UNCIDD/cholera-units: v1.0.0 Initial release

This release contains the code, data, and computational workflows used for the analyses presented in: Defining Epidemiologically Relevant Units of Cholera Transmission in sub-Saharan Africa DiPrete BL, Perez-Saez J, Wohl S, Matteson N, Kim S, Azman AS, Lessler J Under Review Included components This release includes: Datasets used in analysis pipeline Data processing workflows Bayesian Hidden Markov Model implementation in Stan Clustering analyses to define transmission units Simulation studies Figure-generation scripts Reproducibility documentation Software environment specifications Reproducibility The repository contains data and code required to reproduce the analyses and figures presented in the manuscript. Scripts are organized sequentially within the analysis/ directory, beginning with data preparation and ending with figure generation. Datasets are stored within the data/raw directory Citation If you use this repository, please cite both the manuscript and the Zenodo record associated with this release.