# NAITRE-primary
Public repository for the primary mortality analysis of the NAITRE trial: Neonates and Azithromycin: An Innovation in the Treatment of Children
## Description
This repo includes the R code to complete all analyses for the article:
_Neonatal Azithromycin Administration for Prevention of Infant Mortality_, Oldenburg et al. _NEJM Evidence_ 2022. https://doi.org/10.1056/EVIDoa2100054
https://evidence.nejm.org/doi/full/10.1056/EVIDoa2100054
This workflow is also mirrored on a public GitHub repository: https://github.com/proctor-ucsf/NAITRE-primary/blob/main/README.md
## To run the analyses
1. Clone the GitHub repository
2. Download the two analysis datasets under `Data` and save them in a subdirectory named: `NAITRE-primary/data/final`
3. Create a subdirectory to save the analysis output: `NAITRE-primary/output/`
4. Run the `.Rmd` files in the `NAITRE-primary/code/analysis` directory. They will generate `.html` files in the output directory with the results.
We have archived the `.html` output files from the final analysis under `Data/Notebooks` here.
*NOTE: Scripts 7-8 were analyses added only during peer review as robustness checks and to provide contextual information for the discussion.*
## System Requirements
All analyses were run using R software version 4.1.1 on Mac OSX Catalina using the RStudio IDE (https://www.rstudio.com).
```> sessionInfo()```
```R version 4.1.1 (2021-08-10)```
```Platform: x86_64-apple-darwin17.0 (64-bit)```
```Running under: macOS Catalina 10.15.7```
## Installation Guide
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 NAITRE-primary-Config.R.
The installation time should be < 10 minutes total on a typical desktop computer.
