update covid19

CRA_Updated_Version/CRA_Toolbox_bash/Examples/ode_covid19_v3.m

@@ -8,13 +8,13 @@ b1=p(3);
 b2=p(4);
 b2=p(4);
 b3=p(5);
 b3=p(5);
         
         
-N=10^5;
+Norm=10^5;
 
 
-be=be/(N);
-b0=b0/(N);
-b1=b1/(N);
-b2=b2/(N);
-b3=b3/(N);
+be=be/(Norm);
+b0=b0/(Norm);
+b1=b1/(Norm);
+b2=b2/(Norm);
+b3=b3/(Norm);
         
         
 FracSevere = p(6);
 FracSevere = p(6);
 FracCritical = p(7);
 FracCritical = p(7);
@@ -54,7 +54,7 @@ g3=(1/TimeICUDeath)-u;
 
 
 
 
 s0 = (t<Tlock(2)) + s00(1) * (t>=Tlock(2)) * (t<Tlock(3)) + s00(2)*(t>=Tlock(3)) * (t<Tlock(4)) + s00(3)*(t>=Tlock(4));
 s0 = (t<Tlock(2)) + s00(1) * (t>=Tlock(2)) * (t<Tlock(3)) + s00(2)*(t>=Tlock(3)) * (t<Tlock(4)) + s00(3)*(t>=Tlock(4));
-s1 = (t<Tlock(2)) + s11(1) * (t>=Tlock(2)) * (t<Tlock(3)) + s11(2)*(t>=Tlock(3))* (t<Tlock(4)) + s00(3)*(t>=Tlock(4));
+s1 = (t<Tlock(2)) + s11(1) * (t>=Tlock(2)) * (t<Tlock(3)) + s11(2)*(t>=Tlock(3))* (t<Tlock(4)) + s11(3)*(t>=Tlock(4));
 s2 = (t<Tlock(1)) + s22 * (t>=Tlock(1));
 s2 = (t<Tlock(1)) + s22 * (t>=Tlock(1));
 %s3 = (t<Tlock(1)) + s33 * (t>=Tlock(1));
 %s3 = (t<Tlock(1)) + s33 * (t>=Tlock(1));
 
 

CRA_Updated_Version/CRA_Toolbox_bash/compute_MIRI.m

@@ -34,10 +34,16 @@ function compute_MIRI(model,variable_name,current_func,tail_size,current_tm,Nr,N
 nominal_parameters=model.nominal_parameters;
 nominal_parameters=model.nominal_parameters;
 %num_parameters=length(nominal_parameters);
 %num_parameters=length(nominal_parameters);
 nominal_parameters_name=model.nominal_parameters_name;
 nominal_parameters_name=model.nominal_parameters_name;
-derived_parameters=model.derived_parameters;
-derived_parameters_name=model.derived_parameters_name;
-num_parameters=length(nominal_parameters)+length(derived_parameters);
-parameters_name=[nominal_parameters_name derived_parameters_name];
+
+if(isfield(model,'derived_parameters'))
+   derived_parameters=model.derived_parameters;
+   derived_parameters_name=model.derived_parameters_name;
+   num_parameters=length(nominal_parameters)+length(derived_parameters);
+   parameters_name=[nominal_parameters_name derived_parameters_name];
+else
+   num_parameters=length(nominal_parameters);
+   parameters_name=[nominal_parameters_name];
+end
 
 
 obs_name=model.observables_name;
 obs_name=model.observables_name;
 
 
@@ -131,16 +137,20 @@ try
         %[all_xbin_max,all_xbin_min,all_ks_max,all_ks_min]=obj_MIRI.estimate_parampdfs(handles1.nominal_p, handles1.perturbation, Ncloud, handles.XiMax, handles.XiMin);
         %[all_xbin_max,all_xbin_min,all_ks_max,all_ks_min]=obj_MIRI.estimate_parampdfs(handles1.nominal_p, handles1.perturbation, Ncloud, handles.XiMax, handles.XiMin);
         [MIRI_param,CloudCondMin, CloudCondMax]=obj_MIRI.MIRI_computation(all_ks_max,all_ks_min,all_xbin_max,all_xbin_min);
         [MIRI_param,CloudCondMin, CloudCondMax]=obj_MIRI.MIRI_computation(all_ks_max,all_ks_min,all_xbin_max,all_xbin_min);
         
         
-        obj_MIRI_derived=MIRI();
-        [all_xbin_max_d,all_xbin_min_d,all_ks_max_d,all_ks_min_d]=obj_MIRI_derived.estimate_parampdfs(derived_parameters, AllDerivedParam{k,1}, XiMax, XiMin);
-        %[all_xbin_max,all_xbin_min,all_ks_max,all_ks_min]=obj_MIRI.estimate_parampdfs(handles1.nominal_p, handles1.perturbation, Ncloud, handles.XiMax, handles.XiMin);
-        [MIRI_param_d,CloudCondMin_d, CloudCondMax_d]=obj_MIRI_derived.MIRI_computation(all_ks_max_d,all_ks_min_d,all_xbin_max_d,all_xbin_min_d);
+        if(isfield(model,'derived_parameters'))
+           obj_MIRI_derived=MIRI();
+           [all_xbin_max_d,all_xbin_min_d,all_ks_max_d,all_ks_min_d]=obj_MIRI_derived.estimate_parampdfs(derived_parameters, AllDerivedParam{k,1}, XiMax, XiMin);
+           %[all_xbin_max,all_xbin_min,all_ks_max,all_ks_min]=obj_MIRI.estimate_parampdfs(handles1.nominal_p, handles1.perturbation, Ncloud, handles.XiMax, handles.XiMin);
+           [MIRI_param_d,CloudCondMin_d, CloudCondMax_d]=obj_MIRI_derived.MIRI_computation(all_ks_max_d,all_ks_min_d,all_xbin_max_d,all_xbin_min_d);
         
         
         
         
-        MIRI_param=[MIRI_param MIRI_param_d];
+           MIRI_param=[MIRI_param MIRI_param_d];
+           CloudCondMax=[CloudCondMax CloudCondMax_d];
+           CloudCondMin=[CloudCondMin CloudCondMin_d];
+        end
+        
         MIRIT(k,:)=MIRI_param;
         MIRIT(k,:)=MIRI_param;
-        CloudCondMax=[CloudCondMax CloudCondMax_d];
-        CloudCondMin=[CloudCondMin CloudCondMin_d];
+
         CloudCondMaxT=[CloudCondMaxT;CloudCondMax];
         CloudCondMaxT=[CloudCondMaxT;CloudCondMax];
         CloudCondMinT=[CloudCondMinT;CloudCondMin];
         CloudCondMinT=[CloudCondMinT;CloudCondMin];
         mean_CloudMax=mean(CloudCondMaxT);
         mean_CloudMax=mean(CloudCondMaxT);
@@ -153,11 +163,13 @@ try
             ks_param{2,k}(ip,:)=all_ks_min(ip,:);
             ks_param{2,k}(ip,:)=all_ks_min(ip,:);
         end   
         end   
         
         
-        for ip=1:length(derived_parameters)
-            xbin_param_d{1,k}(ip,:)=all_xbin_max_d(ip,:);
-            xbin_param_d{2,k}(ip,:)=all_xbin_min_d(ip,:);
-            ks_param_d{1,k}(ip,:)=all_ks_max_d(ip,:);
-            ks_param_d{2,k}(ip,:)=all_ks_min_d(ip,:);
+        if(isfield(model,'derived_parameters'))
+            for ip=1:length(derived_parameters)
+               xbin_param_d{1,k}(ip,:)=all_xbin_max_d(ip,:);
+               xbin_param_d{2,k}(ip,:)=all_xbin_min_d(ip,:);
+               ks_param_d{1,k}(ip,:)=all_ks_max_d(ip,:);
+               ks_param_d{2,k}(ip,:)=all_ks_min_d(ip,:);
+            end
         end
         end
         
         
    end
    end
@@ -196,8 +208,10 @@ try
    save(fullfile(folder,variable_name,'pdf_eval_func.mat'),'xbinT','ks_y_T');
    save(fullfile(folder,variable_name,'pdf_eval_func.mat'),'xbinT','ks_y_T');
    disp('saving probability density functions of all parameters')
    disp('saving probability density functions of all parameters')
    save(fullfile(folder,variable_name,'pdf_param.mat'),'xbin_param','ks_param');
    save(fullfile(folder,variable_name,'pdf_param.mat'),'xbin_param','ks_param');
-   save(fullfile(folder,variable_name,'pdf_param_derived.mat'),'xbin_param_d','ks_param_d');
    
    
+   if(isfield(model,'derived_parameters'))
+      save(fullfile(folder,variable_name,'pdf_param_derived.mat'),'xbin_param_d','ks_param_d');
+   end
       
       
 catch ME
 catch ME
     
     

CRA_Updated_Version/CRA_Toolbox_bash/compute_R0.m

-function R0=compute_R0(p)%,Tlock2,s02,s12)
+function R0=compute_R0(param)%,Tlock2,s02,s12)
 
 
-be = p(1);
-b0=p(2);
-b1=p(3);
-b2=p(4);
-b3=p(5);
+be = param(1);
+b0=param(2);
+b1=param(3);
+b2=param(4);
+b3=param(5);
         
         
-N=10^5;
-
-be=be/(N);
-b0=b0/(N);
-b1=b1/(N);
-b2=b2/(N);
-b3=b3/(N);
+Norm=10^5; %882000
+%Norm=882000;
+
+be=be/(Norm);
+b0=b0/(Norm);
+b1=b1/(Norm);
+b2=b2/(Norm);
+b3=b3/(Norm);
         
         
-FracSevere = p(6);
-FracCritical = p(7);
+FracSevere = param(6);
+FracCritical = param(7);
 FracMild = 1-FracSevere-FracCritical;
 FracMild = 1-FracSevere-FracCritical;
-FracAsym = p(8);
+FracAsym = param(8);
                
                
-IncubPeriod = p(9);
-DurMildInf = p(10);
+IncubPeriod = param(9);
+DurMildInf = param(10);
 
 
-DurAsym = p(11);
+DurAsym = param(11);
    
    
-DurHosp = p(12);
-TimeICUDeath = p(13);
-ProbDeath=p(14);
-
-PresymPeriod=p(15)*IncubPeriod;
+DurHosp = param(12);
+TimeICUDeath = param(13);
+ProbDeath=param(14);
 
 
+PresymPeriod=param(15)*IncubPeriod;
+%PresymPeriod=param(15);
            
            
 CFR=ProbDeath*FracCritical/100; 
 CFR=ProbDeath*FracCritical/100; 
             
             
@@ -54,4 +55,4 @@ g3=(1/TimeICUDeath)-u;
 %s0 = (t<Tlock1) + s01 * (t>=Tlock1); %* (t<Tlock2) + s01(2)*(t>=Tlock2);
 %s0 = (t<Tlock1) + s01 * (t>=Tlock1); %* (t<Tlock2) + s01(2)*(t>=Tlock2);
 %s1 = (t<Tlock1) + s11 * (t>=Tlock1); %* (t<Tlock2) + s11(2)*(t>=Tlock2);
 %s1 = (t<Tlock1) + s11 * (t>=Tlock1); %* (t<Tlock2) + s11(2)*(t>=Tlock2);
 
 
-R0=N*(((be)/a1)+f*((b0)/g0)+(1-f)*(((b1)/(p1+g1))+(p1/(p1+g1))*(b2/(p2+g2)+ (p2/(p2+g2))*(b3/(u+g3)))));
\ No newline at end of file
+R0=Norm*(((be)/a1)+f*((b0)/g0)+(1-f)*(((b1)/(p1+g1))+(p1/(p1+g1))*(b2/(p2+g2)+ (p2/(p2+g2))*(b3/(u+g3)))));
\ No newline at end of file