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Mads Bahrami

[NB] COVID19 Confirmed Cases: US Counties

Mads Bahrami, Wolfram Research Inc

Posted 2 years ago

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MODERATOR NOTE: coronavirus resources & updates: https://wolfr.am/coronavirus

The COVID19 epidemic data of US counties can be retrieved from Wolfram Data Repository. Note that this dataset is updated daily, by curating the JHU data. In this very short essay, I show how to get county data and do some visualizations.

If you are retrieving the epidemic data on daily bases, I suggest erasing the resource object, to avoid any potential issue with cached data.

Get COVID19 epidemic data from WDR, select California counties

In[]:=

DeleteObject[ResourceObject["Epidemic Data for Novel Coronavirus COVID-19"]];coCases=ResourceData["Epidemic Data for Novel Coronavirus COVID-19","USCounties"]Select#State==

California, United States

ADMINISTRATIVE DIVISION

&,{#County,#ConfirmedCases["LastValue"]}&//Normal;

For coloring and legend, I borrowed some ideas from this community post. In other to figure out how to set limits of bins, one can get some hints from the following code.

Generate list of histogram bins and their heights from the number of confirmed cases, put them in the format of {bin range,height} and return bins with nonzero height:

In[]:=

Select[Transpose[{Partition[First[#],2,1],Last[#]}]&@HistogramList[coCases〚All,2〛],Last[#]>0&]

Out[]=

{{{0,500},46},{{500,1000},4},{{1000,1500},3},{{1500,2000},2},{{2000,2500},1},{{2500,3000},1},{{16000,16500},1}}

Choose 9 color bins, assign corresponding value ranges, and define a color function

In[]:=

colors=ResourceFunction["ColorBrewerData"]["Reds",9];bins={50,100,200,300,500,1000,2000,5000};cfunc[x_]:=Which@@Riffle[Join[x≤#&/@bins,{x>Last[bins]}],colors]

Define legends based on color bins and corresponding values:

In[]:=

legend=SwatchLegend[colors,ToString/@Join[{"<"<>ToString@First[bins]},ToString@#1<>"-"<>ToString@#2&@@@Partition[bins,2,1],{">"<>ToString@Last[bins]}],LegendMarkersGraphics[{EdgeForm[Black],Opacity[1],Rectangle[]}],LegendLabel"Confirmed Cases",LegendFunction(Framed[#,RoundingRadius5]&),LegendMargins5];

Color geo-regions using color bins defined before, and label regions by their name and number of confirmed cases:

In[]:=

Legended[GeoGraphics[{EdgeForm[Black],{GeoStyling[cfunc[#2]],Tooltip[Polygon[#1],Column[{StringDelete[CommonName[#1],", California, United States"],#2}]]}&@@@coCases},PlotLabel"COVID19 cases in California"],legend]

Out[]=

Confirmed Cases

	<50
	50-100
	100-200
	200-300
	300-500
	500-1000
	1000-2000
	2000-5000
	>5000

POSTED BY: Mads Bahrami

11 Replies

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Moderation Team

Moderation Team, WOLFRAM

Posted 2 years ago

-- you have earned *Featured Contributor Badge* Your exceptional post has been selected for our editorial column *Staff Picks* http://wolfr.am/StaffPicks and Your Profile is now distinguished by a *Featured Contributor Badge* and is displayed on the Featured Contributor Board. Thank you!

POSTED BY: Moderation Team

Updating Name

Posted 2 years ago

It appears that Which[] should be replaced by Which@@.

POSTED BY: Updating Name

Mads Bahrami

Mads Bahrami, Wolfram Research Inc

Posted 2 years ago

Good catch! The notebook is revised. Tnx!

POSTED BY: Mads Bahrami

Updating Name

Posted 2 years ago

Hi Mads, I made a copy of your notebook in my cloud account. When I run it I get Which::argctu: Which called with 1 argument. Looks like the definition of `cfunc` is not right.

POSTED BY: Updating Name

Mads Bahrami

Mads Bahrami, Wolfram Research Inc

Posted 2 years ago

Hmmm, I tried on cloud, and it works fine. On cloud, click on "Evaluation", then "Quit Kernel", and then "Evaluate All Cells".

POSTED BY: Mads Bahrami

Rohit Namjoshi

Posted 2 years ago

I made a copy before you fixed the issue with `Which`. Latest version works fine. Thanks!

POSTED BY: Rohit Namjoshi

Rohit Namjoshi

Posted 2 years ago

Hi Mads, I added the following code to show data for any state using `Manipulate`. cases[state_] := ResourceData["Epidemic Data for Novel Coronavirus COVID-19", "USCounties"][ Select[#State == state &], {#County, #ConfirmedCases["LastValue"]} &] // Normal; Manipulate[ GeoRegionValuePlot[Rule @@@ cases[state], GeoLabels -> (Tooltip[#1, Column[{First@CanonicalName@#2, #4}]] &), ColorFunction -> cfunc, ColorFunctionScaling -> False, PlotLegends -> legend, PlotLabel -> "COVID19 cases in " <> First@CanonicalName@state, ImageSize -> Large], {state, EntityClass["AdministrativeDivision", "USStatesAllStates"] // EntityList, ControlType -> PopupMenu}]

Hi Mads,

I added the following code to show data for any state using Manipulate.

cases[state_] := 
  ResourceData["Epidemic Data for Novel Coronavirus COVID-19", "USCounties"][
    Select[#State == state &], {#County, #ConfirmedCases["LastValue"]} &] // Normal;

Manipulate[
  GeoRegionValuePlot[Rule @@@ cases[state], 
  GeoLabels -> (Tooltip[#1, Column[{First@CanonicalName@#2, #4}]] &), 
  ColorFunction -> cfunc,
  ColorFunctionScaling -> False, 
  PlotLegends -> legend, 
  PlotLabel -> "COVID19 cases in " <> First@CanonicalName@state, 
  ImageSize -> Large], 
 {state, EntityClass["AdministrativeDivision", "USStatesAllStates"] // EntityList,
   ControlType -> PopupMenu}]

POSTED BY: Rohit Namjoshi

David G

Posted 2 years ago

I believe there is something wrong with the way GeoRegionValuePlot is displaying colors for some counties. For example if you look at Sonoma county, the confirmed cases is 192 (as of 4/23/2020), but the color doesn't match. There are other counties that show the same issue. Can you explain this?

POSTED BY: David G

Mads Bahrami

Mads Bahrami, Wolfram Research Inc

Posted 2 years ago

Thanks @David G . I will resolve the issue soon (very busy workload today). Quick solution for now: Legended[GeoGraphics[{EdgeForm[ Black], {GeoStyling[cfunc[#2]], Tooltip[Polygon[#1], Column[{StringDelete[CommonName[#1], ", California, United States"], #2}]]} & @@@ coCases}, PlotLabel -> "COVID19 cases in California", ImageSize -> Large], legend]

Thanks @David G . I will resolve the issue soon (very busy workload today). Quick solution for now:

Legended[GeoGraphics[{EdgeForm[
    Black], {GeoStyling[cfunc[#2]], 
      Tooltip[Polygon[#1], 
       Column[{StringDelete[CommonName[#1], 
          ", California, United States"], #2}]]} & @@@ coCases}, 
  PlotLabel -> "COVID19 cases in California", 
  ImageSize -> Large], legend]

POSTED BY: Mads Bahrami