covid19za

Coronavirus COVID-19 (2019-nCoV) Data Repository for South Africa

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Archive Notice

This repository is being prepared for archival. It represents a comprehensive historical record of COVID-19 data collection, analysis, and modeling efforts for South Africa from March 2020 through end of 2021. The data and code are preserved for:

• Historical research and retrospective analysis
• Academic reference and citation
• Public health preparedness and future pandemic response
• Data science education and methodology demonstration
• Transparency and reproducibility of pandemic-era decision support

The repository remains publicly available under open licenses (MIT for code, CC BY-SA 4.0 for data) to ensure long-term accessibility for researchers, policymakers, and the public.

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Table of Contents

• Project Overview
• Historical Context and Impact
• Repository Structure
• Data Availability
• Data Coverage and Completeness
• Technical Documentation
• Data Sources
• Scholarly Work and Citations
• Community Showcase
• Licenses
• Contributors
• Contact

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Project Overview

The Coronavirus COVID-19 Data Repository for South Africa was created, maintained, and hosted by the Data Science for Social Impact (DSFSI) research group at the University of Pretoria, led by Dr. Vukosi Marivate.

Mission and Approach

This repository served as the primary open-access COVID-19 data infrastructure for South Africa, providing:

• Systematically collected data from official sources (NICD, DoH)
• Provincial and district-level granularity for spatial analysis
• Multiple data streams: cases, deaths, recoveries, testing, vaccinations, hospital surveillance, excess mortality, and mobility
• Analysis notebooks for epidemiological modeling and forecasting
• Standardized data formats enabling reproducible research
• Community collaboration through open-source contribution

Key Achievements

• Over 70+ scholarly citations and publications
• Powered 14+ independent web applications and dashboards used by the public
• Daily updates maintained throughout the pandemic (March 2020 onwards)
• Collaboration with 40+ volunteers from academia, industry, and civil society
• Africa-wide model inspiring the broader COVID-19 Africa project
• Published in Data Science Journal (peer-reviewed methodology paper)

Disclaimer: We worked to keep data as accurate as possible. Data was collated from NICD and DoH official reports and statements. Updates occurred only after official announcements to ensure data integrity and traceability.

Related Resources

• Blog Posts:

  • Why we built this and how we are working
  • A call to action across the African continent
  • Data Science thoughts on COVID-19 in South Africa

• Africa-wide Effort: COVID-19 Africa Repository

• Dashboard: COVID-19 Dashboard

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Historical Context and Impact

This repository was established in March 2020 at the onset of the COVID-19 pandemic in South Africa. It filled a critical gap by providing:

1. Open Access to Official Data: Making government health data accessible in machine-readable formats
2. Rapid Response Infrastructure: Enabling real-time analysis by researchers, journalists, and policymakers
3. Transparent Methodology: All data collection, cleaning, and analysis methods documented and open-source
4. Community-Driven Science: Demonstrating collaborative data science for public good
5. African Data Leadership: Setting standards for pandemic data sharing across the continent

The repository supported evidence-based decision-making during the pandemic and continues to serve as a historical record for retrospective analysis and future pandemic preparedness.

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Repository Structure

/data - COVID-19 Datasets

Primary directory containing CSV files for South African COVID-19 data:

• Provincial Timelines: Cumulative confirmed cases, deaths, recoveries, testing, and vaccinations by province
• District Data: Fine-grained geographic data organized by province (Eastern Cape, Free State, Gauteng, KwaZulu-Natal, Limpopo, Mpumalanga, Northern Cape, North West, Western Cape)
• Hospital Surveillance: NICD hospital admission and surveillance data
• Excess Mortality: SAMRC (South African Medical Research Council) excess deaths data
• Mobility Data: Apple, Google, and Facebook mobility indicators
• Health System Data: Public and private hospital facility information
• Official Reports: Archive of DoH PDF reports and extracted data

See Data Availability section for detailed dataset listing.

/notebooks - Analysis and Visualization Notebooks

Jupyter notebooks for epidemiological analysis:

• Growth Analysis: Provincial and international COVID-19 growth comparisons
• Bayesian Inference Models: Statistical modeling of spreading rates
• R0 Estimation: Reproduction number calculations (based on Kevin Systrom’s real-time R0 method)
• Mobility Studies: Correlation between mobility patterns and case trends
• Geospatial Visualization: Choropleth maps and spatial analysis
• Vaccination Analytics: Vaccine rollout tracking and analysis

Usage: Clone the repository and run notebooks locally. Some notebooks fetch external data; others use local /data files.

/modelhub - COVID-19 Forecasting Models

Standardized repository for COVID-19 forecasting and projection models, inspired by the Reich Lab COVID-19 Forecast Hub.

• Model Directory: /modelhub/notebooks/
• Template: model_template.ipynb for standardized model development
• Automation: Models designed for nightly automated execution
• Licensing: Model code (MIT), Model outputs (CC BY-SA 4.0)

/scripts - Data Processing Automation

Python scripts for data collection and processing:

• realtime_r0.py - Automated R0 (effective reproduction number) calculation
• gp_pdf_extractor.py - Extracts COVID-19 data from Gauteng Province PDF reports (requires pdfplumber)
• mobility_scraper.py - Scrapes mobility data from various sources
• sacoronavirus_provincial_vaccine.py - Vaccination data scraper

Dependencies: See individual script headers and /notebooks/covid-model/requirements.txt

/scraper - Media Release Scraper (DEPRECATED)

Go-based CLI tool for scraping NICD/DoH media releases. Note: No longer functional as NICD/DoH stopped providing individual patient data in releases after March 24, 2020.

Build from source: go build in ./scraper directory

/visualisation - Generated Visualizations

Directory for storing output graphics, charts, and visualizations generated from analysis notebooks.

/api - API Components

API-related code and infrastructure for programmatic data access.

/documents - Documentation and Resources

Additional documentation, methodological notes, and resources.

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Data Availability

All datasets are located in the /data directory and are available in CSV format for ease of analysis.

Important Data Caveats

Testing and Reporting Lag: Daily reports reflect new positive test results released by the National Department of Health or NICD, but significant lag exists between test date and reporting date.

Example: In epidemiological Week 1 of 2021 (3-9 Jan), approximately 33,000 new cases were reported in daily announcements. However, the NICD Testing Summary Report for Week 3 of 2021 showed 43,635 positive tests for Week 1. This discrepancy arises because:

• Cases reported in daily announcements may be from prior weeks
• Tests conducted in a given week may only be reported in subsequent weeks

Implication: Temporal analyses must account for reporting lag. The reported date does not necessarily reflect the actual test date or illness onset date.

Active Datasets

Complete, maintained datasets covering the pandemic period:

Dataset	Description	Repository Link	Raw CSV URL
Provincial Confirmed Cases	Cumulative confirmed COVID-19 cases by province over time	Link	CSV
Provincial Recoveries	Cumulative recoveries by province over time	Link	CSV
Provincial Testing	Cumulative COVID-19 tests conducted by province	Link	CSV
Provincial Deaths	Cumulative deaths by province over time	Link	CSV
Vaccination Timeline	COVID-19 vaccination rollout data over time	Link	CSV
Death Statistics	Detailed death statistics and demographics	Link	CSV
Transmission Type	Classification of transmission types (local, imported, etc.)	Link	CSV
Testing Timeline	National-level testing data over time	Link	CSV
District Data	District and subdistrict level data by province	Link	Multiple CSVs
DoH PDF Reports	Department of Health PDF reports and extracted data	Link	Multiple files
DoH WhatsApp Archive	Archive of DoH WhatsApp case update messages	Link	Text files
Health Facilities	Public and private hospital/facility information	Link	CSV
NICD Daily Reports	NICD daily national reports	Link	CSV
NICD Hospital Surveillance	Hospital admission and surveillance data from NICD	Link	CSV
SAMRC Excess Deaths	Excess mortality data by province (SAMRC)	Link	CSV
Mobility Data	Apple, Google, and Facebook mobility indicators	Link	Multiple CSVs

Deprecated Datasets

IMPORTANT NOTE: Since approximately March 24, 2020, individual case-level data was no longer provided by DoH or NICD.

For provincial-level analysis from March 26, 2020 onwards, use the provincial_cumulative_timeline_* datasets. For individual case data up to March 25, 2020, use the confirmed_cases dataset below.

Dataset	Coverage Period	Repository Link	Raw CSV URL
Individual Confirmed Cases	March 5 - March 25, 2020	Link	CSV
Individual Deaths	Limited early period	Link	CSV

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Data Coverage and Completeness

Temporal Coverage

• Primary Data Collection Period: March 2020 - End of 2021
• Individual Case Data: March 5, 2020 - March 25, 2020 (discontinued by authorities)
• Provincial Aggregate Data: March 2020 - End of 2021
• Vaccination Data: Begins with vaccine rollout in 2021
• Hospital Surveillance: Varies by dataset
• Excess Mortality: Provided by SAMRC on periodic basis through 2021

Geographic Coverage

• National Level: All-South Africa aggregates
• Provincial Level: All 9 provinces (Eastern Cape, Free State, Gauteng, KwaZulu-Natal, Limpopo, Mpumalanga, Northern Cape, North West, Western Cape)
• District Level: District and subdistrict data where available (see /data/district_data/)

Data Completeness Notes

1. Reporting Changes: Data collection methods and reporting formats evolved throughout the pandemic
2. Missing Periods: Some datasets may have gaps due to reporting delays or changes in official data release practices
3. Source Dependency: All data depends on official government reporting; accuracy reflects source data quality
4. Backfilling: Some data points were backfilled or corrected in subsequent official reports

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Technical Documentation

Python Environment and Dependencies

Primary Analysis Environment: Python 3.7+

Core Dependencies (for COVID modeling notebooks in /notebooks/covid-model/):

pip install -r notebooks/covid-model/requirements.txt

Key Libraries:

• pandas - Data manipulation and analysis
• numpy - Numerical computing
• scipy - Scientific computing (statistics, interpolation)
• pymc3 - Bayesian statistical modeling
• matplotlib, seaborn - Visualization
• requests - HTTP requests for data fetching
• pdfplumber - PDF data extraction (for GP PDF extractor script)

R Environment

Some notebooks use R for statistical analysis. Required packages vary by notebook.

Data Format Standards

CSV Structure

• Encoding: UTF-8
• Delimiter: Comma (,)
• Date Format: DD-MM-YYYY (primary format, some datasets use YYYY-MM-DD)
• Province Codes: Standard South African province abbreviations (EC, FS, GP, KZN, LP, MP, NC, NW, WC)

District Data Standards

District-level data follows strict standards documented in /data/district_data/README.md:

• Required Columns: date, YYYYMMDD, source
• District Levels:
  • Level 0: Province-level data
  • Level 1: District-level data
  • Level 2: Subdistrict-level data
• Column Management: Do NOT rename existing columns; update friendly names in combined_district_keys.csv
• New Columns: Add at the end before the source column

Source Attribution

Most datasets require source attribution (typically the last column). Each new data point should reference the official report or statement.

Using the Data

Quick Start

# Clone the repository
git clone https://github.com/dsfsi/covid19za.git
cd covid19za

# Install Python dependencies
pip install -r notebooks/covid-model/requirements.txt

# Explore data
cd data
ls -la

# Run analysis notebooks
cd ../notebooks
jupyter notebook

Accessing Raw Data Programmatically

All CSV files can be accessed directly via raw GitHub URLs:

import pandas as pd

# Load provincial confirmed cases
url = "https://raw.githubusercontent.com/dsfsi/covid19za/master/data/covid19za_provincial_cumulative_timeline_confirmed.csv"
df = pd.read_csv(url)

Running Analysis Notebooks

1. Navigate to /notebooks directory
2. Open desired notebook in Jupyter
3. Some notebooks fetch external data; others use local /data files
4. Ensure dependencies are installed

Running Scripts

# Calculate real-time R0
python scripts/realtime_r0.py

# Extract data from Gauteng Province PDFs
pip install pdfplumber
python scripts/gp_pdf_extractor.py

# Scrape mobility data
python scripts/mobility_scraper.py

Data Sources

All data in this repository was collected from official government and public health sources to ensure accuracy and credibility.

Primary Official Sources

Source	Description	URL
NICD	National Institute for Communicable Diseases - Primary source for epidemiological data, alerts, and reports	nicd.ac.za
Department of Health (DoH)	South African National Department of Health - Official health announcements and statistics	health.gov.za
DoH Twitter	Real-time health updates and announcements	@HealthZA
SA Government	Official government media statements and policy announcements	gov.za
SAMRC	South African Medical Research Council - Excess mortality data	samrc.ac.za

Supporting Data Sources

Source	Description	URL
DHIS Data Dictionary	National Department of Health Data Dictionary - Standard health data definitions	dd.dhmis.org
Statistics SA	Statistics South Africa - Demographic and population data	statssa.gov.za
Apple Mobility	Apple mobility trend reports	apple.com/covid19/mobility
Google Mobility	Google Community Mobility Reports	google.com/covid19/mobility
Facebook Data for Good	Facebook mobility and connectivity data	dataforgood.facebook.com
MedPages	South African medical information resource	medpages.info

Data Collection Methodology

1. Daily Monitoring: Official sources were monitored daily for new reports and announcements
2. Manual Verification: Data was manually verified against multiple sources when available
3. Source Attribution: Each data point includes reference to the source document/announcement
4. Version Control: All changes tracked via Git for full transparency and reproducibility
5. Community Review: Open-source model allowed community verification and error reporting

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Scholarly Work and Citations

How to Cite This Repository

For visualizations, notebooks, or web applications:

Data Science for Social Impact Research Group @ University of Pretoria, Coronavirus COVID-19 (2019-nCoV) Data Repository for South Africa. Available on: https://github.com/dsfsi/covid19za.

For academic publications - Journal Article:

@article{marivate2020use,
  Author = {Vukosi Marivate and Herkulaas MvE Combrink},
  Journal = {Data Science Journal},
  Number = {1},
  Pages = {1-7},
  Title = {Use of Available Data To Inform The COVID-19 Outbreak in South Africa: A Case Study},
  Volume = {19},
  Year = {2020},
  DOI = {10.5334/dsj-2020-019},
  URL = {https://doi.org/10.5334/dsj-2020-019}
}

For academic publications - Dataset:

@dataset{marivate_vukosi_2020_3819126,
  author = {Marivate, Vukosi and Arbi, Riaz and Combrink, Herkulaas and
            de Waal, Alta and Dryza, Henkho and Egersdorfer, Derrick and
            Garnett, Shaun and Gordon, Brent and Greyling, Lizel and
            Lebogo, Ofentswe and Mackie, Dave and Merry, Bruce and
            Mkhondwane, S'busiso and Mokoatle, Mpho and Moodley, Shivan and
            Mtsweni, Jabu and Mtsweni, Nompumelelo and Myburgh, Paul and
            Richter, Jannik and Rikhotso, Vuthlari and Rosen, Simon and
            Sefara, Joseph and van der Walt, Anelda and van Heerden, Schalk and
            Welsh, Jay and Hazelhurst, Scott and Petersen, Chad and
            Mbuvha, Rendani and Dhlamini, Nelisiwe and James, Vaibhavi},
  title = {{Coronavirus disease (COVID-19) case data - South Africa}},
  month = mar,
  year = 2020,
  publisher = {Zenodo},
  doi = {10.5281/zenodo.3819126},
  url = {https://doi.org/10.5281/zenodo.3819126}
}

Research Impact

This repository has been cited in over 70+ scholarly publications spanning epidemiology, public health, data science, and social sciences.

Explore citations: Google Scholar

Publications by Repository Team

• Marivate, V., & Combrink, H. M. (2020). “Use of Available Data To Inform The COVID-19 Outbreak in South Africa: A Case Study.” Data Science Journal, 19(1), 1-7. DOI: 10.5334/dsj-2020-019

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Community Showcase

Web Applications and Dashboards

This repository has powered numerous independent projects that made COVID-19 data accessible to the South African public:

#	Project	Description	Links	Creator	Country	Status
1	Covid-19 SA Data	Data visualizations for the COVID-19 outbreak in South Africa	Archive • GitHub	Simon Rosen	South Africa	Archived
2	Covid-19 Testing Map	Map of COVID-19 testing facilities	Archive • GitHub	Yannick Zehnder	Switzerland	Archived
3	Coronavirus Map	Interactive coronavirus mapping tool	Archive • GitHub	Jay Welsh	South Africa	Archived
4	Covid-19 Telegram Bot	Corona virus statistics via Telegram	Bot Link	CodeChap	South Africa	Unknown
5	Xitsonga Dashboard	COVID-19 dashboard in Xitsonga language	Archive	xitsonga.org	South Africa	Archived
6	Hospital Capacity Viz	Mapping local hospital capacity (public and private)	Archive • GitHub	Nompumelelo	South Africa	Archived
7	Covid-19 Trends	COVID-19 analytics dashboard for South Africa	Archive • GitHub	Schalk van Heerden	South Africa	Archived
8	Tshivenda Dashboard	COVID-19 dashboard in Tshivenda language	Archive	luvenda.com	South Africa	Archived
9	Health Facilities Map	Map of health facilities with comparable details	Website • GitHub	Team	South Africa	Active
10	R Interactive Map	Health facilities viewer built with R (afrimapr)	Archive • GitHub	Dr Andy South	United Kingdom	Archived
11	R Number Estimation	Estimating effective reproductive number for SA and provinces (last updated July 2022)	Website	Louis Rossouw	South Africa	Inactive
12	Provincial Modeling	COVID-19 modeling using reported and excess deaths (last updated July 2021)	Website	Louis Rossouw	South Africa	Inactive
13	Provincial Visualization	Deaths, cases, recoveries with mobility data visualization	Archive • GitHub	Christopher Marais	South Africa	Archived
14	Multi-strain Optimization	Differential Evolution for long-term multi-strain modeling	IEEE Paper	CJ Pretorius & MC du Plessis	South Africa	Active

Impact Summary

• 14+ web applications built by independent developers (many now archived as pandemic-era projects)
• Multi-lingual accessibility (English, Xitsonga, Tshivenda)
• International reach (projects from Switzerland, UK, SA)
• Diverse applications: mapping, forecasting, messaging bots, academic research

Note: Many community projects have been archived or discontinued as the active pandemic phase ended. Wayback Machine links are provided where original sites are no longer available.

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Contributing

Note: As this repository transitions to archival status, active contribution may be limited. However, error corrections and data quality improvements are welcome.

Historical Contribution Workflow

During active maintenance, the contribution process was:

How to Contribute

1. Choose or Create an Issue: Browse existing issues or create a new one describing your contribution
2. Assign to Yourself: Take ownership of the issue
3. Adopt a File: Add your name to covid19za_volunteer_adopted_files.csv listing which files you’ll work on
4. Fork the Repository: Create your own fork
5. Make Changes: Ensure data accuracy and include source attribution
6. Submit Pull Request: Follow GitHub PR guidelines

Contribution Guidelines

• Data Accuracy: Verify all data against official sources
• Source Attribution: Include source for every data point
• Format Consistency: Follow existing CSV structure and date formats
• Documentation: Update relevant documentation for significant changes

Resources for Contributors

• Data Science Africa COVID-19 Response
• IndabaX South Africa: Vukosi Marivate - Using data science to inform the COVID-19 outbreak in Africa
• Stanford CS472 Data science and AI for COVID-19

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Contributors

This project was made possible by the dedication of 40+ volunteers from academia, industry, and civil society.

Made with contributors-img.

Full contributor list: GitHub Contributors Graph

Special thanks to all volunteers who contributed data collection, validation, analysis, and development throughout the pandemic.

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Licenses

Code:

Data:

License Details

• Code (MIT License): All software, scripts, and notebooks are licensed under the MIT License, allowing free use, modification, and distribution with attribution
• Data (CC BY-SA 4.0): All datasets are licensed under Creative Commons Attribution-ShareAlike 4.0, requiring attribution and share-alike for derivative works

These open licenses ensure long-term accessibility and reusability for research, education, and public health purposes.

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Project Lead:

• Dr. Vukosi Marivate
  • Email: [email protected]
  • Twitter: @vukosi
  • Affiliation: Data Science for Social Impact Research Group, University of Pretoria

Research Group:

• Data Science for Social Impact (DSFSI)
• Department of Computer Science, University of Pretoria

For Questions:

• Data Issues: Please open a GitHub issue describing the problem
• Research Collaborations: Contact Dr. Vukosi Marivate via email
• General Inquiries: [email protected]

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Acknowledgments and Support

This project was made possible through support from:

Funding and Infrastructure Support

• International Astronomical Union - Astronomy for Development
• Google Cloud Platform

Institutional Support

• University of Pretoria - Hosting and institutional support
• Data Science for Social Impact Research Group - Research leadership and coordination

Community Support

• 40+ volunteer contributors - Data collection, validation, and analysis
• South African data science community - Code reviews, testing, and feedback
• 14+ independent developers - Building applications and tools using this data
• 70+ researchers - Citing and validating this work through scholarly publications

Special Acknowledgment

We acknowledge the critical work of:

• NICD (National Institute for Communicable Diseases) - Primary data collection and public health surveillance
• National Department of Health - Official reporting and public health communication
• SAMRC (South African Medical Research Council) - Excess mortality analysis
• All healthcare workers and public health officials who worked tirelessly during the pandemic

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Repository Metadata

• Repository: github.com/dsfsi/covid19za
• Zenodo DOI: 10.5281/zenodo.3819126
• Data Science Journal DOI: 10.5334/dsj-2020-019
• Primary Language: Python
• Data Format: CSV
• Status: Archival
• Last Active Update: End of 2021 (varies by dataset)

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Additional Resources

Official Dashboards and Tools

• DSFSI COVID-19 Dashboard

Related Projects

• COVID-19 Africa Repository - Africa-wide COVID-19 data effort
• Health Facility Map - South African health facility mapping

Educational Resources

• DSFSI Blog Posts
• Data Science for COVID-19 Course Materials

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This repository stands as a testament to open science, community collaboration, and the power of data to inform public health responses. We hope it continues to serve researchers, educators, and public health professionals for years to come.