UNCIDD/cholera-units

Cholera Transmission Units in Africa # cholera-units Cholera Transmission Units in Africa ### Code accompanying: *Defining Epidemiologically Relevant Units of Cholera Transmission in sub-Saharan Africa* Bethany L. DiPrete, Javier Perez-Saez, Shirlee Wohl, Nathaniel Matteson, Seungwon Kim, Andrew S. Azman, Justin Lessler medRxiv 2025.06.06.25329161; doi: doi.org --- ## Overview This repository contains the data processing, Bayesian modeling, simulation, and visualization workflows used to investigate how the choice of epidemiological unit influences inference about cholera transmission dynamics across sub-Saharan Africa. The analysis combines: - WHO annual cholera case reports - Lineage calls from *Vibrio cholerae* genomic sequence data - Output from phylogeographic reconstructions - Bayesian Hidden Markov Models (HMMs) implemented in Stan - Simulation-based analyses of introductions and transmission --- ## Repository Structure ```text cholera-units/ ├── analysis/ │ ├── 00_functions_settings.R │ ├── 01_initial_data_prep.R │ ├── 02_import_data.R │ ├── 03_create_partitions.R │ ├── 04_hmm_setup.R │ ├── 05_run_hmm.R │ ├── 06_post_hmm_stats.R │ ├── 07_hmm_clustering.R │ ├── 08_phylogeography_clustering.R │ ├── 09_sim_outbreaks_poststan.R │ ├── 10_arrival_times.R │ ├── 11_downsampling_analysis.R │ ├── 12_Figure1.R │ ├── 13_Figure3.R │ ├── 14_Figure4.R │ ├── 15_Figure5.R │ ├── 16_Supplemental_Figures.R │ ├── run_sims/ │ └── stan/ │ └── hmm_fb_model_connectivity.stan │ ├── data/ │ └── raw/ │ ├── who_annual_case_reports.csv │ ├── sequences.csv │ ├── introductions_w.csv │ ├── UN_regions.csv │ └── phylogeography/ │ ├── notebooks/ │ ├── 01_hmm_results.Rmd │ ├── 02_hmm_diagnostics.Rmd │ └── generate_reports/ │ └── README.md ``` --- ## Analysis Workflow ### 1. Data Preparation The workflow begins by harmonizing surveillance and genomic data. | Script | Purpose | |----------|---------- …