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lisphilar / covid19-sir

CovsirPhy: Python library for COVID-19 analysis with phase-dependent SIR-derived ODE models.
https://lisphilar.github.io/covid19-sir/
Apache License 2.0
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[Bug] Wrong vaccination data #1373

Closed eguidotti closed 1 year ago

eguidotti commented 1 year ago

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Summary

Hi @lisphilar, I'm integrating your data in COVID-19 Data Hub and I've found an issue with the vaccination data.

Below I plot the Vaccinated_1st for Location=Domestic from your file: https://github.com/lisphilar/covid19-sir/blob/main/data/japan/covid_jpn_total.csv

vacc

It seems that the data are a mix of cumulative/non-cumulative counts (?) For instance, on 2022-10-10 the number of people with 1 dose is 9744650, but on 2022-10-11 it is 857. And then on 2022-10-16 it is again 9745232.

How should I proceed? Thanks a lot!

Reproducible example script

This is an issue about the data, not the code

The current outputs

See picture above

Expected outputs

No response

Environment

This is an issue about the data, not the code

Package manager (required if installation issue)

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Platform (required if installation issue)

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Additional Context

This is an issue about the data, not the code

lisphilar commented 1 year ago

Thank you for your kind notive. Vaccinated_1st and Vaccinated_2nd were NON-cumulative values. Vaccinated_3rd counts were cumulative values. With #1381, I converted Vaccinated_1st and Vaccinated_2nd to cumulative values. (The last date is 04Feb2023. I will update the dataset in a day.)

lisphilar commented 1 year ago

Data updated. The number of cases: to 05Mar2023, Vaccinated: to 02Mar2023 per primary sources.

Additional infomation: The primaly source has the number of cases with 4th/5th vaccine shots in Japan. Our dataset will provide the data with #1382.

eguidotti commented 1 year ago

Mmm it seems something strange is going on. I tried to plot the data (picture below) and Vaccinated 1 and 2 look weird. In particular, vaccinated 1 is decreasing while it should be cumulative now from my understanding

Thanks a lot for your efforts!

Rplot

lisphilar commented 1 year ago

With #1386, I revised the process of vaccination data integration fully, vaccinated

eguidotti commented 1 year ago

Awesome!

I just noticed that on 2022-01-24 the entry for Hosp_require seems to be a manual entry mistake. The value is 3222100 while I think it should be 322210.

Except from that, I think this issue can be closed. I also checked the data at the prefecture level and they seem ok.

Thanks a lot for your help!