asm-dhs

Repository for investigating the effects of ASM on child health using DHS data across Africa.

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Project Overview

This project will combine:

• Hydrologic watershed data (i.e., spatial hydrologic linkages across space)
• DHS socioeconomic and health data (household-level demographics and health outcomes)
• Artisanal and small-scale mining predictions estimated following Christensen et al. (2025), with extensions
• Regression analysis to estimate the relationship between hydrologic conditions and socioeconomic outcomes

Primary languages: R (analysis, visualization, regression), Python (geospatial preprocessing).

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Repository Structure

asm-dhs/
├── code/
│   ├── cleaning/       # Data ingestion and cleaning scripts
│   ├── analysis/       # Analysis and modeling scripts
│   └── utils/          # Shared helper functions    
├── output/
│   ├── figures/      # Generated plots and maps
│   ├── tables/       # Regression tables, summary statistics
│   └── models/       # Saved model objects (.rds, .rda)
├── docs/             # Project documentation and codebooks
│   └── data-dictionary.md
├── .gitignore
├── .Rprofile
├── asm-dhs.Rproj
├── renv.lock         # R package lock file (generated by renv)
└── README.md

Note on data: Raw and processed data should be stored outside github. Recommended structure:

• data/raw/
• data/temp/
• data/processed/

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Getting Started

Prerequisites

• R ≥ 4.3.0
• renv for R package management
• (Optional) Python ≥ 3.10 with geopandas, rasterio, pandas

Setup

# 1. Clone the repository
git clone https://github.com/<your-username>/asm-dhs.git
cd asm-dhs

# 2. Open asm-dhs.Rproj in RStudio (or start an R session here)

# 3. Restore the R package environment
Rscript -e "renv::restore()"

# 4. (Optional) Set up Python environment
python -m venv .venv
source .venv/bin/activate
pip install -r python/requirements.txt

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Workflow

• Cleaning scripts live under code/cleaning/ and are numbered in run order.
• Analysis scripts live under code/analysis/.
• Shared helpers live under code/utils/.
• Runnable scripts should bootstrap with:

  source(here::here("code", "utils", "config.R"))
  source(here::here("code", "utils", "project_paths.R"))

Scripts should be numbered within subdirectory following the order in which they should be run.

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Reproducibility

This project uses renv to snapshot R package versions. After any package install or update, run:

renv::snapshot()

and commit the updated renv.lock.

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Data storage

See docs/data-dictionary.md for the current data layout.

Contributing

Please read CONTRIBUTING.md before submitting changes. Use task-based branching and tag other contributors for review when merging a branch back to main.