Segregated testing data for some countries

[ImaneElIdrissi]

Some countries report several testing numbers and we would like to add that in the tracker. @angelicambg could you have a look at these websites and see which ones could be automatically scraped? In bold are the countries that are feasible in my opinion.

• [x] Austria: PCR, Antigen - https://www.sozialministerium.at/Informationen-zum-Coronavirus/Neuartiges-Coronavirus-(2019-nCov).html
• [x] Benin: PCR, Rapid test - https://www.gouv.bj/coronavirus/
• [ ] Bhutan: PCR, Rapid test - https://www.facebook.com/MoHBhutan/photos/3641467919248131
• [x] Brazil: PCR, Rapid test -https://qsprod.saude.gov.br/extensions/DEMAS_C19Insumos_TESTES_MX/DEMAS_C19Insumos_TESTES_MX.html
• [x] Czech Republic: PCR, Antigen - https://onemocneni-aktualne.mzcr.cz/covid-19
• [x] Colombia: PCR, Antigen (daily only)- https://twitter.com/MinSaludCol
• [x] Denmark: PCR, Antigen -https://www.sst.dk/en/english/corona-eng/status-of-the-epidemic/covid-19-updates-statistics-and-charts
• [ ] DominicanRepublic: PCR, Antigen (daily only)- https://www.msp.gob.do/web/?page_id=6948#1586785071804-577a2da4-6f72
• [ ] Georgia: PCR, Antigen (daily only)- https://stopcov.ge/en/
• [x] Greece: PCR, Rapid antigen - https://covid19.innews.gr/iframe
• [x] Indonesia: PCR, Rapid antigen - https://covid19.go.id/peta-sebaran
• [x] Italy: PCR, Rapid antigen -https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-json/dpc-covid19-ita-andamento-nazionale-latest.json
• [ ] Jamaica: PCR, Rapid antigen - https://www.moh.gov.jm/?s=COVID-19+Clinical+Management+Summary
• [x] Lithuania: PCR, Rapid antigen - https://osp.stat.gov.lt/praejusios-paros-covid-19-statistika
• [x] Romania: PCR, Rapid antigen - https://stirioficiale.ro/informatii
• [x] Slovakia: PCR, Antigen - https://korona.gov.sk/
• [x] Slovenia: PCR, Rapid test (HAGT) - https://www.nijz.si/sl/dnevno-spremljanje-okuzb-s-sars-cov-2-covid-19
• [x] Spain: PCR, Antigen - https://www.mscbs.gob.es/gabinete/notasPrensa.do
• [x] Switzerland: PCR, Rapid antigen - https://www.covid19.admin.ch/en/overview?ovTime=total

[findanna]

@ImaneElIdrissi and @angelicambg I would narrow it down only to countries that track rapid antigen tests. We should name it Rapid Antigen Test and already think on how to implement the following:

1. How to include it in the current dataset
2. How to showcase it on the shinyapp

Adding @christophsax because it is relevant with the shiny app design.

[christophsax]

@angelicambg let's discuss 2. quickly on Tuesday

[ImaneElIdrissi]

@angelicambg I have updated the list of countries to work on according to @dsbb-finddx comment.

[angelicambg]

@ImaneElIdrissi I have some questions regarding this data. Could you help me?

1. Antigen and Rapid test numbers are the same? i.e. can I store Antigen, Rapid test, Rapid antigen, Rapid test (HAGT) just in one variable called rapid_test, or should I create different variables for each of them?

2. Data for Benin currently is based on Africa CDC, and they show only PCR. Should we take https://www.gouv.bj/coronavirus/ as the source instead of Africa CDC for the current tests_cumulative to also take into account Tests TDR? or should we keep Africa CDC as a source but not include Benin for the segregated tests numbers?

3. For Czech Republic we are only scraping testscumulative = "Provedené PCR testy"_, should I include in test_cumulative the number for Provedené antigenní testy, sotests_cumaltive = "Provedené PCR testy"+ "Provedené antigenní testy".

4. Slovakia same case as Czech Republic

[ImaneElIdrissi]

@angelicambg :

1. One variable called rapid_test is good. The other names Antigen, Rapid antigen and Rapid test (HAGT) are just shortcuts to say rapid tests.

2. Indeed for Benin it would be good to start using https://www.gouv.bj/coronavirus/ for both tests_cumulative and rapid_test (Tests TDR) instead of Africa CDC.

3. For Czech Republic, including in test_cumulative the number for Provedené antigenní testy, sotests_cumaltive = "Provedené PCR testy"+ "Provedené antigenní testy" is I believe the best approach yes. However let's keep the current function for now and we'll integrate the calculation only when implementing the segregation.

4. Slovakia same as Czech Republic.

[ImaneElIdrissi]

@angelicambg , before we close this issue could you double check Denmark (https://www.sst.dk/en/english/corona-eng/status-of-the-epidemic/covid-19-updates-statistics-and-charts) and Greece (https://covid19.innews.gr/iframe)? It seems to me they are easy dashboards? And Peru was removed because the values were not the right ones. Thanks a lot :)

[angelicambg]

• Denmark: Fixed
• Indonesia: Included
• Greece: Included
• Italy: Included
• Colombia: Included using this webpage from INS, extracted from datos.gov.co

[findanna]

@angelicambg I changed the link for Brazil. Can you please update the number for cumulative number of tests and also PCR/RDT?

[findanna]

• [x] Segregated data in processed folder not updating since 24/06/2021 and shinyapp does not show most recent value
• [x] solve the issue of negative values for pcr and rdt test values, calculating the percentage of each daily value from the most recent correct values and apply it on the test_new_corrected column
• [ ] Greece, Benin, Romania are scraped for pcr/rdt numbers but do not show up on the tracker because they are not in the processed folder file

[findanna]

@angelicambg Denmark has updated their data here: https://www.sst.dk/en/english/corona-eng/status-of-the-epidemic/covid-19-updates-statistics-and-charts We have lower values.