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Figures_Appendix_cases7_rho_A14_EPG.m
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Figures_Appendix_cases7_rho_A14_EPG.m
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close all
clear all
load('./Data/tables.mat')
eq = readtable('./Data/relacio_aga.xlsx');
prop = xlsread('./Figures&Tables/Table_incidence_T2.xlsx','Numbers','L:L');
prop = [prop(2:end);prop(1)];
prop = 1./prop;
time = datenum('01/06/2020','dd/mm/yyyy'):datenum('03/09/2020','dd/mm/yyyy');
u = unique(T0827.id_AGA);
pop = 0.*u;
for i = 1:length(u)+1
if i<=length(u)
pop(i) = unique(T0827.popAGA(T0827.id_AGA==u(i)));
else
pop(i) = sum(pop);
end
end
A14_Pc = zeros(length(time),length(u)+1);
A14_CC = zeros(length(time),length(u)+1);
iA14_Pc = zeros(length(time),length(u)+1);
iA14_CC = zeros(length(time),length(u)+1);
cas_Pc = zeros(length(time),length(u)+1);
cas_CC = zeros(length(time),length(u)+1);
icas_Pc = zeros(length(time),length(u)+1);
icas_CC = zeros(length(time),length(u)+1);
cas7_Pc = zeros(length(time),length(u)+1);
cas7_CC = zeros(length(time),length(u)+1);
icas7_Pc = zeros(length(time),length(u)+1);
icas7_CC = zeros(length(time),length(u)+1);
rho_Pc = zeros(length(time),length(u)+1);
rho_CC = zeros(length(time),length(u)+1);
irho_Pc = zeros(length(time),length(u)+1);
irho_CC = zeros(length(time),length(u)+1);
T = T0913;
for i = 1:length(u)+1
for k = 1:length(time)
if i <= length(u)
cas_Pc(k,i) = T.PCRcas(T.id_AGA==u(i) & datenum(T.data)==time(k));
cas_CC(k,i) = T.ClinicsCovid(T.id_AGA==u(i) & datenum(T.data)==time(k));
else
cas_Pc(k,i) = sum(T.PCRcas(datenum(T.data)==time(k)));
cas_CC(k,i) = sum(T.ClinicsCovid(datenum(T.data)==time(k)));
end
[phat, pci] = binofit(cas_Pc(k,i),pop(i),0.05);
icas_Pc(k,i) = mean(abs(pci-phat)*pop(i));
[phat, pci] = binofit(cas_CC(k,i),pop(i),0.05);
icas_CC(k,i) = mean(abs(pci-phat)*pop(i));
if k>6
cas7_Pc(k,i) = 1/7*sum(cas_Pc(k-6:k,i));
cas7_CC(k,i) = 1/7*sum(cas_CC(k-6:k,i));
icas7_Pc(k,i) = 1/7*sqrt(sum(icas_Pc(k-6:k,i).^2));
icas7_CC(k,i) = 1/7*sqrt(sum(icas_CC(k-6:k,i).^2));
end
end
id = 8:length(time);
rho_Pc(id,i) = (cas7_Pc(id,i)+cas7_Pc(id-1,i)+cas7_Pc(id-2,i))./max(cas7_Pc(id-5,i)+cas7_Pc(id-6,i)+cas7_Pc(id-7,i),1);
rho_CC(id,i) = (cas7_CC(id,i)+cas7_CC(id-1,i)+cas7_CC(id-2,i))./max(cas7_CC(id-5,i)+cas7_CC(id-6,i)+cas7_CC(id-7,i),1);
for k = 8:length(time)
k2 = 1/sum(cas7_Pc(k-7:k-5,i));
irho_Pc(k,i) = k2*sqrt(sum((icas7_Pc(k-2:k,i)).^2)+rho_Pc(k,i)^2*sum((icas7_Pc(k-7:k-5,i)).^2));
k2 = 1/sum(cas7_CC(k-7:k-5,i));
irho_CC(k,i) = k2*sqrt(sum((icas7_CC(k-2:k,i)).^2)+rho_CC(k,i)^2*sum((icas7_CC(k-7:k-5,i)).^2));
end
acc = cumsum(cas7_Pc(:,i));
a14 = 0.*acc;
a14(1:14) = acc(1:14);
a14(15:end) = acc(15:end)-acc(1:end-14);
A14_Pc(:,i) = a14/pop(i)*1e5;
acc = cumsum(cas7_CC(:,i));
a14 = 0.*acc;
a14(1:14) = acc(1:14);
a14(15:end) = acc(15:end)-acc(1:end-14);
A14_CC(:,i) = a14/pop(i)*1e5;
for k = 14:length(time)
iA14_Pc(k,i) = sqrt(sum((icas7_Pc(k-13:k,i)).^2))/pop(i)*1e5;
iA14_CC(k,i) = sqrt(sum((icas7_CC(k-13:k,i)).^2))/pop(i)*1e5;
end
end
EPG_Pc = A14_Pc.*rho_Pc;
EPG_CC = A14_CC.*rho_CC;
iEPG_Pc = sqrt(A14_Pc.^2.*(irho_Pc.^2) + rho_Pc.^2.*(iA14_Pc.^2));
iEPG_CC = sqrt(A14_CC.^2.*(irho_CC.^2) + rho_CC.^2.*(iA14_CC.^2));
col = lines(4);
u = [u;0];
Name = cell(length(u),1);
for k = 1:length(u)-1
Name(k) = eq.aga(eq.id_aga==u(k));
end
Name{end} = 'CATALUNYA';
time(1:31)=[];
for k = 1:2
if k==2
s1 = 'i';
else
s1 = '';
end
for i = 1:5
switch i
case 1
s2 = 'cas';
case 2
s2 = 'cas7';
case 3
s2 = 'A14';
case 4
s2 = 'EPG';
case 5
s2 = 'rho';
end
for j = 1:2
if j == 1
s3 = 'Pc';
else
s3 = 'CC';
end
eval([s1 s2 '_' s3 '(1:31,:) = [];'])
end
end
end
%% FIGURA 2A
for id = 1:44
f = figure(1);
clf
plot(time,cas7_Pc(:,id),'linewidth',2,'Color',col(1,:))
hold on
plot(time,prop(id)*cas7_CC(:,id),'linewidth',2,'Color',col(2,:))
opt = {'Pc','CC'};
for s = 1:length(opt)
eval(['x = [cas7_' opt{s} '(:,id)+icas7_' opt{s} '(:,id); flip(cas7_' opt{s} '(:,id)-icas7_' opt{s} '(:,id))];'])
x = x';
x(x<0) = 0;
x(x>10000) = 0;
if s==2
x = x*prop(id);
end
fill([time flip(time)],x,'r','FaceColor',0.5+0.5.*col(s,:),'EdgeColor','none','FaceAlpha',0.5)
end
plot(time,cas7_Pc(:,id),'linewidth',2,'Color',col(1,:))
hold on
plot(time,prop(id)*cas7_CC(:,id),'linewidth',2,'Color',col(2,:))
legend('PCR','EMR','Location','best')
ax = gca;
ax.LineWidth = 1.5;
ax.Box = 'off';
ax.TickDir = 'out';
ax.XLim = [min(time) max(time)];
xt = min(time):7:max(time);
ax.XTick = xt;
XT = cell(length(xt),1);
for kk = 1:length(xt)
XT{kk} = datestr(xt(kk),'dd/mm');
end
ax.XTickLabel = XT;
xtickangle(45)
ylabel('Average cases last 7 days')
title(Name{id})
print(f,['./Figures&Tables/Appendix_cases7/cases7_' num2str(id,'%02u') '.png'],'-dpng','-r600')
f = figure(1);
clf
plot(time,rho_Pc(:,id),'linewidth',2,'Color',col(1,:))
hold on
plot(time,rho_CC(:,id),'linewidth',2,'Color',col(2,:))
opt = {'Pc','CC'};
for s = 1:length(opt)
eval(['x = [rho_' opt{s} '(:,id)+irho_' opt{s} '(:,id); flip(rho_' opt{s} '(:,id)-irho_' opt{s} '(:,id))];'])
x = x';
x(x<0) = 0;
x(x>5) = 5;
fill([time flip(time)],x,'r','FaceColor',0.5+0.5.*col(s,:),'EdgeColor','none','FaceAlpha',0.5)
end
plot(time,rho_Pc(:,id),'linewidth',2,'Color',col(1,:))
hold on
plot(time,rho_CC(:,id),'linewidth',2,'Color',col(2,:))
legend('PCR','EMR','Location','best')
ax = gca;
ax.LineWidth = 1.5;
ax.Box = 'off';
ax.TickDir = 'out';
axis([min(time) max(time) 0 3])
xt = min(time):7:max(time);
ax.XTick = xt;
XT = cell(length(xt),1);
for kk = 1:length(xt)
XT{kk} = datestr(xt(kk),'dd/mm');
end
ax.XTickLabel = XT;
xtickangle(45)
ylabel('Empiric propagation')
title(Name{id})
print(f,['./Figures&Tables/Appendix_rho/rho_' num2str(id,'%02u') '.png'],'-dpng','-r600')
f = figure(1);
clf
plot(time,A14_Pc(:,id),'linewidth',2,'Color',col(1,:))
hold on
plot(time,prop(id)*A14_CC(:,id),'linewidth',2,'Color',col(2,:))
opt = {'Pc','CC'};
for s = 1:length(opt)
eval(['x = [A14_' opt{s} '(:,id)+iA14_' opt{s} '(:,id); flip(A14_' opt{s} '(:,id)-iA14_' opt{s} '(:,id))];'])
x = x';
x(x<0) = 0;
x(x>10000) = 0;
if s==2
x = x*prop(id);
end
fill([time flip(time)],x,'r','FaceColor',0.5+0.5.*col(s,:),'EdgeColor','none','FaceAlpha',0.5)
end
plot(time,A14_Pc(:,id),'linewidth',2,'Color',col(1,:))
hold on
plot(time,prop(id)*A14_CC(:,id),'linewidth',2,'Color',col(2,:))
legend('PCR','EMR','Location','best')
ax = gca;
ax.LineWidth = 1.5;
ax.Box = 'off';
ax.TickDir = 'out';
ax.XLim = [min(time) max(time)];
xt = min(time):7:max(time);
ax.XTick = xt;
XT = cell(length(xt),1);
for kk = 1:length(xt)
XT{kk} = datestr(xt(kk),'dd/mm');
end
ax.XTickLabel = XT;
xtickangle(45)
ylabel('A14')
title(Name{id})
print(f,['./Figures&Tables/Appendix_A14/A14_' num2str(id,'%02u') '.png'],'-dpng','-r600')
f = figure(1);
clf
plot(time,EPG_Pc(:,id),'linewidth',2,'Color',col(1,:))
hold on
plot(time,prop(id)*EPG_CC(:,id),'linewidth',2,'Color',col(2,:))
opt = {'Pc','CC'};
for s = 1:length(opt)
eval(['x = [EPG_' opt{s} '(:,id)+iEPG_' opt{s} '(:,id); flip(EPG_' opt{s} '(:,id)-iEPG_' opt{s} '(:,id))];'])
x = x';
x(x<0) = 0;
x(x>10000) = 0;
if s==2
x = x*prop(id);
end
fill([time flip(time)],x,'r','FaceColor',0.5+0.5.*col(s,:),'EdgeColor','none','FaceAlpha',0.5)
end
plot(time,EPG_Pc(:,id),'linewidth',2,'Color',col(1,:))
hold on
plot(time,prop(id)*EPG_CC(:,id),'linewidth',2,'Color',col(2,:))
legend('PCR','EMR','Location','best')
ax = gca;
ax.LineWidth = 1.5;
ax.Box = 'off';
ax.TickDir = 'out';
ax.XLim = [min(time) max(time)];
xt = min(time):7:max(time);
ax.XTick = xt;
XT = cell(length(xt),1);
for kk = 1:length(xt)
XT{kk} = datestr(xt(kk),'dd/mm');
end
ax.XTickLabel = XT;
xtickangle(45)
ylabel('EPG')
title(Name{id})
print(f,['./Figures&Tables/Appendix_EPG/EPG_' num2str(id,'%02u') '.png'],'-dpng','-r600')
end