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Gabriel Lemieux

[NB] Mapping "Live" COVID Data on a Globe

Gabriel Lemieux

Posted 2 years ago

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

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This document uses the data about the COVID-19 provided by the Johns Hopkins CSSE Github. But any data could be used!

Auto Update your Data

If you have Github installed on your system, you can use the following command to update an initialized copy of the ... university Github repertory (https://github.com/CSSEGISandData/COVID-19).

SetDirectory["path"];RunProcess[{"git","pull"},"StandardOutput"]

Out[]=

Already up to date.

Getting The Map (Without the use of Database)

The following commands allow you to prepare a basic map (cylindric projection) using GEOJSON data files that contain a polygon for each country. The one used here is available on the here: https://cdn.eintel.net/Downloads/coast.geojson . I forgot the original source, I think it was this one: https://datahub.io/core/geo-countries#resource-countries

countryPoly=Import["path","JSON"];countryPolyDs=(Association[Flatten[{"properties"/.#,"geometry"/.#}]]&/@Values[countryPoly[[2]]])//Dataset;

So the database look like that:

countryPolyDs//Take[#,3]&

Out[]=

And all the available countries are named has such:

countriesAvailable=countryPolyDs[;;,"ADMIN"]//Normal;Multicolumn[countriesAvailable,4]

Out[]=

Aruba	Denmark	Laos	Rwanda
Afghanistan	Dominican Republic	Lebanon	Western Sahara
Angola	Algeria	Liberia	Saudi Arabia
Anguilla	Ecuador	Libya	Scarborough Reef
Albania	Egypt	Saint Lucia	Sudan
Aland	Eritrea	Liechtenstein	South Sudan
Andorra	Dhekelia Sovereign Base Area	Sri Lanka	Senegal
United Arab Emirates	Spain	Lesotho	Serranilla Bank
Argentina	Estonia	Lithuania	Singapore
Armenia	Ethiopia	Luxembourg	South Georgia and South Sandwich Islands
American Samoa	Finland	Latvia	Saint Helena
Antarctica	Fiji	Macao S.A.R	Solomon Islands
Ashmore and Cartier Islands	Falkland Islands	Saint Martin	Sierra Leone
French Southern and Antarctic Lands	France	Morocco	El Salvador
Antigua and Barbuda	Faroe Islands	Monaco	San Marino
Australia	Federated States of Micronesia	Moldova	Somaliland
Austria	Gabon	Madagascar	Somalia
Azerbaijan	United Kingdom	Maldives	Saint Pierre and Miquelon
Burundi	Georgia	Mexico	Republic of Serbia
Belgium	Guernsey	Marshall Islands	Sao Tome and Principe
Benin	Ghana	Macedonia	Suriname
Burkina Faso	Gibraltar	Mali	Slovakia
Bangladesh	Guinea	Malta	Slovenia
Bulgaria	Gambia	Myanmar	Sweden
Bahrain	Guinea Bissau	Montenegro	Swaziland
The Bahamas	Equatorial Guinea	Mongolia	Sint Maarten
Bosnia and Herzegovina	Greece	Northern Mariana Islands	Seychelles
Bajo Nuevo Bank (Petrel Is.)	Grenada	Mozambique	Syria
Saint Barthelemy	Greenland	Mauritania	Turks and Caicos Islands
Belarus	Guatemala	Montserrat	Chad
Belize	Guam	Mauritius	Togo
Bermuda	Guyana	Malawi	Thailand
Bolivia	Hong Kong S.A.R.	Malaysia	Tajikistan
Brazil	Heard Island and McDonald Islands	Namibia	Turkmenistan
Barbados	Honduras	New Caledonia	East Timor
Brunei	Croatia	Niger	Tonga
Bhutan	Haiti	Norfolk Island	Trinidad and Tobago
Botswana	Hungary	Nigeria	Tunisia
Central African Republic	Indonesia	Nicaragua	Turkey
Canada	Isle of Man	Niue	Tuvalu
Switzerland	India	Netherlands	Taiwan
Chile	Indian Ocean Territories	Norway	United Republic of Tanzania
China	British Indian Ocean Territory	Nepal	Uganda
Ivory Coast	Ireland	Nauru	Ukraine
Clipperton Island	Iran	New Zealand	United States Minor Outlying Islands
Cameroon	Iraq	Oman	Uruguay
Cyprus No Mans Area	Iceland	Pakistan	United States of America
Democratic Republic of the Congo	Israel	Panama	US Naval Base Guantanamo Bay
Republic of Congo	Italy	Pitcairn Islands	Uzbekistan
Cook Islands	Jamaica	Peru	Vatican
Colombia	Jersey	Spratly Islands	Saint Vincent and the Grenadines
Comoros	Jordan	Philippines	Venezuela
Cape Verde	Japan	Palau	British Virgin Islands
Costa Rica	Baykonur Cosmodrome	Papua New Guinea	United States Virgin Islands
Coral Sea Islands	Siachen Glacier	Poland	Vietnam
Cuba	Kazakhstan	Puerto Rico	Vanuatu
Curaçao	Kenya	North Korea	Wallis and Futuna
Cayman Islands	Kyrgyzstan	Portugal	Akrotiri Sovereign Base Area
Northern Cyprus	Cambodia	Paraguay	Samoa
Cyprus	Kiribati	Palestine	Yemen
Czech Republic	Saint Kitts and Nevis	French Polynesia	South Africa
Germany	South Korea	Qatar	Zambia
Djibouti	Kosovo	Romania	Zimbabwe
Dominica	Kuwait	Russia

The following function gets the polygon data contained in the JSON and prepare Mathematica Polygon objects.

In[]:=

getPoly[target_String]:=If[countryPolyDs[SelectFirst[#ADMINtarget&],#type&]"MultiPolygon",Polygon/@(countryPolyDs[SelectFirst[#ADMINtarget&],#coordinates&]//Normal),Polygon[countryPolyDs[SelectFirst[#ADMINtarget&],#coordinates&]//Normal]];

Now we can create a basemap:

basemap={EdgeForm[{Thin,Black}],FaceForm[White]}~Join~Join[(getPoly/@countriesAvailable)];basemap//Graphics[#,Background->LightBlue,ImageSizeLarge]&//Rasterize

Out[]=

Using ColorData we can add a bit of color on the basemap. I think you are guessing how we will put our data on the map!

{EdgeForm[{Thin,Black}]}~Join~Join[Riffle[getPoly/@countriesAvailable,FaceForm[{#}]&/@ColorData[35,"ColorList"]]]//Graphics[#,Background->LightBlue,ImageSizeLarge]&//Rasterize

Out[]=

Getting the data from the Github repertory

First we load the data from each file, then we will interpret them. We use the interpreter for the number, and we apply the DateObject function on the right columns. The DateObject function will return few errors because of the date formatting that was used in the first versions.

dateAvailable=FileNames[]//StringCases[DigitCharacter..]//DeleteCases[{}];rawData=Import[#,"CSV"]&/@(StringTemplate["``-``-``.csv"]@@#&/@dateAvailable);interpreter={#[[2]],DateObject[#[[3]]],Interpreter["Number"][#[[4]]],Interpreter["Number"][#[[5]]],Interpreter["Number"][#[[6]]]}&;dataFrame=If[MissingQ[#],0,#]&//@ParallelMap[interpreter,Flatten[Rest/@rawData,1]];

Let’s take the data from yesterday, we suppose they are complete. We could use the data from today, but the Github might not have been updated.

In[]:=

dataFrame=DeleteCases[dataFrame,FailureQ[#[[1]]]&];yesterdayData=(GatherBy[Select[dataFrame,DateWithinQ[Yesterday,#[[2]]]&],First]);totalByCountry=Prepend[Total[#[[;;,{3,4,5}]]],#[[1,1]]]&/@yesterdayData;

Some countries won’t be recognized because they are named differently. Here I correct some, but I’ll let few to show the differences.

totalByCountry=totalByCountry/.{"US""United States of America","Korea, South"->"South Korea","Taiwan*""Taiwan"};Grid[{#[[1]],#[[2]],#[[3]],#[[4]]}&/@totalByCountry]

Out[]=

China	71988	3169	60783
Italy	35713	2978	4025
Iran	17361	1135	5389
Spain	13910	623	1081
Germany	12327	28	105
France	9046	148	12
South Korea	8413	84	1540
Switzerland	3028	28	15
United Kingdom	2635	71	67
United States of America	7447	115	106
Netherlands	2053	58	2
Austria	1646	4	9
Norway	1550	6	1
Belgium	1486	14	31
Sweden	1279	10	1
Denmark	1115	4	1
Japan	889	29	144
Malaysia	790	2	60
Cruise Ship	712	7	325
Czechia	464	0	3
Qatar	452	0	4
Portugal	448	2	3
Israel	433	0	11
Greece	418	5	8
Brazil	372	3	2
Finland	336	0	10
Singapore	313	0	114
Pakistan	299	0	2
Ireland	292	2	5
Australia	567	6	23
Romania	260	0	19
Estonia	258	0	1
Bahrain	256	1	88
Poland	251	5	13
Iceland	250	1	5
Chile	238	0	0
Indonesia	227	19	11
Canada	653	8	9
Thailand	212	1	42
Luxembourg	203	2	0
Philippines	202	19	5
Egypt	196	6	32
Iraq	164	12	43
India	156	3	14
Russia	147	0	8
Peru	145	0	1
Kuwait	142	0	15
Lebanon	133	3	3
San Marino	119	11	4
South Africa	116	0	0
United Arab Emirates	113	0	26
Ecuador	111	2	0
Slovakia	105	1	0
Taiwan	100	1	22
Turkey	98	1	0
Colombia	93	0	1
Mexico	93	0	4
Bulgaria	92	2	0
Panama	86	1	0
Armenia	84	0	1
Serbia	83	0	1
Croatia	81	0	4
Argentina	79	2	3
Vietnam	75	0	16
Algeria	74	7	12
Latvia	71	0	1
Brunei	68	0	0
Albania	59	2	0
Hungary	58	1	2
Jordan	52	0	1
Belarus	51	0	5
Sri Lanka	51	0	1
Costa Rica	50	0	0
Uruguay	50	0	0
Cyprus	49	0	0
Morocco	49	2	1
Oman	39	0	12
Bosnia and Herzegovina	38	0	2
Georgia	38	0	1
Venezuela	36	0	0
Cambodia	35	0	1
Kazakhstan	35	0	0
North Macedonia	35	0	1
Senegal	31	0	2
Moldova	30	1	1
Tunisia	29	0	0
Liechtenstein	28	0	0
Guadeloupe	27	0	0
Lithuania	27	0	1
Burkina Faso	20	1	0
New Zealand	20	0	0
Martinique	19	1	0
Uzbekistan	15	0	0
Bangladesh	14	1	3
Jamaica	13	0	2
Bolivia	12	0	0
Reunion	12	0	0
Paraguay	11	0	0
Honduras	9	0	0
Nigeria	8	0	1
Rwanda	8	0	0
Cuba	7	1	0
Trinidad and Tobago	7	0	0
Cote d'Ivoire	6	0	1
Ethiopia	6	0	0
Mongolia	6	0	0
Aruba	4	0	0
Congo (Kinshasa)	4	0	0
Equatorial Guinea	4	0	0
Kyrgyzstan	3	0	0
Mauritius	3	0	0
Mayotte	3	0	0
Tanzania	3	0	0
Barbados	2	0	0
Benin	2	0	0
Liberia	2	0	0
Sudan	2	1	0
Zambia	2	0	0
Djibouti	1	0	0
Gambia, The	1	0	0
Montenegro	1	0	0
Somalia	1	0	0
Guam	0	0	0
The Gambia	0	0	0

Preparing the 2D Map

The 2D map is the important one since it is more useful in many situations to work with two-dimensional representations. Still we will make a 3D globe in the next section!

Countries in the data:

selected=Select[MemberQ[countriesAvailable,#[[1]]]&][totalByCountry[[;;]]];selected[[;;,1]]//Multicolumn[#,4]&

Out[]=

China	Romania	Panama	Burkina Faso
Italy	Estonia	Armenia	New Zealand
Iran	Bahrain	Croatia	Uzbekistan
Spain	Poland	Argentina	Bangladesh
Germany	Iceland	Vietnam	Jamaica
France	Chile	Algeria	Bolivia
South Korea	Indonesia	Latvia	Paraguay
Switzerland	Canada	Brunei	Honduras
United Kingdom	Thailand	Albania	Nigeria
United States of America	Luxembourg	Hungary	Rwanda
Netherlands	Philippines	Jordan	Cuba
Austria	Egypt	Belarus	Trinidad and Tobago
Norway	Iraq	Sri Lanka	Ethiopia
Belgium	India	Costa Rica	Mongolia
Sweden	Russia	Uruguay	Aruba
Denmark	Peru	Cyprus	Equatorial Guinea
Japan	Kuwait	Morocco	Kyrgyzstan
Malaysia	Lebanon	Oman	Mauritius
Qatar	San Marino	Bosnia and Herzegovina	Barbados
Portugal	South Africa	Georgia	Benin
Israel	United Arab Emirates	Venezuela	Liberia
Greece	Ecuador	Cambodia	Sudan
Brazil	Slovakia	Kazakhstan	Zambia
Finland	Taiwan	Senegal	Djibouti
Singapore	Turkey	Moldova	Montenegro
Pakistan	Colombia	Tunisia	Somalia
Ireland	Mexico	Liechtenstein	Guam
Australia	Bulgaria	Lithuania

Some countries were not recognized, I corrected some of them already in the previous section:

Select[¬MemberQ[countriesAvailable,#[[1]]]&][totalByCountry[[;;]]]//Multicolumn[#[[;;,1]],5]&

Out[]=

Cruise Ship	North Macedonia	Reunion	Mayotte	The Gambia
Czechia	Guadeloupe	Cote d'Ivoire	Tanzania
Serbia	Martinique	Congo (Kinshasa)	Gambia, The

Now we are ready to colour our map!

cs=ColorData[{"TemperatureMap",{0,Log[100000]}}];cvmap=(basemap~Join~Join[{FaceForm[cs[If[#[[2]]≠0,Log[#[[2]]],0]]],getPoly[#[[1]]]}&/@selected])//Graphics[#,PlotRange{{-180,180},Automatic},Background->LightBlue,ImageSizeLarge]&;Row[{Rasterize[cvmap,ImageSizeLarge],BarLegend[{"TemperatureMap",{0,Log[100000]}}]},FrameTrue,BackgroundLightBlue]

Globe representation

This step is easier than I was thinking. Using SphericalPlot, we can apply a Texture on the sphere with the right mapping. The Automatic TextureCoordinateFunction from SphericalPlot does the hard work for us! Note the rotation I did on the picture.

Row[{SphericalPlot3D[1,θ,ϕ,AxesFalse,BoxedFalse,MeshStyleDirective[{Opacity[0.25]}],Ba