Antibiotic prescribing in patients with COVID-19: A rapid review and meta-analysis

Purpose of this repository

This repository contains all code and data necessary to reproduce the analyses presented in the manuscript "Antibiotic prescribing in patients with COVID-19: rapid review and meta-analysis" by Langford et al (doi: 10.1016/j.cmi.2020.12.018). This includes every figure and supplementary figure except for figures 1 and 2. Table 1 is generated as part of the dashboard. Supplementary table 1 comprises a subset of the complete dataset found in the directory data.

This repository also contains the code necessary to reproduce the interactive R Shiny dashboard hosted at: https://brxad.shinyapps.io/covid-19-antibiotic/.

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.

Requirements

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.

All required R packages are listed at the top of global.R.

Reproducing the figures

Run manuscript_figs.R.

Running the dashboard

Run app.R.