Primary analysis for the AVENIR trial
This repository includes R code to run all of the analysis for the paper:
O'Brien et al. Azithromycin to reduce mortality: an adaptive cluster-randomized trial (in press).
This work was funded by the Bill & Melinda Gates Foundation (grants OPP1210548 and INV-002454), and was registered under clinical trial NCT04224987
Should you have any questions about the files in this repository, please contact Ben Arnold at UCSF (ben.arnold@ucsf.edu{.email}) or the corresponding author for the paper.
This GitHub repository is mirrored on the Open Science Framework (OSF). The OSF project page includes additional study-related resources, including the compiled HTML computational notebooks created from the .Rmd files, and the final analysis datasets.
Following: https://www.nature.com/documents/nr-software-policy.pdf
All analyses were run using R software version 4.3.2 on macOS Monterey using the RStudio IDE (https://www.rstudio.com).
> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6
You can download and install R from CRAN: https://cran.r-project.org
You can download and install RStudio from their website: https://www.rstudio.com
All R packages required to run the analyses are sourced in the file AVENIR-primary-Config.R.
To reproduce all analyses in the paper, we recommend that you:
- Clone the GitHub repository to your computer
For example, in the location on your computer where you would like to clone the repository, you could type into the Terminal command:
git clone https://github.com/proctor-ucsf/AVENIR-primary.git
- Recreate the exact package environment using the
renvpackage.
You can do this by opening the R project file (AVENIR-primary-analysis.Rproj) in RStudio, loading the renv package, and typing renv::restore() to restore the package environment from the projects renv.lock file.
- All of the analysis scripts should run smoothly (scripts
0-xx.Rmdto9-xx.Rmd) EXCEPT for two of them:1-AVENIR-primary-CONSORT-flow.Rmdand5-AVENIR-primary-enrollment-map.Rmd. Script 1 creates the CONSORT flow numbers and relies on a few idiosyncratic, internal lists to identify clusters that could not be randomized — we did not make those files public. Script 5 relies on GPS information, which are considered identifiable and are not provided in the public datasets. All other scripts will run smoothly. The first script,0-AVENIR-primary-download-public-data.R, will download the public datasets to your local repository in the/datadirectory. The.Rmdfiles will save HTML file output as well as figures and summary estimates in the/outputdirectory.
You can run the .Rmd notebook scripts one-by-one or you can compile AVENIR-primary-run-all.R, which is the file we used to run the final analyses (e.g., from the command line R CMD BATCH AVENIR-primary-run-all.R &).
This project is covered by the CC0 1.0 Universal license.