Xcept-Health/episia

Python toolkit for epidemiological modelling and reporting. SIR/SEIR/SEIRD compartmental models, sensitivity analysis, interactive visualisations, and automated HTML/Markdown/JSON reports, built for low-resource health contexts. **Open-source epidemiology & biostatistics for Python** *epi- (Greek: upon, over, the root of epidemiology) · -sia (African geographic context)* Installation · Quick Start · Modules · Citation · Roadmap --- ## Overview Episia is a Python library for epidemiologists, public health researchers, and biostatisticians. It provides a unified, validated set of tools covering the full analytical workflow from raw surveillance data to statistical analysis, epidemic modeling, and automated report generation. Built on the scientific foundation of OpenEpi, Episia extends it with compartmental epidemic models (SIR/SEIR/SEIRD), Monte Carlo sensitivity analysis, and a modern Python API designed to be both approachable and production-grade. **Designed for:** - Field epidemiologists and biostatisticians working in resource-limited settings - Public health researchers in Africa and around the world - Students and academics in epidemiology and biostatistics - Developers building health analytics applications **Key properties:** - 100% offline zero network dependencies at runtime - Dual visualization backend: Plotly (interactive) and Matplotlib (publication-quality) - Unified result objects: every function returns a rich, serializable result - Self-contained HTML reports with dark/light mode toggle - Terminal loader animation for long-running operations (`EpiLoader`) - Systematic validation against OpenEpi reference implementation - Jupyter notebook support --- ## Validation Episia is systematically validated against OpenEpi, the reference in epidemiology. All results from core functions (risk ratio, odds ratio, confidence intervals, χ² tests, etc.) have been compared and agree with OpenEpi on standard datasets. **Check out the full validation notebook** This notebook reproduces OpenEpi's calculations step by step and demonstrates concordance. --- ## Installation ```bash # Standard install pip install episia # Development install (editable) git clone …