muktaru/who-africa-mortality-analysis

Mortality surveillance analysis for 10 African countries (2000–2019): WHO ANACoD data quality assessment, ICD-10 cause-of-death trends, epidemiological transition analysis, and SDG 3.1–3.4 progress tracking. Python pipeline with reproducible outputs. # WHO Africa Mortality Surveillance Analysis **Author:** Muktar Ahmed, PhD | Postdoctoral Research Fellow, Flinders University **Contact:** Muktar.Ahmed@flinders.edu.au | Google Scholar | ORCID --- ## Overview This repository presents a **complete mortality surveillance analysis** for 10 African countries over 2000–2019, developed as a technical portfolio demonstrating proficiency in: - **WHO ANACoD methodology** — replicating the WHO Analysis of Causes of Death tool in Python to assess vital registration completeness and cause-of-death coding quality - **ICD-10 cause-of-death analysis** — structured classification and trend analysis of mortality by cause group - **SDG progress tracking** — quantitative assessment against SDG 3.1, 3.2, 3.3, and 3.4 targets - **Epidemiological transition analysis** — quantifying the shift from communicable to non-communicable disease burden - **Policy-facing communication** — technical report written for public health decision-makers The analysis uses a dataset **modelled on the WHO Mortality Database** structure, calibrated from GBD 2019 estimates and WHO Global Health Estimates 2024. Instructions for substituting real WHO Mortality Database data are in `data/raw/README_data.md`. --- ## Key Findings | Finding | Value | |---|---| | Countries with ≥90% vital registration completeness | **1/10** (South Africa only) | | Average completeness across 10 countries (2019) | **~40%** | | Communicable disease share of deaths: 2000 → 2019 | **51.2% → 38.3%** | | NCD share of deaths: 2000 → 2019 | **25.8% → 41.9%** | | SDG 3.4 NCD trajectory | **OFF TRACK** (gap: 21.9/100k by 2030) | | Top cause of death (2019) | **All cancers** (CDR 36.7/100k) | --- ## Repository Structure ``` who-africa-mortality-analysis/ ├── README.md # This file ├── run_all_analyses.py # Master runner — executes full pipeline ├── requirements.txt # Python dependencies │ ├── R/ …