the R programming language. 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 analysis script should run with any modern version of R.
The R packages required to reproduce the figures are listed at the top of the analysis script. They must be installed using install.packages or similar functionality within RStudio prior to running the script.
Run analysis.R to create the output figures.
