search

rajeshrinet / pyross

PyRoss: inference, forecasts, and optimised control of epidemiological models in Python. github.com/rajeshrinet/pyross
https://pyross.readthedocs.io
MIT License
169 stars 57 forks source link

Data columns in case files #7

Closed philip-mach closed 4 years ago

philip-mach commented 4 years ago

I noticed the India data has an extra column compared with the China and Italy files. Can you clarify? Maybe a README in the data covid-cases directory?

Thanks.

rajeshrinet commented 4 years ago

@philip-mach thanks for pointing this out. There is now a readme.

The file for India has three columns: days since the first case, date, the number of infected individuals.

The files for China and Italy has two columns: date and number of infected individuals

Mouvoh commented 4 years ago

Hello Sir @rajeshrinet for the SIR and other examples based on India, can we use The Italy file as given or do we have to add the third column please ?

philip-mach commented 4 years ago

If it is running the same code there is no reason to believe that any other country will not need the missing column if you base it off an example that does. I added it for South Africa to make it work. However: things have moved on since then and each country seems to have a different data format.

Look in the Notebook for different countries for a line that starts something like

my_data = np.genfromtxt('../data/covid-cases/

and get some hints from that of how the variability in data format is handled.