Merge branch 'main' into toy-spatial

pyEpiabm/pyEpiabm/property/household_foi.py

@@ -46,8 +46,9 @@ def household_inf(infector, time: float):
     @staticmethod
     def household_susc(infector, infectee, time: float):
         """Calculate the susceptibility of one person to another in a given
-        household. Does not include interventions such as isolation,
-        or whether individual is a carehome resident.
+        household. Intervention parameters are based on the microcell
+        properties of the infectee. Does not include interventions such as
+        isolation, or whether individual is a carehome resident.
 
         Parameters
         ----------
@@ -66,11 +67,11 @@ def household_susc(infector, infectee, time: float):
         """
         household_susceptibility = PersonalInfection.person_susc(
             infector, infectee, time)
-        if (hasattr(infector.microcell, 'distancing_start_time')) and (
-                infector.microcell.distancing_start_time is not None) and (
-                    infector.microcell.distancing_start_time <= time):
-            if (hasattr(infector, 'distancing_enhanced')) and (
-                        infector.distancing_enhanced is True):
+        if (hasattr(infectee.microcell, 'distancing_start_time')) and (
+                infectee.microcell.distancing_start_time is not None) and (
+                    infectee.microcell.distancing_start_time <= time):
+            if (hasattr(infectee, 'distancing_enhanced')) and (
+                        infectee.distancing_enhanced is True):
                 household_susceptibility *= Parameters.instance().\
                     intervention_params['social_distancing'][
                         'distancing_house_enhanced_susc']

pyEpiabm/pyEpiabm/property/place_foi.py

@@ -55,16 +55,14 @@ def place_inf(place, infector, time: float):
         return place_inf
 
     @staticmethod
-    def place_susc(place, infector, infectee,
-                   time: float):
-        """Calculate the susceptibility of a place.
-        Does not include interventions such as isolation,
-        or whether individual is a carehome resident.
+    def place_susc(place, infectee, time: float):
+        """Calculate the susceptibility of a place. Intervention parameters
+        are based on the microcell properties of the infectee. Does not include
+        interventions such as isolation, or whether individual is a carehome
+        resident.
 
         Parameters
         ----------
-        infector : Person
-            Infector
         infectee : Person
             Infectee
         place : Place
@@ -80,11 +78,11 @@ def place_susc(place, infector, infectee,
         """
         place_susc = 1.0
         place_idx = place.place_type.value - 1
-        if (hasattr(infector.microcell, 'distancing_start_time')) and (
-                infector.microcell.distancing_start_time is not None) and (
-                    infector.microcell.distancing_start_time <= time):
-            if (hasattr(infector, 'distancing_enhanced')) and (
-                        infector.distancing_enhanced is True):
+        if (hasattr(infectee.microcell, 'distancing_start_time')) and (
+                infectee.microcell.distancing_start_time is not None) and (
+                    infectee.microcell.distancing_start_time <= time):
+            if (hasattr(infectee, 'distancing_enhanced')) and (
+                        infectee.distancing_enhanced is True):
                 place_susc *= Parameters.instance().\
                              intervention_params[
                              'social_distancing'][
@@ -153,6 +151,6 @@ def place_foi(place, infector, infectee,
 
         infectiousness = (PlaceInfection.place_inf(place, infector, time)
                           * isolation_scale_inf * quarantine_scale)
-        susceptibility = (PlaceInfection.place_susc(place, infector, infectee,
+        susceptibility = (PlaceInfection.place_susc(place, infectee,
                           time) * carehome_scale_susc * quarantine_scale)
         return (infectiousness * susceptibility)

pyEpiabm/pyEpiabm/property/spatial_foi.py

@@ -86,16 +86,15 @@ def spatial_inf(inf_cell, infector,
         return infector.infectiousness * age * closure_spatial
 
     @staticmethod
-    def spatial_susc(susc_cell, infector, infectee, time: float):
+    def spatial_susc(susc_cell, infectee, time: float):
         """Calculate the susceptibility of one cell towards its neighbouring
-        cells.
+        cells. Intervention parameters are based on the microcell properties
+        of the infectee.
 
         Parameters
         ----------
         susc_cell : Cell
             Cell receiving infections
-        infector : Person
-            Infector
         infectee : Person
             Infectee
         time : float
@@ -114,17 +113,17 @@ def spatial_susc(susc_cell, infector, infectee, time: float):
 
         spatial_susc *= Parameters.instance().\
             intervention_params['place_closure']['closure_spatial_params'] \
-            if ((hasattr(infector.microcell, 'closure_start_time'))) and (
-                infector.is_place_closed(
+            if ((hasattr(infectee.microcell, 'closure_start_time'))) and (
+                infectee.is_place_closed(
                     Parameters.instance().intervention_params[
                         'place_closure']['closure_place_type'])) and (
-                        infector.microcell.closure_start_time <= time) else 1
+                        infectee.microcell.closure_start_time <= time) else 1
 
-        if (hasattr(infector.microcell, 'distancing_start_time')) and (
-                infector.microcell.distancing_start_time is not None) and (
-                    infector.microcell.distancing_start_time <= time):
-            if (hasattr(infector, 'distancing_enhanced')) and (
-                        infector.distancing_enhanced is True):
+        if (hasattr(infectee.microcell, 'distancing_start_time')) and (
+                infectee.microcell.distancing_start_time is not None) and (
+                    infectee.microcell.distancing_start_time <= time):
+            if (hasattr(infectee, 'distancing_enhanced')) and (
+                        infectee.distancing_enhanced is True):
                 spatial_susc *= Parameters.instance().\
                     intervention_params['social_distancing'][
                         'distancing_spatial_enhanced_susc']
@@ -196,6 +195,6 @@ def spatial_foi(inf_cell, susc_cell, infector,
             inf_cell, infector, time) * carehome_scale_inf
             * isolation_scale_inf * quarantine_scale)
         susceptibility = (SpatialInfection.spatial_susc(
-            susc_cell, infector, infectee, time)
+            susc_cell, infectee, time)
             * carehome_scale_susc * quarantine_scale)
         return (infectiousness * susceptibility)

pyEpiabm/pyEpiabm/tests/test_unit/test_property/test_household_foi.py

@@ -118,9 +118,9 @@ def test_house_social_distancing(self):
         result = HouseholdInfection.household_susc(
             self.infector, self.infectee, self.time)
 
-        # Normal social distancing
-        self.infector.microcell.distancing_start_time = 1
-        self.infector.distancing_enhanced = False
+        # Normal social distancing of infectee
+        self.infectee.microcell.distancing_start_time = 1
+        self.infectee.distancing_enhanced = False
         distancing_house_susc = pe.Parameters.instance().\
             intervention_params['social_distancing'][
                 'distancing_house_susc']
@@ -129,8 +129,8 @@ def test_house_social_distancing(self):
         self.assertEqual(result*distancing_house_susc,
                          result_distancing)
 
-        # Enhanced social distancing
-        self.infector.distancing_enhanced = True
+        # Enhanced social distancing of infectee
+        self.infectee.distancing_enhanced = True
         distancing_house_enhanced_susc = pe.Parameters.instance().\
             intervention_params['social_distancing'][
                 'distancing_house_enhanced_susc']

pyEpiabm/pyEpiabm/tests/test_unit/test_property/test_place_foi.py

@@ -30,7 +30,7 @@ def setUpClass(cls) -> None:
         cls.time = 1.0
 
     def test_place_susc(self):
-        result = PlaceInfection.place_susc(self.place, self.infector,
+        result = PlaceInfection.place_susc(self.place,
                                            self.infectee, self.time)
         self.assertTrue(result > 0)
         self.assertIsInstance(result, float)
@@ -99,27 +99,28 @@ def test_place_household_quarantine(self):
 
     def test_place_social_distancing(self):
         # Not in social distancing (distancing_start_time = None)
-        result = PlaceInfection.place_susc(self.place, self.infector,
+        result = PlaceInfection.place_susc(self.place,
                                            self.infectee, self.time)
         place_idx = self.place.place_type.value - 1
 
-        # Normal social distancing
-        self.infector.microcell.distancing_start_time = 1
-        self.infector.distancing_enhanced = False
+        # Normal social distancing of infectee
+        self.infectee.microcell.distancing_start_time = 1
+        self.infectee.distancing_enhanced = False
         distancing_place_susc = pe.Parameters.instance().\
             intervention_params['social_distancing'][
                 'distancing_place_susc']
         result_distancing = PlaceInfection.place_susc(
-            self.place, self.infector, self.infectee, self.time)
+            self.place, self.infectee, self.time)
         self.assertEqual(result*distancing_place_susc[place_idx],
                          result_distancing)
-        # Enhanced social distancing
-        self.infector.distancing_enhanced = True
+
+        # Enhanced social distancing of infectee
+        self.infectee.distancing_enhanced = True
         distancing_place_enhanced_susc = pe.Parameters.instance().\
             intervention_params['social_distancing'][
                 'distancing_place_enhanced_susc']
         result_distancing_enhanced = PlaceInfection.place_susc(
-            self.place, self.infector, self.infectee, self.time)
+            self.place, self.infectee, self.time)
         self.assertEqual(result*distancing_place_enhanced_susc[place_idx],
                          result_distancing_enhanced)
 

pyEpiabm/pyEpiabm/tests/test_unit/test_property/test_spatial_foi.py

@@ -35,15 +35,15 @@ def setUp(self) -> None:
 
     def test_spatial_susc(self):
         result = SpatialInfection.spatial_susc(
-            self.cell, self.infector, self.infectee, self.time)
+            self.cell, self.infectee, self.time)
         self.assertTrue(result > 0)
         self.assertIsInstance(result, float)
 
     @patch('pyEpiabm.core.Parameters.instance')
     def test_spatial_susc_no_age(self, mock_params):
         mock_params.return_value.use_ages = False
         result = SpatialInfection.spatial_susc(
-            self.cell, self.infector, self.infectee, self.time)
+            self.cell, self.infectee, self.time)
         self.assertIsInstance(result, float)
         self.assertEqual(result, 1.0)
 
@@ -94,30 +94,51 @@ def test_spatial_case_isolation(self):
 
     def test_spatial_place_closure(self):
         # Update place type, not place closure (closure_start_time = None)
-        self.infector.place_types.append(PlaceType.PrimarySchool)
+        self.infectee.place_types.append(PlaceType.PrimarySchool)
+        self.infector.place_types.append(PlaceType.Workplace)
         result_susc = SpatialInfection.spatial_susc(
-            self.cell, self.infector, self.infectee, self.time)
+            self.cell, self.infectee, self.time)
         result_inf = SpatialInfection.spatial_inf(
             self.cell, self.infector, self.time)
 
         # Update start time
         closure_spatial_params = \
             pe.Parameters.instance().intervention_params[
                 'place_closure']['closure_spatial_params']
-        self.infector.microcell.closure_start_time = 1
+        self.infectee.microcell.closure_start_time = 1
 
-        # Place closure susceptibility
+        # Place closure susceptibility of infectee
+        pe.Parameters.instance().intervention_params[
+            'place_closure']['closure_place_type'] = [1, 2, 3, 4, 5, 6]
         result_closure_susc = SpatialInfection.spatial_susc(
-            self.cell, self.infector, self.infectee, self.time)
+            self.cell, self.infectee, self.time)
         self.assertEqual(result_susc*closure_spatial_params,
                          result_closure_susc)
 
-        # Place closure infectiousness
+        # Place closure infectiousness of infector
+        pe.Parameters.instance().intervention_params[
+            'place_closure']['closure_place_type'] = [1, 2, 3, 4, 5, 6]
         result_closure_inf = SpatialInfection.spatial_inf(
             self.cell, self.infector, self.time)
         self.assertEqual(result_inf*closure_spatial_params,
                          result_closure_inf)
 
+        # Place closure foi, place of infectee and infector closed
+        pe.Parameters.instance().intervention_params[
+            'place_closure']['closure_place_type'] = [1, 2, 3, 4, 5, 6]
+        result_closure_foi = SpatialInfection.spatial_foi(
+            self.cell, self.cell, self.infector, self.infectee, self.time)
+        self.assertEqual(result_susc * closure_spatial_params * result_inf *
+                         closure_spatial_params, result_closure_foi)
+
+        # Place closure foi, place of only infectee closed
+        pe.Parameters.instance().intervention_params['place_closure'][
+            'closure_place_type'] = [1, 2, 3]
+        result_closure_foi = SpatialInfection.spatial_foi(
+            self.cell, self.cell, self.infector, self.infectee, self.time)
+        self.assertEqual(result_susc*result_inf*closure_spatial_params,
+                         result_closure_foi)
+
     def test_spatial_household_quarantine(self):
         # Not in quarantine (quarantine_start_time = None)
         result = SpatialInfection.spatial_foi(
@@ -139,7 +160,7 @@ def test_spatial_household_quarantine(self):
     def test_spatial_social_distancing(self):
         # Not in social distancing (distancing_start_time = None)
         result = SpatialInfection.spatial_susc(
-            self.cell, self.infector, self.infectee, self.time)
+            self.cell, self.infectee, self.time)
 
         # Normal social distancing
         self.infector.microcell.distancing_start_time = 1
@@ -148,17 +169,17 @@ def test_spatial_social_distancing(self):
             intervention_params['social_distancing'][
                 'distancing_spatial_susc']
         result_distancing = SpatialInfection.spatial_susc(
-            self.cell, self.infector, self.infectee, self.time)
+            self.cell, self.infectee, self.time)
         self.assertEqual(result*distancing_spatial_susc,
                          result_distancing)
 
-        # Enhanced social distancing
-        self.infector.distancing_enhanced = True
+        # Enhanced social distancing of infectee
+        self.infectee.distancing_enhanced = True
         distancing_spatial_enhanced_susc = pe.Parameters.instance().\
             intervention_params['social_distancing'][
                 'distancing_spatial_enhanced_susc']
         result_distancing_enhanced = SpatialInfection.spatial_susc(
-            self.cell, self.infector, self.infectee, self.time)
+            self.cell, self.infectee, self.time)
         self.assertEqual(result*distancing_spatial_enhanced_susc,
                          result_distancing_enhanced)