Addition of immunization history class

config_files/immunization_history.toml

@@ -0,0 +1,19 @@
+[vaccine_max_efficacy]
+Pfizer = 0.913
+Moderna = 0.941
+AZ = 0.76
+
+[vaccine_immunity_buildup_days]
+Pfizer = 14
+Moderna = 14
+AZ = 14
+
+[vaccine_efficacy_min_day]
+Pfizer = 180
+Moderna = 180
+AZ = 180
+
+[long_term_vaccine_eff]
+Pfizer = 0.7
+Moderna = 0.7
+AZ = 0.7

config_files/main.toml

@@ -1,20 +1,29 @@
 [simulation_data]
 disease_config_file = "disease.toml"
+immunization_history_config_file = "immunization_history.toml"
 nDays = 50
 nPop = 10000
 vis_default_virus_type = "alpha"
 vis_default_severity = "MILD"
 student_default_virus_type = "alpha"
 num_students = 2000
 max_num_res_students = 500
-v0 = 0
 N_VIS_OPTION = [0, 1, 2, 3]
 N_VIS_PROB = [0.7, 0.17, 0.08, 0.05]
 vis_age_upper = 60
 vis_age_lower = 16
-inf_students_upper = 20
-inf_students_lower = 2
-num_vaccinations = 0
+inf_students_upper = 2
+inf_students_lower = 0
+num_vaccinations = 100
+    [simulation_data.v0_parameters]
+    v0 = 1000
+    v0_interval_start_day = -30
+    v0_interval_end_day = 0
+
+    [simulation_data.vaccine_type]
+    Pfizer = 0.6
+    Moderna = 0.35
+    AZ = 0.05
 
     [simulation_data.variants]
     general = 10
@@ -35,11 +44,6 @@ num_vaccinations = 0
     FOOD = 0.1
     RES = 1
 
-    [simulation_data.vaccine_type]
-    Pfizer = 0.6
-    Moderna = 0.35
-    AZ = 0.05
-
 [policy_data]
 initial_mask_mandate = true
 mask_trigger = 0.3

cv19/immunization_history.py

@@ -0,0 +1,86 @@
+class ImmunizationHistory:
+    """
+    A class designed to keep track of a Person's vaccination history and vaccination parameters.
+
+    Holds the parameters from immunization_history.toml corresponding to the Person's vaccine type,
+    as well as the attributes listed below.
+
+    Attributes
+    ----------
+    vaccinated: :obj:`bool`
+        A variable indicating whether or not the person is vaccinated.
+    list_of_vaccination_dates: :obj:`list` of int
+        A list of a Person's vaccination dates (corresponding to day in simulation).
+    """
+
+    def __init__(self, vaccine_type=None, vaccine_max_efficacy=None, vaccine_immunity_buildup_days=None, long_term_vaccine_eff=None, vaccine_efficacy_min_day=None):
+        """
+        The constructor for the Immunization History class.
+        """
+
+        self.vaccinated = False
+        self.list_of_vaccination_dates = list()
+        self.vaccine_type = vaccine_type
+        self.vaccine_max_efficacy = vaccine_max_efficacy
+        self.vaccine_immunity_buildup_days = vaccine_immunity_buildup_days
+        self.long_term_vaccine_eff = long_term_vaccine_eff
+        self.vaccine_efficacy_min_day = vaccine_efficacy_min_day
+
+    def is_vaccinated(self):
+        """Method to retrieve if a person is vaccinated. Returns True if vaccinated, False if not.
+
+        Returns
+        -------
+        self.vaccinated: :obj:`bool`
+        """
+        return self.vaccinated
+
+    def set_vaccinated(self, day):
+        """Method to set a person to be vaccinated.
+
+        Parameters
+        ----------
+        day: int
+            The day in the simulation when a person is vaccinated.
+
+        Returns
+        -------
+        self.vaccinated: :obj:`bool`
+        """
+
+        self.vaccinated_day = day
+        self.list_of_vaccination_dates.append(self.vaccinated_day)
+        self.vaccinated = True
+
+    def vaccine_efficacy(self, day):
+        """Method to determine what the efficiency of the vaccine based on the type of vaccine administered,
+        and other immunization history parameters.
+
+        Parameters
+        ----------
+        day: int
+            The day in the simulation when a person is vaccinated.
+
+        Returns
+        -------
+        self.current_vaccine_eff: :obj:`float`
+        """
+
+        if self.vaccinated:
+
+            days_since_vaccination = day - self.list_of_vaccination_dates[-1]
+            if days_since_vaccination == 0:
+                self.current_vaccine_eff = 0
+            elif days_since_vaccination <= self.vaccine_immunity_buildup_days:  # linear increase of immunity
+                self.current_vaccine_eff = ((self.vaccine_max_efficacy) / (self.vaccine_immunity_buildup_days)) * days_since_vaccination
+            elif (days_since_vaccination > self.vaccine_immunity_buildup_days) and (days_since_vaccination < self.vaccine_efficacy_min_day):  # calculate linearly decreasing immunity
+                self.current_vaccine_eff = (-(self.vaccine_max_efficacy - self.long_term_vaccine_eff) / (self.vaccine_efficacy_min_day - self.vaccine_immunity_buildup_days))  # slope calculation
+                self.current_vaccine_eff *= days_since_vaccination  # scale by days since vaccination
+                self.current_vaccine_eff += self.vaccine_max_efficacy  # add initial value (which is the max efficacy)
+            else:  # plateau in immunity after and including min_day
+                self.current_vaccine_eff = self.long_term_vaccine_eff
+
+            return self.current_vaccine_eff
+
+        else:
+            return 0

cv19/interaction_sites.py

@@ -466,7 +466,7 @@ def site_interaction(self, will_go_array, day, personal, grade_code):
 
                 if person_1_infected != person_2_infected:
                     # Have an interaction between those people
-                    did_infect = self.interact(p1_obj, p2_obj)
+                    did_infect = self.interact(p1_obj, p2_obj, day=day)
                     if did_infect:
                         if person_1_infected:
                             new_infections[person_2_index] = True
@@ -525,15 +525,17 @@ def calc_interactions(self, site_day_pop):
 
         return number_of_interactions
 
-    def interact(self, person_1, person_2):
-        """Method that models the interaction between two people.
-
+    def interact(self, person_1, person_2, day):
+        """
+        Method that models the interaction between two people.
         Parameters
         ----------
         person_1 : :obj:`cv19.person.Person`
             First person in the two-way interaction.
         person_2 : :obj:`cv19.person.Person`
             Second person in the two-way interaction.
+        day : int
+            The day value that this function is being called on in the encompassing simulation class. Used to determine vaccine efficacy of interacting individuals.
 
         Returns
         -------
@@ -566,11 +568,8 @@ def interact(self, person_1, person_2):
                 if p2_mask:
                     spread_prob *= (1 - P2_OUTWARD_EFF)
 
-        p1_vaccinated1 = person_1.is_vaccinated()
-        p2_vaccinated1 = person_2.is_vaccinated()
-
-        p1_vaccine_eff = person_1.vaccine_type_efficiency() if p1_vaccinated1 else 0
-        p2_vaccine_eff = person_2.vaccine_type_efficiency() if p2_vaccinated1 else 0
+        p1_vaccine_eff = person_1.immunization_history_obj.vaccine_efficacy(day)
+        p2_vaccine_eff = person_2.immunization_history_obj.vaccine_efficacy(day)
 
         spread_prob *= ((1 - p1_vaccine_eff) * (1 - p2_vaccine_eff))
 
@@ -615,8 +614,7 @@ def house_interact(self, day):
                     virus_name = self.variant_code_map[virus_id]
 
                     infection_chance = self.base_infection_spread_prob[virus_name] * self.house_infection_spread_factor
-                    person_vaccinated = housemembers[person].is_vaccinated()
-                    person_vaccine_eff = housemembers[person].vaccine_type_efficiency() if person_vaccinated else 0
+                    person_vaccine_eff = housemembers[person].immunization_history_obj.vaccine_efficacy(day)
                     infection_chance *= (1 - person_vaccine_eff)
                     caught_infection = random() < infection_chance
 
@@ -667,8 +665,7 @@ def student_house_interact(self, day):
                     virus_name = self.variant_code_map[virus_id]
 
                     infection_chance = self.base_infection_spread_prob[virus_name] * self.house_infection_spread_factor
-                    person_vaccinated = housemembers[person].is_vaccinated()
-                    person_vaccine_eff = housemembers[person].vaccine_type_efficiency() if person_vaccinated else 0
+                    person_vaccine_eff = housemembers[person].immunization_history_obj.vaccine_efficacy(day)
                     infection_chance *= (1 - person_vaccine_eff)
                     caught_infection = random() < infection_chance
                     if caught_infection:

cv19/person.py

@@ -1,6 +1,7 @@
 from random import random
 
 import numpy as np
+from .immunization_history import ImmunizationHistory
 
 
 class Person(object):
@@ -17,11 +18,11 @@ class Person(object):
 
     """
 
-    def __init__(self, index, sim_obj, infected=False, recovered=False, dead=False, hospitalized=False, ICU=False,
-                 quarantined=False, quarantined_day=None, infected_day=None, recovered_day=None, death_day=None,
-                 others_infected=None, cure_days=None, recent_infections=None, vaccinated=False, vaccine_type=None,
+    def __init__(self, index, sim_obj, infected=False, recovered=False, dead=False, hospitalized=False, ICU=False, quarantined=False,
+                 quarantined_day=None, infected_day=None, recovered_day=None, death_day=None, others_infected=None,
+                 cure_days=None, recent_infections=None, vaccine_info=None,
                  age=None, job=None, house_index=0, isolation_tendencies=None, case_severity=None, mask_type=None,
-                 has_mask=True, virus_type=None, days_until_symptoms=None):
+                 has_mask=True, virus_type=None):
         """Method to load in attributes from the provided simulation class object.
 
         Sets all objects in the "person_data" dictionary key as self attributes of the
@@ -45,10 +46,8 @@ def __init__(self, index, sim_obj, infected=False, recovered=False, dead=False,
             Determines if person is quarentined or not, defaults False.
         quarantined_day : int
             The day a person is put into quarantine, defaults None.
-        vaccinated : bool
-            Determines if a person is vaccinated or not, defaults to True.
-        vaccine_type : string
-            Determines type of vaccine received by person, defaults to None.
+        vaccine_info : dict
+            Dictionary containing vaccine parameters, defaults None.
         infected_day : int
             The day a person is infected, defaults None.
         recovered_day : int
@@ -90,8 +89,7 @@ def __init__(self, index, sim_obj, infected=False, recovered=False, dead=False,
         self.others_infected = [] if others_infected is None else others_infected
         self.cure_days = cure_days
         self.recent_infections = recent_infections
-        self.vaccinated = vaccinated
-        self.vaccine_type = vaccine_type
+        self.immunization_history_obj = ImmunizationHistory(**vaccine_info) if vaccine_info is not None else ImmunizationHistory()
         self.index = index
         self.age = age
         self.job = job
@@ -100,7 +98,7 @@ def __init__(self, index, sim_obj, infected=False, recovered=False, dead=False,
         self.case_severity = case_severity
         self.mask_type = mask_type
         self.show_symptoms = False
-        self.days_until_symptoms = days_until_symptoms
+        self.days_until_symptoms = None
         self.knows_infected = False
         self.will_get_symptoms = False
         self.has_mask = has_mask
@@ -769,45 +767,3 @@ def update_lockdown_days(self, lockdown_level):
         elif self.days_in_lockdown != 0:
             self.days_in_lockdown -= 1
         return self.days_in_lockdown
-
-    def is_vaccinated(self):
-        """Method to retrieve if a person is vaccinated. Returns True if vaccinated, False if not.
-
-        Returns
-        -------
-        self.vaccinated: :obj:`bool`
-        """
-        return self.vaccinated
-
-    def set_vaccinated(self, day):
-        """Method to set a person to be vaccinated.
-
-        Parameters
-        ----------
-        day: int
-            The day in the simulation when a person is vaccinated.
-
-        Returns
-        -------
-        self.vaccinated: :obj:`bool`
-        """
-        # Make sure person is not already vaccinated.
-        if not self.is_vaccinated():
-            self.vaccinated_day = day
-            self.vaccinated = True
-
-    def vaccine_type_efficiency(self):
-        """Method to determines what the efficiency of the vaccine based on the type of vaccine administered.
-
-        Returns
-        -------
-        self.sim_obj.vaccine_eff[self.vaccine_type]: :obj:`float`
-        """
-        if self.vaccinated:
-            try:
-                return self.sim_obj.vaccine_eff[self.vaccine_type]
-            except KeyError as e:
-                raise ValueError((f"'{self.vaccine_type}' is not a valid vaccine type "
-                                  "and has no associated efficiency.")) from e
-        else:
-            return 1