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Bernat Espigulé

[NB] Propagation risk of COVID-19 by local contact in Spain

Bernat Espigulé, Universitat de Barcelona

Posted 2 years ago

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AUTHORS's GitHub Repository: github.com/espigule/SARS-CoV-2SpainMarch_2020*

Animated GIF Propagation risk of COVID-19

Source

A team of researchers from Spain presented an interactive map: deim.urv.cat/~alephsys/COVID-19/spain/en/. And since their numerical data is freely available to everyone as an excel file I decided to take it a look in a Mathematica notebook. The following is the exploration I made with GeoGraphics using their estimated propagation risk of COVID-19 by local contact in Spain (14 - 18 March).

Importing the raw data

In[]:=

path=NotebookDirectory[];

In[]:=

rawdata14t18=Import["https://deim.urv.cat/~alephsys/COVID-19/spain/resources/Risk_Municipio_2020_03_14-18.xlsx"]

Out[]=

{{{,% Riesgo SARS-CoV-2,,,,},

⋯7156⋯

,{Zucaina,1.×

-7

,1.×

-7

,1.×

-7

,1.×

-7

,1.×

-7

}}}

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In[]:=

dates=rawdata14t18[[1,2,2;;]]

Out[]=



Sat 14 Mar 2020 00:00:00GMT+1.

Sun 15 Mar 2020 00:00:00GMT+1.

Mon 16 Mar 2020 00:00:00GMT+1.

Tue 17 Mar 2020 00:00:00GMT+1.

Wed 18 Mar 2020 00:00:00GMT+1.



Data Curation

Propagation risk time series:

In[]:=

ts1418=ParallelMap[#[[1]]->TimeSeries[#[[2;;6]],{dates}]&,rawdata14t18[[1,3;;]]];

Interpreter[Restricted[“City”,Entity[“Country”,”Spain”]]][“municipality”]

In order to get Wolfram’s city interpreter working properly I removed diacritics and other language variants:

In[]:=

cleanNames1=RemoveDiacritics/@Map[StringRiffle@Reverse[StringSplit[#,", "]]&,Map[StringSplit[#,"/"][[-1]]&,Map[StringReplace[#,"-"" "]&,rawdata14t18[[1,3;;,1]]]]];

In[]:=

cleanNames1

In[]:=

cleanNames2=RemoveDiacritics/@Map[StringRiffle@Reverse[StringSplit[#,", "]]&,Map[StringSplit[#,"/"][[-1]]&,Map[StringSplit[#,"-"][[-1]]&,rawdata14t18[[1,3;;,1]]]]];

In[]:=

cleanNames2

In[]:=

cleanNames3=RemoveDiacritics/@Map[StringSplit[#,"/"][[-1]]&,Map[StringReplace[StringDelete[#,{"O ","Los ","El "," el","La ","L ","Las "," al"," las"," la"," l"," de"," d"," y"," i"}],"-"" "]&,Map[StringRiffle@Reverse[StringSplit[#,", "]]&,rawdata14t18[[1,3;;,1]]]]];

In[]:=

cleanNames3

In[]:=

municipalities=ParallelMap[{#[[1]],interpreted=DeleteDuplicates[Interpreter[Restricted["City",Entity["Country","Spain"]]][DeleteDuplicates[#[[2;;]]]]];Select[interpreted,FailureQ[#]==False&]}&,Transpose[{rawdata14t18[[1,3;;,1]],cleanNames1,cleanNames2,cleanNames3}]]

Out[]=

Ollauri,

Ollauri

,{Haro,{}},Gimileo,

Gimileo

,Briñas,

Brinas

,Casalarreina,

Casalarreina

,Anguciana,

Anguciana

,Labastida/Bastida,

La Bastida

,

⋯7142⋯

,Yunta, La,

La Yunta

,Zamarra,

Zamarra

,Zaorejas,

Zaorejas

,Zapardiel de la Cañada,

Zapardiel de la Canada

,Zarza de Pumareda, La,

La Zarza de Pumareda

,Zorita del Maestrazgo,

Zorita del Maestrazgo

,Zucaina,

Zucaina



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There is 6551 municipalities with non-ambiguous interpretations:

In[]:=

municipalities1=Flatten/@Select[municipalities,Length[#[[-1]]]1&]

And 43 municipalities with more than one possible interpretation that need hand curation:

In[]:=

Select[municipalities,Length[#[[-1]]]>1&]

In[]:=

municipalities2="Rozas de Madrid, Las",

Las Rozas de Madrid

CITY

,"Valencia de las Torres",

Valencia de las Torres

CITY

,"Arcos, Los",

Los Arcos

CITY

,"Uharte-Arakil",

Uharte-Arakil

CITY

,"Herrera, La",

La Herrera

CITY

,"Fuente-Álamo",

Fuente Alamo de Murcia

CITY

,"Corral-Rubio",

Corral-Rubio

CITY

,"Santos, Los",

Los Santos

CITY

,"Granada, La",

La Granada

CITY

,"Font-rubí",

Font-rubi

CITY

,"Serrada, La",

La Serrada

CITY

,"Cerro, El",

El Cerro

CITY

,"Zarza, La",

La Zarza

CITY

,"Vélez-Málaga",

Velez-Malaga

CITY

,"Peñarroya-Pueblonuevo",

Penarroya-Pueblonuevo

CITY

,"Valls dAguilar, Les",

Les Valls d'Aguilar

CITY

,"Serna, La",

La Serna

CITY

,"Fuente-Olmedo",

Fuente-Olmedo

CITY

,"Majadas, Las",

Las Majadas

CITY

,"Antigua, La",

La Antigua

CITY

,"San Pedro de la Nave-Almendra",

San Pedro de la Nave-Almendra

CITY

,"Calahorra, La",

La Calahorra

CITY

,"Oliva, La",

Oliva

CITY

,"Foz-Calanda",

Foz-Calanda

CITY

,"Alamedilla, La",

La Alamedilla

CITY

,"Galera, La",

La Galera

CITY

,"Grado, El",

El Grado

CITY

,"Vélez-Rubio",

Velez-Rubio

CITY

,"Robleda-Cervantes",

Robleda-Cervantes

CITY

,"Zarza, La",

La Zarza

CITY

,"Zarza-Capilla",

Zarza-Capilla

CITY

,"Marines, Los",

Los Marines

CITY

,"Valde-Ucieza",

Valde-Ucieza

CITY

,"Torre, La",

La Torre

CITY

,"Cuervo, El",

El Cuervo

CITY

,"Saceda-Trasierra",

Saceda-Trasierra

CITY

,"Atalaya, La",

La Atalaya

CITY

,"Azanuy-Alins",

Azanuy-Alins

CITY

,"Figuera, La",

La Figuera

CITY

,"Frontera, La",

Frontera

CITY

,"Garganta, La",

La Garganta

CITY

,"Olmos, Los",

Los Olmos

CITY

,"Villa del Campo",

Villa del Campo

CITY



Despite this effort about 12% of these municipalities were not interpreted at all :

In[]:=

Length@Select[municipalities,Length[#[[-1]]]==0&]

Out[]=

562

In[]:=

Select[municipalities,Length[#[[-1]]]==0&][[All,1]]

Curated Dataset

In[]:=

dataset14t18=Dataset[Map[<|"Municipality"->#[[-1]],"Propagation"->#[[1]]/.ts1418|>&,Join[municipalities1,municipalities2]]]

In[]:=

dataset14t18=Import[path<>"dataset14t18.m"]

Out[]=

Municipality

Propagation

Ollauri

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Gimileo

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Brinas

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Casalarreina

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Anguciana

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



La Bastida

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Zarraton

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Villalba de Rioja

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



San Asensio

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Castanares de Rioja

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Briones

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Cuzcurrita de Rio Tiron

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



San Sebastian de la Gomera

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Arjonilla

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Santo Domingo de la Calzada

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



San Vicente de la Sonsierra

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Leiva

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Miranda de Ebro

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Rodezno

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



Banares

TimeSeries

Time: 14 Mar 2020 to 18 Mar 2020
Data points: 5



showing 1–20 of 6594

Data Visualization

Iberian Peninsula

In[]:=

GeoGraphics[(* Legend *)legend=MapIndexed[{EdgeForm[Directive[Thin,Black]],FaceForm[ColorData["Rainbow"][If[(10+Log[#1])/7<0,0.0001,(10+Log[#1])/7]]],Disk[GeoPosition[{37.5,.75First[#2]-1}],.2 If[(10+Log[#1])/7<0,0.001,(10+Log[#1])/7]],Inset[Style[ToString[100#]<>" %",White],GeoPosition[{37.2,.75First[#2]-1}]]}&,{0.0001,0.00025,0.0005,0.001,0.005,0.015,0.025,0.035}],(* GeoStyling *)styling={GeoBackgroundGeoStyling["StreetMapNoLabels",GeoStylingImageFunction(ImageAdjust@ColorNegate@ColorConvert[#1,"Grayscale"]&)],GeoScaleBarPlaced[{"Metric","Imperial"},{Left,Top}],GeoRange{{35,45.5},{-11,5.5}},GeoRangePaddingFull,ImageSize800}]

Out[]=