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get_covid_argentina.m
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get_covid_argentina.m
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function [tableConfirmed_AR,tableDeaths_AR,tableRecovered_AR,time_AR] = get_covid_argentina( source, directory , Recovered_jh)
% get_covid_argentina() gets Argentina data from the COVID-19 epidemy from [1].
% Based on E. Cheynet's work [2].
%
% References:
% [1] https://github.com/SistemasMapache/Covid19arData/blob/master/CSV/Covid19arData%20-%20historico.csv
% [2] https://github.com/ECheynet/SEIR
%
% Version: 001
% Date: 2020/04/01
% Author: Rodrigo Gonzalez <rodralez@frm.utn.edu.ar>
% URL: https://github.com/rodralez/navego
%% Input handling
if nargin < 1
source = 'offline';
directory = './';
end
fprintf('get_covid_argentina: getting data %s...\n', source)
%%
province_ar = {'CABA';'Buenos Aires';'Catamarca';'Chaco';'Chubut'; ... Capital Federal
'Córdoba';'Corrientes';'Entre Ríos';'Formosa';'Jujuy';'La Pampa'; ...
'La Rioja';'Mendoza';'Misiones';'Neuquén';'Río Negro';'Salta'; ...
'San Juan';'San Luis';'Santa Cruz';'Santa Fe';'Santiago del Estero';...
'Tierra del Fuego';'Tucumán'; ''};
population_ar = [ 3075646; 17541141; 415438; 1204541; 618994; ...
3760450; 1120801; 1385961; 605193; 770881; 358428;...
393531; 1990338; 1261294; 664057; 747610; 1424397;...
781217; 508328; 365698; 3536418; 978313;...
173432; 1694656; 45376763; ];
%% RECOVERIES TABLE IS EMPTY
if ( strcmp (source, 'online'))
% Import the data
url = 'https://docs.google.com/spreadsheets/d/16-bnsDdmmgtSxdWbVMboIHo5FRuz76DBxsz_BbsEVWA/export?format=csv&id=16-bnsDdmmgtSxdWbVMboIHo5FRuz76DBxsz_BbsEVWA&gid=0';
% url = 'https://github.com/raw/SistemasMapache/Covid19arData/master/CSV/Covid19arData - historico.csv';
name = 'Covid19arData - historico.csv';
filename = [directory , name ];
websave( filename, url );
opts = detectImportOptions(filename);
% Specify file level properties
opts.ExtraColumnsRule = "ignore";
opts.EmptyLineRule = "read";
% Create input table with data in file
tableData = readtable(filename, opts);
tableData.Properties.VariableNames(1) = {'Dates'};
tableData.Properties.VariableNames(4) = {'CountryRegion'};
tableData.Properties.VariableNames(5) = {'ProvinceState'};
tableData.Properties.VariableNames(8) = {'NewActives'};
tableData.Properties.VariableNames(10) = {'NewDeaths'};
% Days in currect time series
FIRST_DAY = table2array(tableData(1,1));
LAST_DAY = table2array(tableData(end,1));
DAYS = days (LAST_DAY - FIRST_DAY) + 1;
% Country cells
country_c = cell(1, 25);
[country_c{:}] = deal('Argentina');
% Vartype cells
vartype_c = cell(1, DAYS+3);
[vartype_c{:}] = deal('double');
vartype_c(1) = {'string'};
vartype_c(2) = {'string'};
% Confirmed table
tableConfirmed_AR = table('Size', [25 DAYS+3], 'VariableTypes', vartype_c );
tableConfirmed_AR.Properties.VariableNames(1:3) = {'ProvinceState','CountryRegion','Population'};
tableConfirmed_AR.CountryRegion = country_c';
tableConfirmed_AR.ProvinceState = province_ar;
tableConfirmed_AR.Population = population_ar;
% Daytime cells
for ddx = 1:DAYS
time_s = ['Day_',datestr(FIRST_DAY+ddx-1,'dd_mm_yy') ];
tableConfirmed_AR.Properties.VariableNames(3+ddx) = { time_s };
end
% Deaths table
tableDeaths_AR = table('Size', [25 DAYS+3], 'VariableTypes', vartype_c );
tableDeaths_AR.Properties.VariableNames(1:3) = {'ProvinceState','CountryRegion','Population'};
tableDeaths_AR.CountryRegion = country_c';
tableDeaths_AR.ProvinceState = province_ar;
tableDeaths_AR.Population = population_ar;
% Daytime cells
for ddx = 1:DAYS
time_s = ['Day_',datestr(FIRST_DAY+ddx-1,'dd_mm_yy') ];
tableDeaths_AR.Properties.VariableNames(3+ddx) = { time_s };
end
% Recovery table
% Recovered series starts on 14/03/2020, filled by hand
recovered_ar = [zeros(1,12), 1, 1, 1, 3, 3, 3, 3, 3, 27, 51, 52, 52, 72, 72, 72, ...
91, 228, 240, 248, 256, 266, 279, 280, 325, 338, 358, 365, 375, 440, ...
468, 515, 559, 596, 631, 666, 685, 709, 737. 840 ]; % , 872, 919, 976
tableRecovered_AR = table('Size', [1 DAYS+3], 'VariableTypes', vartype_c );
tableRecovered_AR.Properties.VariableNames(1:3) = {'ProvinceState','CountryRegion','Population'};
tableRecovered_AR.CountryRegion = {'Argentina'};
tableRecovered_AR.ProvinceState = {''};
tableRecovered_AR.Population = tableDeaths_AR.Population(25);
diff = size(tableRecovered_AR(1,4:end), 2) - size(recovered_ar, 2);
idx = find (Recovered_jh == recovered_ar(end)) -1 ;
jdx = diff + idx;
fill_r = Recovered_jh(idx+1:jdx) ;
% fill_z = zeros (1, size(tableRecovered_AR(1,4:end), 2) - size(recovered_ar, 2) ) ;
tableRecovered_AR(1,4:end) = num2cell( [recovered_ar, fill_r ] );
% Daytime cells
for ddx = 1:DAYS
time_s = ['Day_',datestr(FIRST_DAY+ddx-1,'dd_mm_yy') ];
tableRecovered_AR.Properties.VariableNames(3+ddx) = { time_s };
end
% Index for Indeterminado
hdx = ~ (contains( tableData.ProvinceState, 'Indeterminado' ) );
% Index for badspelled provinces
bdx = (contains( tableData.ProvinceState, 'Tierra Del Fuego' ) );
tableData.ProvinceState (bdx) = {'Tierra del Fuego'};
bdx = (contains( tableData.ProvinceState, 'Santiago Del Estero' ) );
tableData.ProvinceState (bdx) = {'Santiago del Estero'};
if any(tableData.NewActives(~hdx))
error('get_covid_argentina: data in NewActives for "Indeterminado".')
end
if any(tableData.NewDeaths(~hdx))
error('get_covid_argentina: data in NewDeaths for "Indeterminado".')
end
%% Fill table with cases per day
for idx = 1:DAYS
ldx = table2array ( tableData(:,1) ) == FIRST_DAY + idx - 1;
% Do not select Indeterminado
ldx = ldx & hdx;
provinces = tableData.ProvinceState(ldx);
new_actives = tableData.NewActives(ldx);
new_deaths = tableData.NewDeaths(ldx);
for pdx = 1:size(provinces, 1)
cdx = contains( tableConfirmed_AR.ProvinceState, provinces(pdx) );
tableConfirmed_AR(cdx, idx+3) = num2cell ( table2array ( tableConfirmed_AR(cdx, idx+3)) + new_actives(pdx) );
tableDeaths_AR(cdx, idx+3) = num2cell ( table2array ( tableDeaths_AR(cdx, idx+3)) + new_deaths(pdx) );
end
end
for idx = 2:DAYS
ldx = table2array( tableConfirmed_AR(: , idx+3) ) == 0;
tableConfirmed_AR(ldx , idx+3) = tableConfirmed_AR(ldx , idx+3-1) ;
tableConfirmed_AR(~ldx , idx+3) = array2table( ...
table2array(tableConfirmed_AR(~ldx , idx+3-1)) + table2array(tableConfirmed_AR(~ldx , idx+3)));
ldx = table2array( tableDeaths_AR(: , idx+3) ) == 0;
tableDeaths_AR(ldx , idx+3) = tableDeaths_AR(ldx , idx+3-1) ;
tableDeaths_AR(~ldx , idx+3) = array2table( ...
table2array(tableDeaths_AR(~ldx , idx+3-1)) + table2array(tableDeaths_AR(~ldx , idx+3)));
end
total_c = sum ( table2array(tableConfirmed_AR(1:24, 3:end) ) );
tableConfirmed_AR( 25, 3:end ) = array2table( total_c );
total_c = sum ( table2array(tableDeaths_AR(1:24, 3:end) ) );
tableDeaths_AR( 25, 3:end ) = array2table( total_c );
%% TIME
time_AR = FIRST_DAY:LAST_DAY;
%% SAVE TABLES
save tableConfirmed_AR tableConfirmed_AR
save tableRecovered_AR tableRecovered_AR
save tableDeaths_AR tableDeaths_AR
save time_AR time_AR
% time_series_covid19_confirmed_global.csv
name = 'time_series_covid19_confirmed_ARG.csv';
filename = [directory , name ];
writetable(tableConfirmed_AR, filename );
name = 'time_series_covid19_recovered_ARG.csv';
filename = [directory , name ];
writetable(tableRecovered_AR, filename );
name = 'time_series_covid19_deaths_ARG.csv';
filename = [directory , name ];
writetable(tableDeaths_AR, filename );
elseif (strcmp (source, 'offline') )
%% LOAD TABLES
load tableConfirmed_AR
load tableRecovered_AR
load tableDeaths_AR
load time_AR
else
error('get_covid_argentina: bad source.')
end
disp('get_covid_argentina: exit.')
end