k-dilillo/Estimating-COVID19-Exposure-in-Kenya
Domain:
healthcareRecord type:
project
Creator:
k-d
Host:
# 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 |
|--------|--------------------|--------| …