update korona

code/korona_final.py

@@ -276,6 +276,28 @@
 status_hospitalized_severe[hosp_p_severe] = 1 
 
 
+# now remove people from home recovery
+inc_home = np.where(home_recovery_period < 0.5)[0]
+status_home[inc_home] = 0
+status_active[inc_home] = 0
+
+# now remove living/deceased from hospitals
+inc_hosp_dead = np.where(hospitalization_period_dead < 0.5)[0]
+status_hospitalized_dead[inc_hosp_dead] = 0
+status_dead[inc_hosp_dead] = 1
+status_active[inc_hosp_dead] = 0
+
+inc_hosp_critical = np.where(hospitalization_period_critical < 0.5)[0]
+status_hospitalized_critical[inc_hosp_critical] = 0
+status_immune[inc_hosp_critical] = 1
+status_active[inc_hosp_critical] = 0
+
+inc_hosp_severe = np.where(hospitalization_period_severe < 0.5)[0]
+status_hospitalized_severe[inc_hosp_severe] = 0 
+status_immune[inc_hosp_severe] = 1
+status_active[inc_hosp_severe] = 0
+
+
 Nactive   = np.sum(status_active)
 Nincubation =  np.sum(status_incubation)
 Ninfectious = np.sum(status_infectious)
@@ -642,11 +664,11 @@
 
     # ukrepi 16. marca
     if day == 4:
-        rands = rands/np.random.uniform(3.0,4.5) # /8.
+        rands = rands/np.random.uniform(3.5,4.5) # /8.
 
-    # ukrepi 18.marca
+    # ukrepi 20.marca
     if day == 8:
-        rands = rands/np.random.uniform(1.2,3.) # /2.
+        rands = rands/np.random.uniform(1.5,3.) # /2.
 
     random_sample = np.random.random(N)
     rands_input = (rands - rands.astype(np.int32)>random_sample) + rands.astype(np.int32)
@@ -665,16 +687,16 @@
 print ""
 print "Saving fields"
 # save fields
-np.savetxt("./2020_03_29/tab_days_{:03d}.txt".format(run),tab_days,fmt='%8d')
-np.savetxt("./2020_03_29/tab_active_{:03d}.txt".format(run),tab_active,fmt='%8d')
-np.savetxt("./2020_03_29/tab_infectious_{:03d}.txt".format(run),tab_infectious,fmt='%8d')
-np.savetxt("./2020_03_29/tab_incubation_{:03d}.txt".format(run),tab_incubation,fmt='%8d')
-np.savetxt("./2020_03_29/tab_symptoms_{:03d}.txt".format(run),tab_symptoms,fmt='%8d')
-np.savetxt("./2020_03_29/tab_hospitalized_{:03d}.txt".format(run),tab_hospitalized,fmt='%8d')
-np.savetxt("./2020_03_29/tab_icu_{:03d}.txt".format(run), tab_icu,fmt='%8d')
-np.savetxt("./2020_03_29/tab_dead_{:03d}.txt".format(run), tab_dead,fmt='%8d')
-np.savetxt("./2020_03_29/tab_immune_{:03d}.txt".format(run), tab_immune,fmt='%8d')
-np.savetxt("./2020_03_29/tab_susceptible_{:03d}.txt".format(run), tab_susceptible,fmt='%8d')
+np.savetxt("./2020_04_03/tab_days_{:03d}.txt".format(run),tab_days,fmt='%8d')
+np.savetxt("./2020_04_03/tab_active_{:03d}.txt".format(run),tab_active,fmt='%8d')
+np.savetxt("./2020_04_03/tab_infectious_{:03d}.txt".format(run),tab_infectious,fmt='%8d')
+np.savetxt("./2020_04_03/tab_incubation_{:03d}.txt".format(run),tab_incubation,fmt='%8d')
+np.savetxt("./2020_04_03/tab_symptoms_{:03d}.txt".format(run),tab_symptoms,fmt='%8d')
+np.savetxt("./2020_04_03/tab_hospitalized_{:03d}.txt".format(run),tab_hospitalized,fmt='%8d')
+np.savetxt("./2020_04_03/tab_icu_{:03d}.txt".format(run), tab_icu,fmt='%8d')
+np.savetxt("./2020_04_03/tab_dead_{:03d}.txt".format(run), tab_dead,fmt='%8d')
+np.savetxt("./2020_04_03/tab_immune_{:03d}.txt".format(run), tab_immune,fmt='%8d')
+np.savetxt("./2020_04_03/tab_susceptible_{:03d}.txt".format(run), tab_susceptible,fmt='%8d')
 
 # np.savetxt("./save/day_infected_{:03d}.txt".format(run),day_infected) 
 # np.savetxt("./save/rands_input_{:03d}.txt".format(run),rands)  

code/korona_final_spike.py

@@ -665,16 +665,16 @@
 print ""
 print "Saving fields"
 # save fields
-np.savetxt("./2020_03_29/tab_days_{:03d}.txt".format(run),tab_days,fmt='%8d')
-np.savetxt("./2020_03_29/tab_active_{:03d}.txt".format(run),tab_active,fmt='%8d')
-np.savetxt("./2020_03_29/tab_infectious_{:03d}.txt".format(run),tab_infectious,fmt='%8d')
-np.savetxt("./2020_03_29/tab_incubation_{:03d}.txt".format(run),tab_incubation,fmt='%8d')
-np.savetxt("./2020_03_29/tab_symptoms_{:03d}.txt".format(run),tab_symptoms,fmt='%8d')
-np.savetxt("./2020_03_29/tab_hospitalized_{:03d}.txt".format(run),tab_hospitalized,fmt='%8d')
-np.savetxt("./2020_03_29/tab_icu_{:03d}.txt".format(run), tab_icu,fmt='%8d')
-np.savetxt("./2020_03_29/tab_dead_{:03d}.txt".format(run), tab_dead,fmt='%8d')
-np.savetxt("./2020_03_29/tab_immune_{:03d}.txt".format(run), tab_immune,fmt='%8d')
-np.savetxt("./2020_03_29/tab_susceptible_{:03d}.txt".format(run), tab_susceptible,fmt='%8d')
+np.savetxt("./save_spike/tab_days_{:03d}.txt".format(run),tab_days,fmt='%8d')
+np.savetxt("./save_spike/tab_active_{:03d}.txt".format(run),tab_active,fmt='%8d')
+np.savetxt("./save_spike/tab_infectious_{:03d}.txt".format(run),tab_infectious,fmt='%8d')
+np.savetxt("./save_spike/tab_incubation_{:03d}.txt".format(run),tab_incubation,fmt='%8d')
+np.savetxt("./save_spike/tab_symptoms_{:03d}.txt".format(run),tab_symptoms,fmt='%8d')
+np.savetxt("./save_spike/tab_hospitalized_{:03d}.txt".format(run),tab_hospitalized,fmt='%8d')
+np.savetxt("./save_spike/tab_icu_{:03d}.txt".format(run), tab_icu,fmt='%8d')
+np.savetxt("./save_spike/tab_dead_{:03d}.txt".format(run), tab_dead,fmt='%8d')
+np.savetxt("./save_spike/tab_immune_{:03d}.txt".format(run), tab_immune,fmt='%8d')
+np.savetxt("./save_spike/tab_susceptible_{:03d}.txt".format(run), tab_susceptible,fmt='%8d')
 
 # np.savetxt("./save/day_infected_{:03d}.txt".format(run),day_infected) 
 # np.savetxt("./save/rands_input_{:03d}.txt".format(run),rands)  

code/korona_final_tracing.py

@@ -280,6 +280,28 @@
 status_hospitalized_severe[hosp_p_severe] = 1 
 
 
+# now remove people from home recovery
+inc_home = np.where(home_recovery_period < 0.5)[0]
+status_home[inc_home] = 0
+status_active[inc_home] = 0
+
+# now remove living/deceased from hospitals
+inc_hosp_dead = np.where(hospitalization_period_dead < 0.5)[0]
+status_hospitalized_dead[inc_hosp_dead] = 0
+status_dead[inc_hosp_dead] = 1
+status_active[inc_hosp_dead] = 0
+
+inc_hosp_critical = np.where(hospitalization_period_critical < 0.5)[0]
+status_hospitalized_critical[inc_hosp_critical] = 0
+status_immune[inc_hosp_critical] = 1
+status_active[inc_hosp_critical] = 0
+
+inc_hosp_severe = np.where(hospitalization_period_severe < 0.5)[0]
+status_hospitalized_severe[inc_hosp_severe] = 0 
+status_immune[inc_hosp_severe] = 1
+status_active[inc_hosp_severe] = 0
+
+
 Nactive   = np.sum(status_active)
 Nincubation =  np.sum(status_incubation)
 Ninfectious = np.sum(status_infectious)

code/plot_data_share.py

@@ -12,7 +12,7 @@
 import os
 import datetime
 
-run = 15
+run = 17
 
 save_data = False
 #%% READ REAL DATA
@@ -26,10 +26,13 @@
 data_icu = data_stats["state.icu"][17:]
 data_cases = data_stats["tests.positive.todate"][17:]
 data_dead = data_stats["state.deceased.todate"][17:]
+#data_cases_new = data_stats["tests.positive"][17:]
 data_days = np.arange(0,data_hospitalised.shape[0])
+Ndata = len(data_dead)
+
 
 #%% READ SIMULATED DATA
-days = np.loadtxt("./2020_03_29/tab_days_4453.txt")
+days = np.loadtxt("./2020_04_03/tab_days_002.txt")
 Nt =days.shape[0]
 
 N = 5000
@@ -43,27 +46,54 @@
 immune = np.zeros((N,days.shape[0]))
 susceptible = np.zeros((N,days.shape[0]))
 
+inc_dead_data = data_dead.values>0
+inc_icu_data = data_icu.values>0
 
+blah = np.zeros((2,N))
 
 j = 0
 for i in range(N):
     print(i)
-    if os.path.exists("./2020_03_29/tab_active_{:03d}.txt".format(i)):
+    if os.path.exists("./2020_04_03/tab_active_{:03d}.txt".format(i)):
+
+        active[j,:] = np.loadtxt("./2020_04_03/tab_active_{:03d}.txt".format(i))
+        infectious[j,:] = np.loadtxt("./2020_04_03/tab_infectious_{:03d}.txt".format(i))
+        incubation[j,:] = np.loadtxt("./2020_04_03/tab_incubation_{:03d}.txt".format(i))
+        symptoms[j,:] = np.loadtxt("./2020_04_03/tab_symptoms_{:03d}.txt".format(i))
+        hospitalized[j,:] = np.loadtxt("./2020_04_03/tab_hospitalized_{:03d}.txt".format(i))
+        icu[j,:] = np.loadtxt("./2020_04_03/tab_icu_{:03d}.txt".format(i))
+        dead[j,:] = np.loadtxt("./2020_04_03/tab_dead_{:03d}.txt".format(i))
+        immune[j,:] = np.loadtxt("./2020_04_03/tab_immune_{:03d}.txt".format(i))
+        susceptible[j,:] = np.loadtxt("./2020_04_03/tab_susceptible_{:03d}.txt".format(i))
 
-        active[j,:] = np.loadtxt("./2020_03_29/tab_active_{:03d}.txt".format(i))
-        infectious[j,:] = np.loadtxt("./2020_03_29/tab_infectious_{:03d}.txt".format(i))
-        incubation[j,:] = np.loadtxt("./2020_03_29/tab_incubation_{:03d}.txt".format(i))
-        symptoms[j,:] = np.loadtxt("./2020_03_29/tab_symptoms_{:03d}.txt".format(i))
-        hospitalized[j,:] = np.loadtxt("./2020_03_29/tab_hospitalized_{:03d}.txt".format(i))
-        icu[j,:] = np.loadtxt("./2020_03_29/tab_icu_{:03d}.txt".format(i))
-        dead[j,:] = np.loadtxt("./2020_03_29/tab_dead_{:03d}.txt".format(i))
-        immune[j,:] = np.loadtxt("./2020_03_29/tab_immune_{:03d}.txt".format(i))
-        susceptible[j,:] = np.loadtxt("./2020_03_29/tab_susceptible_{:03d}.txt".format(i))
 
+        dead_model = dead[j,:Ndata] > 0
+        icu_model = icu[j,:Ndata] > 0       
+
+        inc_dead_all = inc_dead_data & dead_model
+        inc_icu_all = inc_icu_data & icu_model
+
+        #print dead[j,:Ndata][inc_dead_all]
+        #print (data_dead.values)[inc_dead_all]   
+
+        #print icu[j,:Ndata][inc_icu_all]
+        #print (data_icu.values)[inc_icu_all]      
+
+        sum1 = ((np.log((data_dead.values)[inc_dead_all]) - np.log(dead[j,:Ndata][inc_dead_all]))**2).sum()
+        sum2 = (((np.log(data_icu.values)[inc_icu_all]) - np.log(icu[j,:Ndata][inc_icu_all]))**2).sum()       
+        #print sum1, sum2
+        #print ""
+        blah[0,j] = i
+        blah[1,j] = sum1 + sum2 
         j += 1
     else:
         continue
-print(j)
+
+print blah[1,:j]
+print np.percentile(blah[1,:j],15)
+
+
+
 
 #%% COMPUTE PARAMETERS
 active_median = np.median(active[:j],axis=0)
@@ -200,8 +230,8 @@
 
 # simulated values
 # plt.fill_between(days,active_01,active_99,color="blue",alpha=0.1)
-#plt.fill_between(days,active_05,active_95,color="blue",alpha=0.2)
-#plt.plot(days,active_median,label="Active",color="blue",lw=3)
+plt.fill_between(days,active_25,active_75,color="blue",alpha=0.2)
+plt.plot(days,active_median,label="Active",color="blue",lw=3)
 
 # plt.fill_between(days,symptoms_01,symptoms_99,color="green",alpha=0.1)
 plt.fill_between(days,symptoms_25,symptoms_75,color="green",alpha=0.2)
@@ -246,6 +276,7 @@
 plt.grid(b=True, which='major', color='grey', linestyle='-')
 plt.grid(b=True, which='minor', color='grey', linestyle='--')
 plt.ylim([1,10**5])
+plt.xlim([-3,Nt+3])
 plt.legend()
 fig.savefig("potek_pandemije{:02d}.png".format(run),dpi=250)