Update US case counts source

nextstrain / forecasts-ncov

SARS-CoV-2 variant growth rates and frequency forecasts

https://nextstrain.org/sars-cov-2/forecasts/

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Update US case counts source #16

Open joverlee521 opened 1 year ago

joverlee521 commented 1 year ago

Our current US case count source was no longer updated as of 10/20/2022.

There is a new CDC data source, but this reports cases by week instead of by day.

joverlee521 commented 1 year ago

I did not notice the US case counts was no longer updated because the automated pipeline only notifies when the upload has updated the file on S3. It does not send notifications when the file is identical to the S3 file. This should be changed so that we get alerted if the case counts do not get updated.

joverlee521 commented 1 year ago

Alternative sources:

NYTimes has a public repo for US case counts, but the daily counts are cumulative
John Hopkins has a public repo for case counts, with US case counts split by county and wide date columns with daily counts that are cumulative

marlinfiggins commented 1 year ago

I'd recommend the NYT's case data. Their us-states.csv seems to be basically exactly what we need other than just taking a diff for cases between consecutive days.