medaed89/algeria-climate-leishmaniasis

Reproducible analysis of climate and cutaneous leishmaniasis in Algeria, 2000–2024 # Climate and cutaneous leishmaniasis in Algeria Reproducibility repository for: > **Temperature seasonality and spatial confounding of cutaneous leishmaniasis in Algeria: a source-verified national panel, 2000–2024** The repository contains the final 48-wilaya × 25-year analysis panel, MATLAB code for the reported models, independent Python implementations of the spatial models, and the corresponding results and figures. ## Repository structure ```text . ├── code/ │ ├── matlab/ reported NB2, Mundlak, spatial and diagnostic analyses │ └── python/ independent BYM2, MCMC, figures and data utilities ├── data/ finalized analysis inputs ├── figures/ publication figures ├── results/ │ ├── matlab/ reported numerical outputs │ ├── python/ independent spatial-model checks │ └── tables/ supporting descriptive tables └── tests/ fast integrity and repository checks ``` Only finalized, analysis-ready files are included. Raw surveillance bulletins and ERA5 downloads are not redistributed; their public sources are described in `data/README.md`. ## Requirements ### MATLAB - MATLAB R2020b or later - Statistics and Machine Learning Toolbox - Optimization Toolbox ### Python - Python 3.11 - Packages pinned in `requirements.txt` Create an isolated environment from the repository root: ```bash python -m venv .venv python -m pip install --upgrade pip python -m pip install -r requirements.txt ``` Install `requirements-era5.txt` only when repeating the ERA5-Land extraction or rebuilding the polygon contiguity graph. ## Reproduce the reported MATLAB analysis The master script resolves every path from its own location, so it can be launched from any MATLAB working directory: ```matlab run("code/matlab/MASTER_final_analysis.m") ``` Outputs are written to `results/matlab/`. The primary spatial specification is the BYM2 convolution implemented by `fitBYM2true.m`. The distinct scaled Leroux sensitivity is im …