Merge pull request #164 from ggrrll/master

improved & fixed v. of E > I transition
GiulioRossetti · May 19, 2020 · 9e80267 · 9e80267
2 parents dea8c6e + 77be272
commit 9e80267
Showing 1 changed file with 6 additions and 11 deletions.
diff --git a/ndlib/models/epidemics/SEIRModel.py b/ndlib/models/epidemics/SEIRModel.py
@@ -79,23 +79,18 @@ def iteration(self, node_status=True):
                 if self.params['model']['tp_rate'] == 1:
                     if eventp < 1 - (1 - self.params['model']['beta']) ** len(infected_neighbors):
                         actual_status[u] = 2  # Exposed
-                        self.progress[u] = 0
+                        self.progress[u] =  self.actual_iteration # save time of exposure t_i
                 else:
                     if eventp < self.params['model']['beta'] * triggered:
                         actual_status[u] = 2  # Exposed
-                        self.progress[u] = 0
+                        self.progress[u] =  self.actual_iteration # save time of exposure t_i
 
             elif u_status == 2:
 
-                # not sure whether this line is correct – to be tested
-                if eventp < 1 - np.exp(- self.actual_iteration / self.params['model']['alpha']): 
-                    actual_status[u] = 1  # Infected    
-
-                # if self.progress[u] < 1:
-                #     self.progress[u] += self.params['model']['alpha']
-                # else:
-                #     actual_status[u] = 1  # Infected
-                #     del self.progress[u]
+                # apply prob. of infection, after (t - t_i) 
+                if eventp < 1 - np.exp(- (self.actual_iteration - self.progress[u]) / self.params['model']['alpha']): 
+                    actual_status[u] = 1  # Infected
+                    del self.progress[u]
 
             elif u_status == 1:
                 if eventp < self.params['model']['gamma']: