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https://github.com/dsfsi/covid19za

Coronavirus COVID-19 (2019-nCoV) Data Repository and Dashboard for South Africa
https://github.com/dsfsi/covid19za

coronavirus covid-19 covid-data covid19 covid19-data dashboard data-science dataset doh doi dsfsi-datasets health nicd south-africa

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

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



[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3819126.svg)](https://doi.org/10.5281/zenodo.3819126) [![dsJournal](https://img.shields.io/badge/DSJournal-10.5334-B31B1B.svg)](https://doi.org/10.5334/dsj-2020-019)



Give Feedback 📑: [DSFSI Resource Feedback Form](https://docs.google.com/forms/d/e/1FAIpQLSf7S36dyAUPx2egmXbFpnTBuzoRulhL5Elu-N1eoMhaO7v10w/formResponse){:target="_blank"}



Coronavirus COVID-19 (2019-nCoV) Data Repository for South Africa created, maintained and hosted by [Data Science for Social Impact research group](https://dsfsi.github.io/), led by Dr. Vukosi Marivate, at the University of Pretoria.



**Disclaimer:** We have worked to keep the data as accurate as possible. We collate the COVID 19 reporting data from NICD and DoH. We only update that data once there is an official report or statement. For the other data, we work to keep the data as accurate as possible. If you find errors. Make a pull request.



*If you use this repo for any research/development/innovation, please contact us (see contacts below)*



See our blog posts:

* [Why we built this and how we are working](https://dsfsi.github.io/blog/covid19za-dashboard/),

* [How this is a call to action across the African continent](https://dsfsi.github.io/blog/covida19africa-call-to-action/)

* [A few weeks in, Data Science thoughts on COVID-19 in South Africa](https://dsfsi.github.io/blog/a-few-weeks-in-covid19/)



*If you are interested in the **Africa-wide effort**:* Go to [https://github.com/dsfsi/covid19africa](https://github.com/dsfsi/covid19africa)



For information on daily updates on the repo, go to [https://twitter.com/vukosi/status/1239184086633242630?s=20](https://twitter.com/vukosi/status/1239184086633242630?s=20)



## Licenses



Code [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)  | Data [![License: CC BY-SA 4.0](https://img.shields.io/badge/License-CC%20BY--SA%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-sa/4.0/)



## Data Available [[/data](/data)]



Please note that these reports are the daily reports as released by the National Department of Health or the NICD. The new cases reported are based on new positive test reports released. However, there may be significant lag from when the patient was tested. As an example in epidemiological Week 1 of 2021 (3-9 Jan) approximately 33k new cases were reported on the daily announcement. However, the NICD Testing Summary Report for Week 3 of 2021 (which also reports the two previous weeks) shows that the number of positive tests was 43635 for Week 1 of 2021. The difference is due to the lag in testing being done -- some of the 33k cases reported on the daily announcments were actually from prior weeks while a large number of people were tested between 3-9 January, but the cases were only reported from the 10th onwards. Care needs to be taken in doing some analyses to take this into account. 



### Active

| dataset         | url | raw_url[file] |

|-----------------|-----|---------------|

| provincial_cumulative_timeline_confirmed|  [provincial_cumulative_timeline_confirmed](/data/covid19za_provincial_cumulative_timeline_confirmed.csv)   |       [provincial_cumulative_timeline_confirmed.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/covid19za_provincial_cumulative_timeline_confirmed.csv)         |

| provincial_cumulative_timeline_recoveries|  [provincial_cumulative_timeline_recoveries](/data/covid19za_provincial_cumulative_timeline_recoveries.csv)   |       [provincial_cumulative_timeline_recoveries.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/covid19za_provincial_cumulative_timeline_recoveries.csv)         |

| provincial_cumulative_timeline_testing|  [provincial_cumulative_timeline_testing](/data/covid19za_provincial_cumulative_timeline_testing.csv)   |       [provincial_cumulative_timeline_testing.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/covid19za_provincial_cumulative_timeline_testing.csv)         |

| provincial_cumulative_timeline_deaths|  [provincial_cumulative_timeline_deaths](/data/covid19za_provincial_cumulative_timeline_deaths.csv)   |       [provincial_cumulative_timeline_deaths.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/covid19za_provincial_cumulative_timeline_deaths.csv)         |

| vaccination |  [covid19za_timeline_vaccination](/data/covid19za_timeline_vaccination.csv)   |       [covid19za_timeline_vaccination.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/covid19za_timeline_vaccination.csv)         |

| death_statistics |  [covid19za_timeline_death_statistics](/data/covid19za_timeline_death_statistics.csv)   |       [covid19za_timeline_death_statistics.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/covid19za_timeline_deaths.csv)         |

| transmission_type |  [covid19za_timeline_transmission_type](/data/covid19za_timeline_transmission_type.csv)   |       [covid19za_timeline_transmission_type.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/covid19za_timeline_transmission_type.csv)         |

| testing |  [covid19za_timeline_testing](/data/covid19za_timeline_testing.csv)   |       [covid19za_timeline_testing.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/covid19za_timeline_testing.csv)         |

| district_data |  [district_data](/data/district_data/)   |            |

|   DoH PDFs and Extracted CSVs |  [doh_pdf](/data/doh_pdf)   |              |

|   DoH Whatsapp case update archive |  [doh_whatsapp](/data/doh_whatsapp)   |              |

|   health facility data [public and private] |  [health_system_za_hospitals_v1](/data/health_system_za_hospitals_v1.csv)   |         [health_system_za_hospitals_v1.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/health_system_za_hospitals_v1.csv)       |

|   nicd_daily_national_report |  [nicd_daily_national_report](/data/nicd_daily_national_report.csv)   |         [nicd_daily_national_report.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/nicd_daily_national_report.csv)       |

|   nicd_hospital_surveillance_data |  [nicd_hospital_surveillance_data](/data/nicd_hospital_surveillance_data.csv)   |         [nicd_hospital_surveillance_data.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/nicd_hospital_surveillance_data.csv)       |

|   samrc_excess_deaths_province |  [samrc_excess_deaths_province](/data/samrc_excess_deaths_province.csv)   |         [samrc_excess_deaths_province.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/samrc_excess_deaths_province.csv)       |

|   Apple, Google, Facebook Mobility Data |  [mobility](/data/mobility)   |              |

### Deprecated

**NOTE:** Since around 24 March 2020, we have not gotten individual case data from DoH or NICD. For now if you need provincial counts use the *provincial_cumulative_timeline*. For individual cases up to 25 March 2020, use the *confirmed_cases*.

| dataset         | url | raw_url[file] |

|-----------------|-----|---------------|

| confirmed_cases* [updated to 25 March 2020] |  [covid19za_timeline_confirmed](/data/covid19za_timeline_confirmed.csv)   |       [covid19za_timeline_confirmed.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/covid19za_timeline_confirmed.csv)         |

| deaths |  [covid19za_timeline_deaths](/data/covid19za_timeline_deaths.csv)   |       [covid19za_timeline_deaths.csv](https://raw.githubusercontent.com/dsfsi/covid19za/master/data/covid19za_timeline_deaths.csv)         |



\* NICD no longer gives individual case data. Please use **provincial_cumulative_timeline** from 26 March 2020 onwards.



## Dashboard

* Google Data Studio Dashboard [URL link](https://dsfsi.github.io/covid19za-dash/)



## Data Sources:

* NICD - South Africa [URL](https://www.nicd.ac.za/media/alerts/)

* Department of Health - South Africa [Main Site](http://www.health.gov.za/), [Twitter](https://twitter.com/HealthZA/)

* South African Government Media Statements [URL](https://www.gov.za/media-statements)

* National Department of Health Data Dictionary [URL](https://dd.dhmis.org/)

* MedPages [URL](https://www.medpages.info/sf/index.php?page=homepage)

* Statistics South Africa [URL](http://www.statssa.gov.za/)



## Contributing

### Options

* *I want to help, but don't have an idea:* You can take a look at the issues to see which one you might be interested in tackling.

* *I have an idea or new feature:* Create a new issue first, assign it to yourself and then fork the repo.



### Adopting a file

Once you have chosen how you are going to contribute, you must list which files you will be working on by adding your name to the adopt-a-file csv file. Edit [covid19za_volunteer_adopted_file](https://github.com/dsfsi/covid19za/blob/master/covid19za_volunteer_adopted_files.csv).



### Submitting Changes [Pull Request]

* See https://opensource.com/article/19/7/create-pull-request-github

### Resources [Get some ideas]

* [Data Science Africa COVID-19 Response](https://www.youtube.com/watch?v=9o0sa7gypMc)

* [IndabaX South Africa: Vukosi Marivate - Using data science to inform the COVID-19 outbreak in Africa](https://www.youtube.com/watch?v=DZOpypSA85I)

* [Stanford \<\> CS472 Data science and AI for COVID-19](https://sites.google.com/view/data-science-covid-19)

## Contributors

[![Contributors](https://contributors-img.web.app/image?repo=dsfsi/covid19za)](https://github.com/dsfsi/covid19za/graphs/contributors)

Made with [contributors-img](https://contributors-img.web.app).

* See https://github.com/dsfsi/covid19za/graphs/contributors



## Contact

* Vukosi Marivate - [email protected], [@vukosi](https://twitter.com/vukosi)



## Citing the dataset

**On a visualisation/notebook/webapp:**



> 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.



**In a publication**



Data Science Journal



>@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},

    url = {[https://doi.org/10.5334/dsj-2020-019](https://doi.org/10.5334/dsj-2020-019)}

}



and 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](https://doi.org/10.5281/zenodo.3819126)}

}



## Showcase



### Web Projects



Some of COVID-19 Data for South Africa (data in this repo) is currently being used by other independent projects shown in the table below :



| Project Name  | Project Description |  Project Demo    |    Project owner |    Country   |

| ------------- | ------------- |------------|-----------------|------------------|

| 1. Covid-19 SA Data | Data visualizations corresponding to the current Covid-19 outbreak in South Africa |  [[Website](https://covid19data.co.za/)],[[GitHub Repo](https://github.com/SimonRosen173/Covid19SAData_JS)]| [Simon Rosen](https://github.com/SimonRosen173)| South Africa |

| 2. Covid-19 testing areas| A Covid-19 Testing Facilities Map |[[Website](https://www.ineff.ch/cov19testmap/)],[[GitHub Repo](https://github.com/IneffableKoD/cov19testmap)]| [Yannick Zehnder](https://github.com/IneffableKoD/) | Switzerland |

| 3. Covid-19 Map| A Coronavirus Map | [[Website](https://coronamap.co.za)] [[GitHub Repo](https://github.com/JayWelsh/coronamap)] | Jay Welsh | South Africa |

| 4. Covid-19 Telegram Bot| Corona virus statistics via Telegram | [Link](https://t.me/CoronaZABot) | CodeChap | South Africa |

| 5. Covid-19 Xitsonga Dashboard | Xitsonga Dashboard | [Link](http://xitsonga.org/covid19) | xitsonga.org | South Africa |

| 6. Hospitals' capacity to respond to Covid-19 | Data visualization mapping local hospitals (private ad public) in South Africa | [[Map Viz](https://elolelo.github.io/covid19/)] ,[[Repo](https://github.com/elolelo/covid19)] |[Nompumelelo](https://github.com/elolelo)|South Africa |

| 7. Covid-19 Trends | Covid-19 analytics dashboard for South Africa | [[Website]](http://www.covid19trends.co.za) [[Repo]](https://github.com/heerden/Covid19TrendsZA) | [Schalk van Heerden](https://github.com/heerden) | South Africa | 

| 8. Covid-19 Tshivenda Dashboard | Tshivenda Dashboard | [Link](http://luvenda.com/covid/) | luvenda.com | South Africa |

| 9. Map of Health facilites around me  | Map showing comparable details of hospitals around my location in response to Covid-19  | [[Webpage](https://dsfsi.github.io/healthfacilitymap/)] , [[GitHub Repo](https://github.com/dsfsi/healthfacilitymap)] | [These authors](https://dsfsi.github.io/blog/mapping-healthsystem/)  | South Africa |

|10. R-based Interactive health facilties Map | Afrimapr, mapping health facilities using R-building blocks |[[Webpage](https://andysouth.shinyapps.io/hosp-viewer-SA-v02/)] [[Repo](https://github.com/afrimapr/afrimapr_dev/tree/master/hospitals-viewer-south-africa/hosp-viewer-SA-v02)] | [Dr Andy South](http://andysouth.co.uk/)  |  United Kingdom |

|11. Estimating the Reproductive Number of COVID-19 | Estimating effective reproductive number for SA, it's provinces and other countries. |  [[Website](https://unsupervised.online/static/covid-19/estimating_r_za.html)] | [Louis Rossouw](https://github.com/lrossouw) | South Africa |

|12. Modelling COVID-19 in South Africa at a Provincial Level | Modelling COVID-19 in South Africa at a Provincial Level using reported and excess deaths. |  [[Website](https://unsupervised.online/static/covid-19/modelling_covid-19_in_south_africa_at_a_provincial_level.html)] | [Louis Rossouw](https://github.com/lrossouw) | South Africa |

|13. South African Provincial COVID-19 Visualization | Visualize deaths, cases and recoveries alongside mobility data on a provincial level. Additionally, visualize cahnge of cases over a weekly basis. |  [[Website](http://3.140.191.119:8050/)] | [Christopher Marais](https://github.com/ChristopherMarais/Panthera_interview_gcm) | South Africa |

|14. Differential Evolution to Optimize A Long-term Multi-strain Model of COVID-19 in South Africa | Uses Differential Evolution (an Evolutionary Optimization Algorithm) for data fitting and parameter estimation. | [[Website](https://ieeexplore.ieee.org/document/9925558)] | CJ Pretorius and MC du Plessis | South Africa |



### Scholarly Work



See [Google Scholar](https://scholar.google.com/scholar?cites=16177923666716456587&as_sdt=2005&sciodt=0,5&hl=en)



## Support 



We want to acknowledge support from these organisations



* [International Astronomical Union - Astronomy for Development](http://www.astro4dev.org/)

* [Google Cloud Platform](http://cloud.google.com/)