Immune fraction read from a file

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

@@ -37,6 +37,7 @@
     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

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