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Good question. The NYT dataset contains a list of anomalies (https://github.com/nytimes/covid-19-data/tree/master/rolling-averages) that I'm excluding from my visualisation. If I included them, there are many cases in which counties have large increases that mess up the seven day average for that week (with flashes of black or purple). This means that a number of cases aren't represented, although I'm not sure what could be done about that (maybe, as a rough approximation, divide them between the days of the previous month?).
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