Change france regional cases data source

[PaulC91]

It looks like the yaml files get_france_regional_cases() reads from are no longer being updated so we need another data source.

The opencovid19-fr github has a csv compiling data for regions and districts but there are often several entries for each day from various sources so this would require some work to get a daily de-duplicated number.

@patrickbarks you mentioned the french gov website is now publishing csv files, should we switch to that?

[patrickbarks]

Actually, frustratingly, I haven't been able to find France regional case counts from after 2020-03-25.

In that 'key figures' .csv you link to (also available from data.gouv.fr), confirmed cases are missing for most regions after 2020-03-25.

There are three other regional/departmental datasets from Santé publique France, but none include counts of confirmed cases:

• hospitalizations (counts of hospitalizations, number on ventilation, and hospital deaths)
• emergency and urgent care (counts of emergency room visits, medical acts, etc.)
• test results by city laboratories only (includes warning "does not list all the tests carried out in France"; only lists ~17k positive test results as of 2020-04-05, so definitely a small subset)

There are also two gov dashboards (here and here), but again no regional case counts :(

[patrickbarks]

Based on this report from yesterday, Santé publique France no longer counts cases per se, but rather estimates them from the city laboratory tests and the hospitalization counts:

Since March 26, 2020, the numbers of confirmed COVID-19 cases have been estimated at the national level taking into account count data from city medical laboratories and patients hospitalized for COVID-19 ...

Patients with signs of COVID-19 are no longer systematically confirmed by a biological test ...

The number of confirmed cases in France therefore no longer satisfactorily reflects the dynamics of the epidemic.

[briatte]

Is this issue still alive? The data source indicated in the script seems alive: https://raw.githubusercontent.com/opencovid19-fr/data/master/dist/chiffres-cles.csv

It looks like the data can also be accessed from there: https://geodes.santepubliquefrance.fr/#c=news

… although I don't see an API.

[patrickbarks]

These sources have the same problems noted above.

In chiffres-cles.csv, daily confirmed cases and daily deaths were only tracked at the regional level until ~2020-03-25 (except for a few regions that report their own figures sporadically).

And geodes.santepubliquefrance.fr does not contain daily cases or deaths by region/department.

[briatte]

Thanks @patrickbarks for your answer.

I now see the issue with the opencovid19-fr data.

Re: Géodes, I do seem to get some data out of it: https://geodes.santepubliquefrance.fr/index.php#c=indicator&i=covid_hospit_incid.incid_dc&s=2020-04-28&t=a01&view=map1

Nombre quotidien de personnes nouvellement décédées pour COVID-19

Goes from March 19 to today, for both régions and départements.