armelbatchi/agroecology-ssa-transitions-code

R code and supporting materials for a multi-country study of agroecological transitions and food system resilience in Sub-Saharan Africa # Agroecological Transitions in Sub-Saharan Africa — Public Code Repository This repository contains the public code used for the manuscript on agroecological transitions and food system resilience in Sub-Saharan Africa. ## Repository contents - `Figures_agroeconomic-paper_public.Rmd` — figure-generation workflow - `Code_supplementary_information_public.Rmd` — supplementary analyses workflow - `README.md` — repository overview and usage notes - `.gitignore` — protects local private data and generated outputs from accidental upload - `LICENSE` — code license - `CITATION.cff` — citation metadata for the repository ## Important data note This public repository does **not** include raw household-level data. The underlying study data contain sensitive and potentially identifying information and should remain local and private. Do **not** upload raw data, participant-level data, exact site identifiers, GPS files, or confidential records to GitHub. ## How to use this repository 1. Clone or download the repository locally. 2. Keep your de-identified working datasets in a local `data/` folder that is **not** tracked by GitHub. 3. Open the R Markdown files in RStudio. 4. Update any local file references if needed so they point to your private local `data/` folder. 5. Run the scripts locally to generate figures and supplementary outputs. ## Expected local input files The scripts are designed to use local input files stored in a private `data/` directory. These files are not included in the public repository. Expected filenames include: - `data/deidentified_analytic_dataset.csv` - `data/hdds_long.csv` - `data/yield_stability_long.csv` - `data/practice_adoption_by_country.csv` - `data/sites_public.csv` - `data/figure3_yields.csv` - `data/figure4_biodiversity.csv` - `data/figure5_soil_health.csv` - `data/figure6_income.csv` - `data/figure6_dietary_diversity.csv` - `data/figure6_gender.csv` - `data/figure6_yield_stability.csv` ## Reproducibility All analyses were con …