COVID-19 US County Death Timeline Plots
COVID-19 US County Death Timeline Plots
Bob Sandheinrich
Create timeline plots of New York Times county-by-county data for COVID-19 deaths.
Retrieve Data
Retrieve Data
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AbsoluteTiming[timeseries=ResourceFunction["NYTimesCOVID19Data"]["USCountiesTimeSeries"];]
Plotting Tools
Plotting Tools
Making log trend lines
Making log trend lines
This is pretty hacky—Epilog with DateListLogPlot is not easy to use, but I experimentally found some values that look alright.
Decide how long the trend lines should be and define a vertical offset (the offset was chosen experimentally and may need to be adjusted):
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$linedays=30;$startlinevalue=2.5;
Define functions for making trendlines and labeling them:
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makeline[a_]:=N@{Darker[ColorData["TemperatureMap"][1/2+1/(a/2)],.2],Line[{{Now,$startlinevalue},{Now+Quantity[$linedays,"Days"],$startlinevalue+($linedays/a)}}],Text["Doubles every "<>ToString[a]<>" days",textlocation[a]]}
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textlocation[a_]:=If[2^($linedays/a)<100,{Now+Quantity[$linedays,"Days"],$startlinevalue+($linedays/a)},With[{d=First[x/.NSolve[2^(x/a)100.&&x>0,x]]},{Now+Quantity[d-5,"Days"],N@Log[2,100]}]]
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$plotopts=Sequence@@{FrameTicks{None, Automatic},PlotRange{Automatic,{5,Automatic}},PlotLegendsNone,PlotLabelsPlaced[Automatic,Right,StringDelete[CommonName[#],", United States"]&],Epilog{Dashed,makeline/@{3,5,10}},ImageSize800};
Select Data
Select Data
Select only data for counties that have had a minimum number of deaths for a minimum number of days, then align the first timestamp of each time series using the TimeSeriesAlign resource function:
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$mindeaths=10;$mindays=18;
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highdeaths=timeseries[All,ResourceFunction["TimeSeriesSelect"][#Deaths,#2>$mindeaths&]&][Select[#["PathLength"]>$mindays&]/*ResourceFunction["TimeSeriesAlign"]];
Create a Plot
Create a Plot
Create a plot:
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DateListLogPlot[highdeaths,$plotopts]
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Deploy a Web Form
Deploy a Web Form
Export the data to a static cloud object to make the performance reasonable:
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dataco=CloudExport[timeseries,"WXF","COVID19/CountyTimeSeries/data.wxf"];
Deploy a form:
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CloudDeploy[FormFunction[{"County"RepeatingElement["USCounty"]},With[{data=Import[dataco]},With[{selected=data[KeyTake[#County],ResourceFunction["TimeSeriesSelect"][#Deaths,#2>$mindeaths&]&][Select[#["PathLength"]>$mindays&]/*ResourceFunction["TimeSeriesAlign"]]},If[!MissingQ[selected]&&Length[selected]>0,DateListLogPlot[selected,$plotopts],CloudPut[#County->selected,"COVID19/CountyTimeSeries/lastfailure"];"No data found"]]]&,"CloudCDFElement",AppearanceRules<|"Title""US County COVID-19 Death Timeline","Description""NY Times Data updated: "<>DateString[]|>],"COVID19/CountyTimeSeries/form",Permissions"Public"]
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Any time the results do not contain data, it logs it here:
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CloudGet["COVID19/CountyTimeSeries/lastfailure"]
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{}MissingNotAvailable,Select[#1[PathLength]>2&]/*