Merge pull request #52 from djgroen/immune

Preseeded Immunity

covid_data/disease_covid19.yml

@@ -43,6 +43,7 @@ incubation_period: 4 # https://www.ams.edu.sg/view-pdf.aspx?file=media%5c5558_fi
 # Fei Zhou et al. The Lancet vol. 395.
 period_to_hospitalisation: 14.0 #this is period to ICU.
 immunity_duration: 273.0
+immunity_fraction: 0.0
 mutations:
   alpha:
     infection_rate: 0.112

covid_data/disease_measles.yml

@@ -30,6 +30,7 @@ mild_recovery_period: 14.0      # Mild measles cases may have a shorter recovery
 incubation_period: 10.0         # Measles' incubation period, from virus exposure to symptom onset, is around 10 to 14 days (range: 7 to 21 days).
 period_to_hospitalisation: 7.0  # The time to hospitalisation varies; severe cases may require it within days, while mild cases may not need hospitalisation.  
 immunity_duration: 9125.0       # Natural immunity after measles recovery is usually lifelong, but waning immunity can occur over decades. MMR vaccination provides long-lasting immunity, often for life.
+immunity_fraction: 0.8          # The initial fraction of the population that is immune to measles due to vaccination or prior infection.
 genotypes:
   D4:
     infection_rate: 0.12

facs/base/disease.py

@@ -23,6 +23,7 @@ class Disease:
     mortality_period: float
     period_to_hospitalisation: float
     immunity_duration: float
+    immunity_fraction: float
 
     hospital: list[float] = field(default_factory=list, init=False, repr=False)
     mortality: list[float] = field(default_factory=list, init=False, repr=False)
@@ -54,6 +55,9 @@ def __post_init__(self):
             if getattr(self, attr) == 0:
                 warnings.warn(f"{attr} is zero", RuntimeWarning)
 
+        if self.immunity_fraction < 0 or self.immunity_fraction > 1:
+            raise ValueError("Immunity fraction must be between 0 and 1")
+
     def array_sanity_check(self, array: list[list[float]], name: str):
         """Sanity check for Hospitalisation and Mortality parameters."""
 

facs/base/person.py

@@ -11,6 +11,7 @@
 import numpy as np
 import yaml
 
+from facs.readers.read_disease_yml import read_disease_yml
 from .needs import Needs
 from .location_types import building_types_dict, building_types_data
 from .utils import (
@@ -26,6 +27,7 @@
     from .house import House
     from .household import Household
     from .location import Location
+    from .disease import Disease
 
 
 needs = Needs("covid_data/needs.csv", list(building_types_dict.keys()))
@@ -34,6 +36,9 @@
     vac_data = yaml.safe_load(f)
     antivax_chance = vac_data["antivax_fraction"]
 
+immune_duration = read_disease_yml("covid_data/disease_covid19.yml").immunity_duration
+immunity_fraction = read_disease_yml("covid_data/disease_covid19.yml").immunity_fraction
+
 
 @dataclass
 class Person:
@@ -69,6 +74,10 @@ def __post_init__(self):
         if np.random.rand() < antivax_chance:  # 5% are antivaxxers.
             self.antivax = True
 
+        if np.random.rand() < 0.5:  # 50% immune initially
+            self.status = "immune"
+            self.phase_duration = np.random.poisson(immune_duration)
+
         self.age = np.random.choice(91, p=self.ages)  # age in years
         self.job = np.random.choice(4, 1, p=[0.865, 0.015, 0.08, 0.04])[0]
         # 0=default, 1=teacher (1.5%), 2=shop worker (8%), 3=health worker (4%)
@@ -210,7 +219,7 @@ def recover(self, e, location):
             e.time, self.location.location_x, self.location.location_x, location, e.rank
         )
 
-    def progress_condition(self, e, t, disease):
+    def progress_condition(self, e, t, disease: Disease):
         """Progress the condition of a person."""
         if self.status_change_time > t:
             return

facs/readers/read_disease_yml.py

@@ -19,11 +19,12 @@ def read_disease_yml(ymlfile: str) -> Disease:
         data["mortality_period"],
         data["period_to_hospitalisation"],
         data["immunity_duration"],
+        data["immunity_fraction"],
     )
-    
+
     disease.add_mortality_chances(data["mortality"])
     disease.add_hospitalisation_chances(data["hospitalised"])
-    
+
     if "mutations" in data:
         # Handle mutations
         disease.add_mutations(data["mutations"])
@@ -32,7 +33,7 @@ def read_disease_yml(ymlfile: str) -> Disease:
         disease.add_genotypes(data["genotypes"])
     else:
         print("No mutations or genotypes provided")
-    
+
     print(disease)
-    
+
     return disease

tests/test_disease.py

@@ -20,6 +20,7 @@ def disease():
         mortality_period=20.0,
         period_to_hospitalisation=25.0,
         immunity_duration=30.0,
+        immunity_fraction=0.5,
     )
 
 
@@ -30,7 +31,7 @@ def test_disease_initialization(disease: Disease):
         repr(disease) == "Disease(infection_rate=0.05, "
         "incubation_period=5.0, mild_recovery_period=10.0, "
         "recovery_period=15.0, mortality_period=20.0, "
-        "period_to_hospitalisation=25.0, immunity_duration=30.0)"
+        "period_to_hospitalisation=25.0, immunity_duration=30.0, immunity_fraction=0.5)"
     )
 
 
@@ -86,6 +87,7 @@ def test_disease_initialisation_warn_zero_parameters():
             mortality_period=20.0,
             period_to_hospitalisation=25.0,
             immunity_duration=30.0,
+            immunity_fraction=0.5,
         )
 
 
@@ -101,6 +103,7 @@ def test_disease_initialisation_fail_negative_parameters():
             mortality_period=20.0,
             period_to_hospitalisation=25.0,
             immunity_duration=30.0,
+            immunity_fraction=0.5,
         )
 
 
@@ -116,6 +119,23 @@ def test_disease_initialisation_fail_string_parameters():
             mortality_period=20.0,
             period_to_hospitalisation=25.0,
             immunity_duration=30.0,
+            immunity_fraction=0.5,
+        )
+
+
+def test_disease_initialisation_invalid_immunity_fraction():
+    """Test Disease initialization with string parameters."""
+
+    with pytest.raises(TypeError):
+        Disease(
+            infection_rate="0.05",
+            incubation_period=5.0,
+            mild_recovery_period=10.0,
+            recovery_period=15.0,
+            mortality_period=20.0,
+            period_to_hospitalisation=25.0,
+            immunity_duration=30.0,
+            immunity_fraction=1.5,
         )
 
 
@@ -131,6 +151,7 @@ def test_disease_initialisation_fail_list_parameters():
             mortality_period=20.0,
             period_to_hospitalisation=25.0,
             immunity_duration=30.0,
+            immunity_fraction=0.5,
         )
 
 

tests/test_household.py

@@ -106,6 +106,8 @@ def test_evolve(mock_probability, sample_house, sample_ages):
 
     household = Household(sample_house, sample_ages, size=3)
     household.agents[0].status = "infectious"
+    household.agents[1].status = "susceptible"
+    household.agents[2].status = "susceptible"
     household.evolve(eco, disease)
 
     assert mock_probability.call_count == 2