k-dilillo/Estimating-COVID19-Exposure-in-Kenya

# Estimating-COVID19-Exposure-in-Kenya --- ## Overview This repository contains all code to reproduce the analysis and figures in the manuscript: **"Estimating SARS-CoV-2 exposure in asymptomatic hospitalized children with cancer in Western Kenya: a retrospective analysis of serological data"** --- ## Repository structure ``` ├── scripts/ # R scripts (run in order) ├── data/ │ ├── raw/ # Downloaded .xlsx input — see Data section (not tracked in git) │ └── processed/ # Generated by scripts (not tracked in git) ├── results/ # Generated by scripts (not tracked in git) │ ├── figures/ # PDF figure outputs │ └── tables/ # CSV outputs │ └── supp_figures/ # PDF supplementary figure outputs ├── renv/ # renv enviornment files └── renv.lock # R package lockfile ``` --- ## Requirements All analyses were conducted in R version 4.5.1 on macOS Sonoma (14.6.1) Dependencies are managed with `renv`. To restore the exact package versions used in the analysis: 1. Clone the GitHub repo 2. Restore project dependencies: ```r if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv") renv::restore() ``` 3. Load all packages before running any scripts: ```r source("scripts/00_load_packages.R") ``` --- ## Data Serology data and associated metadata are publicly available in the Supporting Information of the manuscript. **Download the `.xslx` files from the manuscript and store in the `data/raw/` directory** --- ## Reproducing the figures Run scripts sequentially, ensuring all required upstream scripts (as indicated by dependencies in the script names) are executed first. Each script saves its outputs to `results/main_figures/`, `results/supp_figures/`, and `results/tables/`, as appropriate. Figures and tables will be stored as PDF and CSV files, respectively. #### Main tables & figures | Table/Figure | Description | Script | |--------|--------------------|--------| …