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outbreak-info / outbreak.info

During outbreaks of emerging diseases such as COVID-19, efficiently collecting, sharing, and integrating data is critical to scientific research. outbreak.info is a resource to aggregate all this information into a single location.
https://outbreak.info/
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Use Johns Hopkins CSSE data for Puerto Rico cases instead of New York Times #356

Open sacundim opened 3 years ago

sacundim commented 3 years ago

The daily new cases time series for Puerto Rico on Outbreak.info is at this URL:

It currently looks like this:

Screen Shot 2021-05-08 at 1 04 46 PM

From the note at the bottom and my own analysis of the chart, the data shown for Puerto Rico is from the New York Times. But the New York Times' data set's Puerto Rico data set is, to put it charitably, baroque, because its daily case numbers up to Nov. 6, 2020 are PCR + serological, but since Nov. 7, 2020 are PCR + antigens. This is because around that date, the Puerto Rico Department of Health revised the way that it classifies cases in order to incorporate cases found by antigen testing. Nov. 6 daily report (data up to Nov. 5):

Puerto Rico Department of Health, Nov. 6 daily report (data up to Nov. 5)

Nov. 7 daily report: (data up to Nov. 6):

Puerto Rico Department of Health, Nov. 7 daily report (data up to Nov. 6)

While aggregators like the COVID Tracking Project and Johns Hopkins CSSE retroactively reviewed their Puerto Rico time series so as to make it PCR + antigen the whole way through, the New York Times has strangely decided to carry on with a time series whose meaning completely changes on that date.

If we assume that PCR + antigens case count is preferable to PCR + antigens + serological, then Johns Hopkins CSSE has an accurate time series for Puerto Rico. But even if we assume that PCR + antigens + serological is preferable, NYT doesn't have that...

More info in this Twitter thread I wrote a couple of months ago:

gkarthik commented 3 years ago

Hey @sacundim, thank you for the detailed explanation! I wasn't aware of this change on Nov 6th. We are in the process of switching to JHU data for US states, and counties as well. However, this could take a while but that should fix this issue. I will keep you updated!