Time-series data of cumulative number of recovered/fatal cases as well as confirmed cases

[lisphilar]

Datasets of cumulative number of COVID-19 confirmed/recovered/fatal cases accelerated studies of data analysis with math models. Regarding monkeypox, "Confirmed" is now provided at this great repository, and addition of "Recovered" and "Fatal" is expected.

I think we have two choices for improvement.

1. add a script for calculation for internal-use of developers and run the script after linelist updates
2. provide users with Python/R interface for calculation

My trial suggested a few lines of Python codes is required for calculation. https://gist.github.com/lisphilar/ae24c369d21cfeb89a673de1f6edb2b9

Note:

• Staus = "confirmed" or "suspected": confirmed cases
• Outcome = Recovered: recovered cases
• Outcome = Deaths: fatal cases
• "active" means "confirmed but not recovered/fatal" cases
• "in-active" means "recovered or fatal cases"
• minimum date of ["Date_onset", "Date_confirmation", "Date_hospitalisation", "Date_isolation", "Date_death", "Date_last_modified"] can be regarded as the infection date (This may require discussion for aggregation.)
• recovery date is recorded in Date_last_modified column

[lisphilar]

@jim-sheldon If I understand the changes on 23Sep2022 correctly, we will close this issue and move forward to https://github.com/globaldothealth/monkeypox/issues/201?

Recovered data may be difficult due to https://github.com/globaldothealth/monkeypox/issues/177