From efc41c069c69be36f529c0d0e39a107cb8192e1c Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 31 Oct 2022 18:53:43 -0400
Subject: [PATCH 01/14] Updating vax branch to include Immunization History
 class.

---
 .../immunization_history_parameters.toml      | 19 +++++
 config_files/main.toml                        | 20 +++--
 cv19/immunization_history.py                  | 76 +++++++++++++++++++
 cv19/interaction_sites.py                     | 20 ++---
 cv19/person.py                                | 54 ++-----------
 cv19/population.py                            | 50 +++++++++---
 cv19/simulation.py                            | 42 +++++++++-
 7 files changed, 203 insertions(+), 78 deletions(-)
 create mode 100644 config_files/immunization_history_parameters.toml
 create mode 100644 cv19/immunization_history.py

diff --git a/config_files/immunization_history_parameters.toml b/config_files/immunization_history_parameters.toml
new file mode 100644
index 0000000..00574b4
--- /dev/null
+++ b/config_files/immunization_history_parameters.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
diff --git a/config_files/main.toml b/config_files/main.toml
index 2cb4418..e7b6d30 100644
--- a/config_files/main.toml
+++ b/config_files/main.toml
@@ -1,19 +1,28 @@
 [simulation_data]
 disease_config_file = "disease.toml"
+immunization_history_config_file = "immunization_history_parameters.toml"
 nDays = 100
 nPop = 10000
 vis_default_virus_type = "alpha"
 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
+inf_students_upper = 2
+inf_students_lower = 0
 num_vaccinations = 0
+    [simulation_data.v0_parameters]
+    v0 = 10000
+    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
@@ -34,11 +43,6 @@ 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
diff --git a/cv19/immunization_history.py b/cv19/immunization_history.py
new file mode 100644
index 0000000..eb212fe
--- /dev/null
+++ b/cv19/immunization_history.py
@@ -0,0 +1,76 @@
+class Immunization_History:
+
+    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):
+        '''
+        A class designed to keep track of a Person's vaccination history and vaccination parameters.
+
+        Holds the parameters from immunization_history_parameters.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).
+        '''
+
+        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 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:
+
+            days_since_vaccination = day - self.list_of_vaccination_dates[-1]
+            if (days_since_vaccination) == 0:
+                self.current_vax_eff = 0
+            elif (days_since_vaccination) <= self.vaccine_immunity_buildup_days:
+                self.current_vax_eff = ((self.vaccine_max_efficacy) / (self.vaccine_immunity_buildup_days)) * days_since_vaccination
+            elif (days_since_vaccination) >= self.vaccine_efficacy_min_day:
+                self.current_vax_eff = self.long_term_vaccine_eff
+            else:
+                self.current_vax_eff = (-(self.vaccine_max_efficacy - self.long_term_vaccine_eff) / (self.vaccine_efficacy_min_day - self.vaccine_immunity_buildup_days))
+                self.current_vax_eff *= days_since_vaccination
+                self.current_vax_eff += self.vaccine_max_efficacy
+
+            return self.current_vax_eff
+
+        else:
+            return 0
diff --git a/cv19/interaction_sites.py b/cv19/interaction_sites.py
index b55db76..da8a87a 100644
--- a/cv19/interaction_sites.py
+++ b/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)
                     if did_infect:
                         if person_1_infected:
                             new_infections[person_2_index] = True
@@ -522,7 +522,7 @@ def calc_interactions(self, site_day_pop):
 
         return number_of_interactions
 
-    def interact(self, person_1, person_2):
+    def interact(self, person_1, person_2, day):
         '''Method that models the interaction between two people.
 
         Parameters
@@ -563,11 +563,11 @@ 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_vaccinated1 = person_1.immunization_history_obj.is_vaccinated()
+        p2_vaccinated1 = person_2.immunization_history_obj.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) if p1_vaccinated1 else 0
+        p2_vaccine_eff = person_2.immunization_history_obj.vaccine_efficacy(day) if p2_vaccinated1 else 0
 
         spread_prob *= ((1 - p1_vaccine_eff) * (1 - p2_vaccine_eff))
 
@@ -612,8 +612,8 @@ 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_vaccinated = housemembers[person].immunization_history_obj.is_vaccinated()
+                    person_vaccine_eff = housemembers[person].immunization_history_obj.vaccine_efficacy(day) if person_vaccinated else 0
                     infection_chance *= (1 - person_vaccine_eff)
                     caught_infection = random() < infection_chance
 
@@ -664,8 +664,8 @@ 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_vaccinated = housemembers[person].immunization_history_obj.is_vaccinated()
+                    person_vaccine_eff = housemembers[person].immunization_history_obj.vaccine_efficacy(day) if person_vaccinated else 0
                     infection_chance *= (1 - person_vaccine_eff)
                     caught_infection = random() < infection_chance
                     if caught_infection:
diff --git a/cv19/person.py b/cv19/person.py
index 92f8710..64203a1 100644
--- a/cv19/person.py
+++ b/cv19/person.py
@@ -1,6 +1,7 @@
 from random import random
 
 import numpy as np
+from .immunization_history import Immunization_History
 
 
 class Person(object):
@@ -19,7 +20,7 @@ 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,
+                 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):
         '''Method to load in attributes from the provided simulation class object.
@@ -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 = Immunization_History(**vaccine_info)
         self.index = index
         self.age = age
         self.job = job
@@ -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
diff --git a/cv19/population.py b/cv19/population.py
index 018da84..3f0ee6b 100644
--- a/cv19/population.py
+++ b/cv19/population.py
@@ -37,7 +37,6 @@ def __init__(self, sim_obj):
         self.set_demographic_parameters()
 
         self.nPop = sim_obj.nPop  # total population
-        self.v0 = sim_obj.v0  # initial vaccinated
 
         # Student parameter
         self.nStudents = sim_obj.num_students  # full capacity ~ 24k students
@@ -99,7 +98,25 @@ def __init__(self, sim_obj):
 
         mask_type_arr = np.random.choice(a=self.mask_options, p=self.mask_weights, size=self.nPop)
         has_mask_arr = np.random.uniform(size=self.nPop) < self.prob_has_mask
+
+        self.v0 = sim_obj.v0_parameters["v0"]  # initial vaccinated
         vaccine_type_arr = np.random.choice(a=self.vaccine_options, p=self.vaccine_weights, size=self.nPop)
+        if self.v0 > self.nPop:
+            self.v0 = self.nPop  # make sure maximum initially vaccinated people <= population size
+        v0_lower = sim_obj.v0_parameters["v0_interval_start_day"]
+        v0_upper = sim_obj.v0_parameters["v0_interval_end_day"]
+        vaccination_date_arr = np.zeros(self.v0)
+        if v0_upper <= 0:
+
+            if v0_lower < v0_upper:
+                vaccination_date_arr = np.random.uniform(low=v0_lower, high=v0_upper, size=self.v0)
+            else:
+                vaccination_date_arr = np.ones(self.v0) * v0_lower
+        else:
+            if v0_lower >= 0:
+                vaccination_date_arr = np.zeros(self.v0)
+            else:
+                vaccination_date_arr = np.random.uniform(low=v0_lower, high=0, size=self.v0)
 
         # Initialize the house index and size for the loop
         houseIndex = 0
@@ -111,6 +128,13 @@ def __init__(self, sim_obj):
                 houseIndex += 1
                 houseSize = self.household[houseIndex]
 
+            vaccine_type = vaccine_type_arr[i]
+            individual_vaccine_info = {"vaccine_type": vaccine_type,
+                                       "vaccine_max_efficacy": self.vaccine_parameters["vaccine_max_efficacy"][vaccine_type],
+                                       "vaccine_immunity_buildup_days": self.vaccine_parameters["vaccine_immunity_buildup_days"][vaccine_type],
+                                       "long_term_vaccine_eff": self.vaccine_parameters["long_term_vaccine_eff"][vaccine_type],
+                                       "vaccine_efficacy_min_day": self.vaccine_parameters["vaccine_efficacy_min_day"][vaccine_type]}
+
             # MAKE A PERSON
             newPerson = Person(index=i,
                                sim_obj=sim_obj,
@@ -130,8 +154,7 @@ def __init__(self, sim_obj):
                                age=age_arr[i],
                                job=job_arr[i],
                                house_index=houseIndex,
-                               vaccinated=False,
-                               vaccine_type=vaccine_type_arr[i],
+                               vaccine_info=individual_vaccine_info,
                                isolation_tendencies=isolation_tend_arr[i],
                                case_severity=case_severity_arr[i],
                                mask_type=mask_type_arr[i],
@@ -176,6 +199,13 @@ def __init__(self, sim_obj):
                 studHouseIndex += 1
                 studHouseSize = self.stud_houses[studHouseIndex]
 
+            vaccine_type = vaccine_type_arr[i]
+            individual_vaccine_info = {"vaccine_type": vaccine_type,
+                                       "vaccine_max_efficacy": self.vaccine_parameters["vaccine_max_efficacy"][vaccine_type],
+                                       "vaccine_immunity_buildup_days": self.vaccine_parameters["vaccine_immunity_buildup_days"][vaccine_type],
+                                       "long_term_vaccine_eff": self.vaccine_parameters["long_term_vaccine_eff"][vaccine_type],
+                                       "vaccine_efficacy_min_day": self.vaccine_parameters["vaccine_efficacy_min_day"][vaccine_type]}
+
             newStudent = Person(index=i,
                                 sim_obj=sim_obj,
                                 infected=False,
@@ -194,8 +224,7 @@ def __init__(self, sim_obj):
                                 age=student_age[i - self.nPop + self.nStudents],  # adjust for index inconsistency
                                 job='Student',
                                 house_index=studHouseIndex,
-                                vaccinated=False,
-                                vaccine_type=vaccine_type_arr[i],
+                                vaccine_info=individual_vaccine_info,
                                 isolation_tendencies=isolation_tend_arr[i],
                                 case_severity=student_case_severity_arr[i - self.nPop + self.nStudents],  # adjust for index inconsistency
                                 mask_type=mask_type_arr[i],
@@ -266,8 +295,8 @@ def __init__(self, sim_obj):
 
         # Vaccinate first v0 people
         v_indices = sample(range(self.nPop), self.v0)
-        for i in v_indices:
-            self.population[i].set_vaccinated(day=0)
+        for index, i in enumerate(v_indices):
+            self.population[i].immunization_history_obj.set_vaccinated(day=int(vaccination_date_arr[index]))
             self.vaccinated[i] = i
 
     def load_attributes_from_sim_obj(self, sim_obj):
@@ -302,9 +331,10 @@ def load_attributes_from_sim_obj(self, sim_obj):
         self.mask_weights = np.array([self.mask_type[key] for key in constants.MASK_OPTIONS])
         self.mask_options = constants.MASK_OPTIONS
 
-        # format vaccine weights
+        # format vaccine parameters
         self.vaccine_weights = np.array([self.sim_obj.vaccine_type[key] for key in constants.VACCINE_OPTIONS])
         self.vaccine_options = constants.VACCINE_OPTIONS
+        self.vaccine_parameters = sim_obj.immunization_history_parameters
 
     def set_demographic_parameters(self):
         '''Method to open disease parameters from the TOML file.
@@ -892,7 +922,7 @@ def update_vaccinated(self, day):
         '''
 
         non_vaccinated = np.array([index for index in range(self.nPop)
-                                   if not self.population[index].is_vaccinated()])
+                                   if not self.population[index].immunization_history_obj.is_vaccinated()])
 
         num_vacc = self.sim_obj.num_vaccinations
         num_to_vaccinate = num_vacc if len(non_vaccinated) >= num_vacc else len(non_vaccinated)
@@ -902,7 +932,7 @@ def update_vaccinated(self, day):
         for index in self.to_vaccinate:
             person_to_vaccinate = self.population[index]
 
-            person_to_vaccinate.set_vaccinated(day)
+            person_to_vaccinate.immunization_history_obj.set_vaccinated(day)
             self.vaccinated[index] = index
 
     def change_mask_wearing(self):
diff --git a/cv19/simulation.py b/cv19/simulation.py
index 18747bc..5ab4109 100644
--- a/cv19/simulation.py
+++ b/cv19/simulation.py
@@ -78,6 +78,7 @@ def __init__(self, config_file, config_dir="", verbose=False):
         self.config_dir = config_dir
         self.load_general_parameters(config_file)
         self.load_disease_parameters(self.disease_config_file)
+        self.load_immunization_parameters(self.immunization_history_config_file)
 
         self.init_classes()  # Have to initalize the classes after we have all of the parameters
 
@@ -189,6 +190,43 @@ def load_disease_parameters(self, filename):
                 with open(filepath, 'rb') as file:
                     self.disease_parameters = tomli.load(file)
 
+    def load_immunization_parameters(self, config_file_name):
+        ''' Method to load in attributes from the immunization history configuration file.
+
+        All parameters in the file are loaded into the object, and parameter names
+        are taken from dictionary keys.
+
+        Parameters
+        ----------
+        filename : str
+            Path to the immunization history configuration file.
+        '''
+
+        # If path is absolute, use it.
+        if Path(config_file_name).is_absolute():
+            with open(config_file_name, 'rb') as file:
+                self.immunization_history_parameters = tomli.load(file)
+
+        # Assume that the configuration filename is relative to path of main config.
+        # If not set, assume relative to working directory.
+        # Last attempt try relative to cv19 project directory.
+        else:
+            filepath = Path(self.config_dir, config_file_name)
+            try:
+                with open(filepath, 'rb') as file:
+                    self.immunization_history_parameters = tomli.load(file)
+
+                return
+
+            except FileNotFoundError:
+                warnings.warn((f"Unable to find file: {filepath} "
+                               "assuming directory is relative to main config. "
+                               "Attempting read relative to CV19ROOT directory."))
+
+                filepath = Path(CV19ROOT, config_file_name)
+                with open(filepath, 'rb') as file:
+                    self.immunization_history_parameters = tomli.load(file)
+
     def init_classes(self):
         ''' Method that links the policy, population, and interaction sites class objects with
         the Simulation class (serves as pointer variables).
@@ -369,7 +407,9 @@ def run(self, fail_on_rerun=True):
                 visitor = Person(index=visitors_ind[i], sim_obj=self, infected=True, 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, age=vis_age[i],
+                                 cure_days=None, recent_infections=None,
+                                 vaccine_info={"vaccine_type": None, "vaccine_max_efficacy": None,
+                                               "vaccine_immunity_buildup_days": None, "long_term_vaccine_eff": None, "vaccine_efficacy_min_day": None}, age=vis_age[i],
                                  job="Visitor", house_index=None, isolation_tendencies=0.2,
                                  case_severity='Mild', has_mask=True, virus_type="alpha")
                 self.pop.population.append(visitor)

From 4c53d0907e5ec1328c05679042668706815d1509 Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 31 Oct 2022 20:16:37 -0400
Subject: [PATCH 02/14] Added comments throughout vaccine class changes.

---
 cv19/immunization_history.py | 17 +++++++++--------
 cv19/person.py               |  2 +-
 cv19/population.py           | 25 ++++++++++++++-----------
 cv19/simulation.py           |  2 +-
 4 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/cv19/immunization_history.py b/cv19/immunization_history.py
index eb212fe..e7ee4a7 100644
--- a/cv19/immunization_history.py
+++ b/cv19/immunization_history.py
@@ -49,11 +49,12 @@ def set_vaccinated(self, day):
         self.vaccinated = True
 
     def vaccine_efficacy(self, day):
-        '''Method to determines what the efficiency of the vaccine based on the type of vaccine administered.
+        '''Method to determines what the efficiency of the vaccine based on the type of vaccine administered, and other
+        immunization history parameters.
 
         Returns
         -------
-        self.sim_obj.vaccine_eff[self.vaccine_type]: :obj:`float`
+        self.current_vax_eff: :obj:`float`
         '''
 
         if self.vaccinated:
@@ -61,14 +62,14 @@ def vaccine_efficacy(self, day):
             days_since_vaccination = day - self.list_of_vaccination_dates[-1]
             if (days_since_vaccination) == 0:
                 self.current_vax_eff = 0
-            elif (days_since_vaccination) <= self.vaccine_immunity_buildup_days:
+            elif (days_since_vaccination) <= self.vaccine_immunity_buildup_days:  # linear increase of immunity
                 self.current_vax_eff = ((self.vaccine_max_efficacy) / (self.vaccine_immunity_buildup_days)) * days_since_vaccination
-            elif (days_since_vaccination) >= self.vaccine_efficacy_min_day:
+            elif (days_since_vaccination) >= self.vaccine_efficacy_min_day:  # plateau in immunity after min_day
                 self.current_vax_eff = self.long_term_vaccine_eff
-            else:
-                self.current_vax_eff = (-(self.vaccine_max_efficacy - self.long_term_vaccine_eff) / (self.vaccine_efficacy_min_day - self.vaccine_immunity_buildup_days))
-                self.current_vax_eff *= days_since_vaccination
-                self.current_vax_eff += self.vaccine_max_efficacy
+            else:  # calculate linearly decreasing immunity
+                self.current_vax_eff = (-(self.vaccine_max_efficacy - self.long_term_vaccine_eff) / (self.vaccine_efficacy_min_day - self.vaccine_immunity_buildup_days))  # slope calculation
+                self.current_vax_eff *= days_since_vaccination  # scale by days since vaccination
+                self.current_vax_eff += self.vaccine_max_efficacy  # add initial value (which is the max efficacy)
 
             return self.current_vax_eff
 
diff --git a/cv19/person.py b/cv19/person.py
index 64203a1..2f591f2 100644
--- a/cv19/person.py
+++ b/cv19/person.py
@@ -89,7 +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.immunization_history_obj = Immunization_History(**vaccine_info)
+        self.immunization_history_obj = Immunization_History(**vaccine_info)  # create immunization history object
         self.index = index
         self.age = age
         self.job = job
diff --git a/cv19/population.py b/cv19/population.py
index 3f0ee6b..4eb0691 100644
--- a/cv19/population.py
+++ b/cv19/population.py
@@ -103,19 +103,21 @@ def __init__(self, sim_obj):
         vaccine_type_arr = np.random.choice(a=self.vaccine_options, p=self.vaccine_weights, size=self.nPop)
         if self.v0 > self.nPop:
             self.v0 = self.nPop  # make sure maximum initially vaccinated people <= population size
-        v0_lower = sim_obj.v0_parameters["v0_interval_start_day"]
-        v0_upper = sim_obj.v0_parameters["v0_interval_end_day"]
-        vaccination_date_arr = np.zeros(self.v0)
-        if v0_upper <= 0:
+        v0_lower = sim_obj.v0_parameters["v0_interval_start_day"]  # lower bound on v0 range
+        v0_upper = sim_obj.v0_parameters["v0_interval_end_day"]  # upper bound on v0 range
+        vaccination_date_arr = np.zeros(self.v0)  # initialize v0 dates array
+        if v0_lower <= 0 and v0_upper <= 0:  # v0 bounds cannot be greater than 0
 
-            if v0_lower < v0_upper:
+            if v0_lower < v0_upper:  # v0_lower should be smaller (more negative) than v0_upper
                 vaccination_date_arr = np.random.uniform(low=v0_lower, high=v0_upper, size=self.v0)
-            else:
+            if v0_lower > v0_upper:  # flip the bounds to set the range of v0
+                vaccination_date_arr = np.random.uniform(low=v0_upper, high=v0_lower, size=self.v0)
+            else:  # they are equal to each other:
                 vaccination_date_arr = np.ones(self.v0) * v0_lower
         else:
-            if v0_lower >= 0:
+            if v0_lower >= 0:  # if v0_lower is > 0, make all individuals vaccinated on day 0
                 vaccination_date_arr = np.zeros(self.v0)
-            else:
+            else:  # if only v0_upper is > 0, set 0 as upper bound and proceed
                 vaccination_date_arr = np.random.uniform(low=v0_lower, high=0, size=self.v0)
 
         # Initialize the house index and size for the loop
@@ -128,12 +130,13 @@ def __init__(self, sim_obj):
                 houseIndex += 1
                 houseSize = self.household[houseIndex]
 
-            vaccine_type = vaccine_type_arr[i]
+            vaccine_type = vaccine_type_arr[i]  # vaccine type from vaccine type arr
             individual_vaccine_info = {"vaccine_type": vaccine_type,
                                        "vaccine_max_efficacy": self.vaccine_parameters["vaccine_max_efficacy"][vaccine_type],
                                        "vaccine_immunity_buildup_days": self.vaccine_parameters["vaccine_immunity_buildup_days"][vaccine_type],
                                        "long_term_vaccine_eff": self.vaccine_parameters["long_term_vaccine_eff"][vaccine_type],
                                        "vaccine_efficacy_min_day": self.vaccine_parameters["vaccine_efficacy_min_day"][vaccine_type]}
+            # set up dictionary of vaccination parameters for immunization history object
 
             # MAKE A PERSON
             newPerson = Person(index=i,
@@ -204,7 +207,7 @@ def __init__(self, sim_obj):
                                        "vaccine_max_efficacy": self.vaccine_parameters["vaccine_max_efficacy"][vaccine_type],
                                        "vaccine_immunity_buildup_days": self.vaccine_parameters["vaccine_immunity_buildup_days"][vaccine_type],
                                        "long_term_vaccine_eff": self.vaccine_parameters["long_term_vaccine_eff"][vaccine_type],
-                                       "vaccine_efficacy_min_day": self.vaccine_parameters["vaccine_efficacy_min_day"][vaccine_type]}
+                                       "vaccine_efficacy_min_day": self.vaccine_parameters["vaccine_efficacy_min_day"][vaccine_type]}  # set up immunization history object parameters as dictionary
 
             newStudent = Person(index=i,
                                 sim_obj=sim_obj,
@@ -295,7 +298,7 @@ def __init__(self, sim_obj):
 
         # Vaccinate first v0 people
         v_indices = sample(range(self.nPop), self.v0)
-        for index, i in enumerate(v_indices):
+        for index, i in enumerate(v_indices):  # set vaccinated date based on vaccination_date_arr
             self.population[i].immunization_history_obj.set_vaccinated(day=int(vaccination_date_arr[index]))
             self.vaccinated[i] = i
 
diff --git a/cv19/simulation.py b/cv19/simulation.py
index 5ab4109..438bdc9 100644
--- a/cv19/simulation.py
+++ b/cv19/simulation.py
@@ -78,7 +78,7 @@ def __init__(self, config_file, config_dir="", verbose=False):
         self.config_dir = config_dir
         self.load_general_parameters(config_file)
         self.load_disease_parameters(self.disease_config_file)
-        self.load_immunization_parameters(self.immunization_history_config_file)
+        self.load_immunization_parameters(self.immunization_history_config_file)  # load immunization history files
 
         self.init_classes()  # Have to initalize the classes after we have all of the parameters
 

From 3eff0a5506538f137596917c0ddbe1b14525b078 Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 31 Oct 2022 20:30:16 -0400
Subject: [PATCH 03/14] Change how visitors' vaccine objects are initialized.

---
 cv19/simulation.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cv19/simulation.py b/cv19/simulation.py
index 438bdc9..8eb20ef 100644
--- a/cv19/simulation.py
+++ b/cv19/simulation.py
@@ -408,8 +408,8 @@ def run(self, fail_on_rerun=True):
                                  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={"vaccine_type": None, "vaccine_max_efficacy": None,
-                                               "vaccine_immunity_buildup_days": None, "long_term_vaccine_eff": None, "vaccine_efficacy_min_day": None}, age=vis_age[i],
+                                 vaccine_info={"vaccine_type": "Pfizer", "vaccine_max_efficacy": 0.913,
+                                               "vaccine_immunity_buildup_days": 14, "long_term_vaccine_eff": 0.7, "vaccine_efficacy_min_day": 180}, age=vis_age[i],
                                  job="Visitor", house_index=None, isolation_tendencies=0.2,
                                  case_severity='Mild', has_mask=True, virus_type="alpha")
                 self.pop.population.append(visitor)

From 7e80eedfdd8342d955267fe1850b1859c1805be5 Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 31 Oct 2022 20:38:57 -0400
Subject: [PATCH 04/14] Add class docstring for Immunization history and fix
 initialization of object in person constructor.

---
 cv19/immunization_history.py | 25 ++++++++++++++-----------
 cv19/person.py               |  3 ++-
 2 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/cv19/immunization_history.py b/cv19/immunization_history.py
index e7ee4a7..2f924f4 100644
--- a/cv19/immunization_history.py
+++ b/cv19/immunization_history.py
@@ -1,18 +1,21 @@
 class Immunization_History:
+    '''
+    A class designed to keep track of a Person's vaccination history and vaccination parameters.
 
-    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):
-        '''
-        A class designed to keep track of a Person's vaccination history and vaccination parameters.
+    Holds the parameters from immunization_history_parameters.toml corresponding to the Person's vaccine type,
+    as well as the attributes listed below.
 
-        Holds the parameters from immunization_history_parameters.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).
+    '''
 
-        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
diff --git a/cv19/person.py b/cv19/person.py
index 2f591f2..d5eea17 100644
--- a/cv19/person.py
+++ b/cv19/person.py
@@ -89,7 +89,8 @@ 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.immunization_history_obj = Immunization_History(**vaccine_info)  # create immunization history object
+        # create immunization history object
+        self.immunization_history_obj = Immunization_History(**vaccine_info) if vaccine_info != None else Immunization_History()
         self.index = index
         self.age = age
         self.job = job

From 5e627951f7741e98f1aa0ff9f1988906fdcb965b Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 31 Oct 2022 20:46:33 -0400
Subject: [PATCH 05/14] Pull request issue fixes.

---
 cv19/person.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cv19/person.py b/cv19/person.py
index d5eea17..97c568c 100644
--- a/cv19/person.py
+++ b/cv19/person.py
@@ -90,7 +90,7 @@ def __init__(self, index, sim_obj, infected=False, recovered=False, dead=False,
         self.cure_days = cure_days
         self.recent_infections = recent_infections
         # create immunization history object
-        self.immunization_history_obj = Immunization_History(**vaccine_info) if vaccine_info != None else Immunization_History()
+        self.immunization_history_obj = Immunization_History(**vaccine_info) if vaccine_info is not None else Immunization_History()
         self.index = index
         self.age = age
         self.job = job

From 4b199cca78c4119ad2ddb0a82791e5b5bf5df4d2 Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 31 Oct 2022 20:48:35 -0400
Subject: [PATCH 06/14] Small fix

---
 cv19/immunization_history.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cv19/immunization_history.py b/cv19/immunization_history.py
index 2f924f4..df497bb 100644
--- a/cv19/immunization_history.py
+++ b/cv19/immunization_history.py
@@ -15,7 +15,7 @@ class Immunization_History:
 
     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. 
+        The constructor for the Immunization History class.
         '''
 
         self.vaccinated = False

From 274bb0847f64cb63bee0c99c2d3e299be2daa5e4 Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 31 Oct 2022 20:55:46 -0400
Subject: [PATCH 07/14] Amend test files to include new config files so that
 the code actually works ...

---
 test/testing_config_files/main_quarantine_1.toml | 1 +
 test/testing_config_files/main_quarantine_2.toml | 1 +
 2 files changed, 2 insertions(+)

diff --git a/test/testing_config_files/main_quarantine_1.toml b/test/testing_config_files/main_quarantine_1.toml
index 8410658..28e6d21 100644
--- a/test/testing_config_files/main_quarantine_1.toml
+++ b/test/testing_config_files/main_quarantine_1.toml
@@ -1,5 +1,6 @@
 [simulation_data]
 disease_config_file = "disease_quarantine_1.toml"
+immunization_history_config_file = "immunization_history_parameters.toml"
 nDays = 50 ## needs to be at least max infectious time (29 days) + quarantine_time (14 days)
 nPop = 10000
 vis_default_virus_type = "alpha"
diff --git a/test/testing_config_files/main_quarantine_2.toml b/test/testing_config_files/main_quarantine_2.toml
index e0e07a5..2dd25d2 100644
--- a/test/testing_config_files/main_quarantine_2.toml
+++ b/test/testing_config_files/main_quarantine_2.toml
@@ -1,5 +1,6 @@
 [simulation_data]
 disease_config_file = "disease_quarantine_1.toml"
+immunization_history_config_file = "immunization_history_parameters.toml"
 nDays = 30
 nPop = 10000
 vis_default_virus_type = "alpha"

From 47a31f396aa74204b5617461450b5b82d16ea6bc Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 31 Oct 2022 21:03:16 -0400
Subject: [PATCH 08/14] Fix simulation unit test issue

---
 .../immunization_history_parameters_test.toml | 19 +++++++++++++++++++
 .../main_quarantine_1.toml                    |  2 +-
 .../main_quarantine_2.toml                    |  2 +-
 3 files changed, 21 insertions(+), 2 deletions(-)
 create mode 100644 test/testing_config_files/immunization_history_parameters_test.toml

diff --git a/test/testing_config_files/immunization_history_parameters_test.toml b/test/testing_config_files/immunization_history_parameters_test.toml
new file mode 100644
index 0000000..00574b4
--- /dev/null
+++ b/test/testing_config_files/immunization_history_parameters_test.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
diff --git a/test/testing_config_files/main_quarantine_1.toml b/test/testing_config_files/main_quarantine_1.toml
index 28e6d21..3a6568a 100644
--- a/test/testing_config_files/main_quarantine_1.toml
+++ b/test/testing_config_files/main_quarantine_1.toml
@@ -1,6 +1,6 @@
 [simulation_data]
 disease_config_file = "disease_quarantine_1.toml"
-immunization_history_config_file = "immunization_history_parameters.toml"
+immunization_history_config_file = "immunization_history_parameters_test.toml"
 nDays = 50 ## needs to be at least max infectious time (29 days) + quarantine_time (14 days)
 nPop = 10000
 vis_default_virus_type = "alpha"
diff --git a/test/testing_config_files/main_quarantine_2.toml b/test/testing_config_files/main_quarantine_2.toml
index 2dd25d2..bd5bc7d 100644
--- a/test/testing_config_files/main_quarantine_2.toml
+++ b/test/testing_config_files/main_quarantine_2.toml
@@ -1,6 +1,6 @@
 [simulation_data]
 disease_config_file = "disease_quarantine_1.toml"
-immunization_history_config_file = "immunization_history_parameters.toml"
+immunization_history_config_file = "immunization_history_parameters_test.toml"
 nDays = 30
 nPop = 10000
 vis_default_virus_type = "alpha"

From 659bbf6a8cf0774096a7a7fe9b17350dab397c8e Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 31 Oct 2022 21:06:22 -0400
Subject: [PATCH 09/14] More unit test issues ...

---
 test/testing_config_files/main_quarantine_1.toml | 5 ++++-
 test/testing_config_files/main_quarantine_2.toml | 5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/test/testing_config_files/main_quarantine_1.toml b/test/testing_config_files/main_quarantine_1.toml
index 3a6568a..291d138 100644
--- a/test/testing_config_files/main_quarantine_1.toml
+++ b/test/testing_config_files/main_quarantine_1.toml
@@ -7,7 +7,6 @@ vis_default_virus_type = "alpha"
 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
@@ -15,6 +14,10 @@ vis_age_lower = 16
 inf_students_upper = 20
 inf_students_lower = 2
 num_vaccinations = 0
+    [simulation_data.v0_parameters]
+    v0 = 10000
+    v0_interval_start_day = -30
+    v0_interval_end_day = 0
 
     [simulation_data.variants]
     general = 1000
diff --git a/test/testing_config_files/main_quarantine_2.toml b/test/testing_config_files/main_quarantine_2.toml
index bd5bc7d..51d9161 100644
--- a/test/testing_config_files/main_quarantine_2.toml
+++ b/test/testing_config_files/main_quarantine_2.toml
@@ -7,7 +7,6 @@ vis_default_virus_type = "alpha"
 student_default_virus_type = "alpha"
 num_students = 2000
 max_num_res_students = 500
-v0 = 0
 N_VIS_OPTION = [0]
 N_VIS_PROB = [1]
 vis_age_upper = 60
@@ -15,6 +14,10 @@ vis_age_lower = 16
 inf_students_upper = 20
 inf_students_lower = 2
 num_vaccinations = 0
+    [simulation_data.v0_parameters]
+    v0 = 10000
+    v0_interval_start_day = -30
+    v0_interval_end_day = 0
 
     [simulation_data.variants]
     general = 0

From 2a8dfaad3f163b64bf5ef864c5998b2de06c4398 Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 23 Jan 2023 18:43:28 -0500
Subject: [PATCH 10/14] amending pr due to feedback, small syntax and
 organization changes

---
 ...ameters.toml => immunization_history.toml} |  0
 config_files/main.toml                        |  2 +-
 cv19/immunization_history.py                  | 24 ++++-----
 cv19/interaction_sites.py                     | 12 +++--
 cv19/person.py                                |  2 +-
 cv19/population.py                            | 54 +++++++++++--------
 cv19/simulation.py                            |  6 ++-
 7 files changed, 56 insertions(+), 44 deletions(-)
 rename config_files/{immunization_history_parameters.toml => immunization_history.toml} (100%)

diff --git a/config_files/immunization_history_parameters.toml b/config_files/immunization_history.toml
similarity index 100%
rename from config_files/immunization_history_parameters.toml
rename to config_files/immunization_history.toml
diff --git a/config_files/main.toml b/config_files/main.toml
index e7b6d30..713a3c8 100644
--- a/config_files/main.toml
+++ b/config_files/main.toml
@@ -1,6 +1,6 @@
 [simulation_data]
 disease_config_file = "disease.toml"
-immunization_history_config_file = "immunization_history_parameters.toml"
+immunization_history_config_file = "immunization_history.toml"
 nDays = 100
 nPop = 10000
 vis_default_virus_type = "alpha"
diff --git a/cv19/immunization_history.py b/cv19/immunization_history.py
index df497bb..dcf662b 100644
--- a/cv19/immunization_history.py
+++ b/cv19/immunization_history.py
@@ -1,4 +1,4 @@
-class Immunization_History:
+class ImmunizationHistory:
     '''
     A class designed to keep track of a Person's vaccination history and vaccination parameters.
 
@@ -52,7 +52,7 @@ def set_vaccinated(self, day):
         self.vaccinated = True
 
     def vaccine_efficacy(self, day):
-        '''Method to determines what the efficiency of the vaccine based on the type of vaccine administered, and other
+        '''Method to determine what the efficiency of the vaccine based on the type of vaccine administered, and other
         immunization history parameters.
 
         Returns
@@ -63,18 +63,18 @@ def vaccine_efficacy(self, day):
         if self.vaccinated:
 
             days_since_vaccination = day - self.list_of_vaccination_dates[-1]
-            if (days_since_vaccination) == 0:
-                self.current_vax_eff = 0
-            elif (days_since_vaccination) <= self.vaccine_immunity_buildup_days:  # linear increase of immunity
-                self.current_vax_eff = ((self.vaccine_max_efficacy) / (self.vaccine_immunity_buildup_days)) * days_since_vaccination
-            elif (days_since_vaccination) >= self.vaccine_efficacy_min_day:  # plateau in immunity after min_day
-                self.current_vax_eff = self.long_term_vaccine_eff
-            else:  # calculate linearly decreasing immunity
-                self.current_vax_eff = (-(self.vaccine_max_efficacy - self.long_term_vaccine_eff) / (self.vaccine_efficacy_min_day - self.vaccine_immunity_buildup_days))  # slope calculation
+            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_vax_eff *= days_since_vaccination  # scale by days since vaccination
-                self.current_vax_eff += self.vaccine_max_efficacy  # add initial value (which is the max efficacy)
+                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_vax_eff
+            return self.current_vaccine_eff
 
         else:
             return 0
diff --git a/cv19/interaction_sites.py b/cv19/interaction_sites.py
index da8a87a..2f7197e 100644
--- a/cv19/interaction_sites.py
+++ b/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, day)
+                    did_infect = self.interact(p1_obj, p2_obj, day=day)
                     if did_infect:
                         if person_1_infected:
                             new_infections[person_2_index] = True
@@ -531,6 +531,8 @@ def interact(self, person_1, person_2, day):
             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
         -------
@@ -566,8 +568,8 @@ def interact(self, person_1, person_2, day):
         p1_vaccinated1 = person_1.immunization_history_obj.is_vaccinated()
         p2_vaccinated1 = person_2.immunization_history_obj.is_vaccinated()
 
-        p1_vaccine_eff = person_1.immunization_history_obj.vaccine_efficacy(day) if p1_vaccinated1 else 0
-        p2_vaccine_eff = person_2.immunization_history_obj.vaccine_efficacy(day) 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))
 
@@ -613,7 +615,7 @@ def house_interact(self, day):
 
                     infection_chance = self.base_infection_spread_prob[virus_name] * self.house_infection_spread_factor
                     person_vaccinated = housemembers[person].immunization_history_obj.is_vaccinated()
-                    person_vaccine_eff = housemembers[person].immunization_history_obj.vaccine_efficacy(day) 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
 
@@ -665,7 +667,7 @@ def student_house_interact(self, day):
 
                     infection_chance = self.base_infection_spread_prob[virus_name] * self.house_infection_spread_factor
                     person_vaccinated = housemembers[person].immunization_history_obj.is_vaccinated()
-                    person_vaccine_eff = housemembers[person].immunization_history_obj.vaccine_efficacy(day) 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:
diff --git a/cv19/person.py b/cv19/person.py
index 97c568c..e09fe90 100644
--- a/cv19/person.py
+++ b/cv19/person.py
@@ -1,7 +1,7 @@
 from random import random
 
 import numpy as np
-from .immunization_history import Immunization_History
+from .immunization_history import ImmunizationHistory
 
 
 class Person(object):
diff --git a/cv19/population.py b/cv19/population.py
index 4eb0691..af84296 100644
--- a/cv19/population.py
+++ b/cv19/population.py
@@ -98,27 +98,10 @@ def __init__(self, sim_obj):
 
         mask_type_arr = np.random.choice(a=self.mask_options, p=self.mask_weights, size=self.nPop)
         has_mask_arr = np.random.uniform(size=self.nPop) < self.prob_has_mask
-
-        self.v0 = sim_obj.v0_parameters["v0"]  # initial vaccinated
+        
+        #Prepare vaccination date array for population initialization
         vaccine_type_arr = np.random.choice(a=self.vaccine_options, p=self.vaccine_weights, size=self.nPop)
-        if self.v0 > self.nPop:
-            self.v0 = self.nPop  # make sure maximum initially vaccinated people <= population size
-        v0_lower = sim_obj.v0_parameters["v0_interval_start_day"]  # lower bound on v0 range
-        v0_upper = sim_obj.v0_parameters["v0_interval_end_day"]  # upper bound on v0 range
-        vaccination_date_arr = np.zeros(self.v0)  # initialize v0 dates array
-        if v0_lower <= 0 and v0_upper <= 0:  # v0 bounds cannot be greater than 0
-
-            if v0_lower < v0_upper:  # v0_lower should be smaller (more negative) than v0_upper
-                vaccination_date_arr = np.random.uniform(low=v0_lower, high=v0_upper, size=self.v0)
-            if v0_lower > v0_upper:  # flip the bounds to set the range of v0
-                vaccination_date_arr = np.random.uniform(low=v0_upper, high=v0_lower, size=self.v0)
-            else:  # they are equal to each other:
-                vaccination_date_arr = np.ones(self.v0) * v0_lower
-        else:
-            if v0_lower >= 0:  # if v0_lower is > 0, make all individuals vaccinated on day 0
-                vaccination_date_arr = np.zeros(self.v0)
-            else:  # if only v0_upper is > 0, set 0 as upper bound and proceed
-                vaccination_date_arr = np.random.uniform(low=v0_lower, high=0, size=self.v0)
+        vaccination_date_arr = self.set_v0_parameters(self,sim_obj)
 
         # Initialize the house index and size for the loop
         houseIndex = 0
@@ -298,9 +281,10 @@ def __init__(self, sim_obj):
 
         # Vaccinate first v0 people
         v_indices = sample(range(self.nPop), self.v0)
-        for index, i in enumerate(v_indices):  # set vaccinated date based on vaccination_date_arr
-            self.population[i].immunization_history_obj.set_vaccinated(day=int(vaccination_date_arr[index]))
-            self.vaccinated[i] = i
+        for i,v in enumerate(v_indices):
+        # set vaccinated date based on vaccination_date_arr
+            self.population[v].immunization_history_obj.set_vaccinated(day=int(vaccination_date_arr[i]))
+            self.vaccinated[v] = v
 
     def load_attributes_from_sim_obj(self, sim_obj):
         '''Method to load in attributes from the provided simulation class object.
@@ -373,6 +357,30 @@ def set_demographic_parameters(self):
 
         # Cast this so they can be used as ints
         self.house_options = [int(x) for x in constants.HOUSE_OPTIONS]
+        
+    def set_v0_parameters(self,sim_obj):
+        '''Method to set up initially vaccinated population array.
+        
+        Returns
+        -------
+        vaccination_date_arr: :obj:`np.array` of :obj:`int`
+        '''
+        
+        self.v0 = sim_obj.v0_parameters["v0"]  # initial vaccinated
+        
+        v0_lower = sim_obj.v0_parameters["v0_interval_start_day"]  # lower bound on v0 range
+        v0_upper = sim_obj.v0_parameters["v0_interval_end_day"]  # upper bound on v0 range
+        vaccination_date_arr = np.zeros(self.v0)  # initialize v0 dates array
+        
+        if v0_lower <= 0 and v0_upper <= 0:  # v0 bounds cannot be greater than 0
+
+            if v0_lower < v0_upper:  # v0_lower should be smaller (more negative) than v0_upper
+                vaccination_date_arr = np.random.uniform(low=v0_lower, high=v0_upper, size=self.v0)
+                
+            else:  # they are equal to each other:
+                vaccination_date_arr = np.ones(self.v0) * v0_lower
+                
+        return vaccination_date_arr
 
     def get_population_size(self):
         '''Method to return population size.
diff --git a/cv19/simulation.py b/cv19/simulation.py
index 8eb20ef..3ba6c86 100644
--- a/cv19/simulation.py
+++ b/cv19/simulation.py
@@ -12,6 +12,7 @@
 from .population import Population
 from .policy import Policy
 from .interaction_sites import InteractionSites
+from .data import constants
 
 
 class Simulation():
@@ -403,13 +404,14 @@ def run(self, fail_on_rerun=True):
             num_vis = np.random.choice(a=self.N_VIS_OPTION, p=self.N_VIS_PROB)
             visitors_ind = [x for x in range(self.nPop, self.nPop + num_vis)]
             vis_age = np.random.choice(a=self.pop.age_options, p=self.pop.age_weights, size=num_vis)
+            vis_vaccine_type = np.random.choice(a=constants.VACCINE_OPTIONS,p=self.vaccine_type,size=num_vis)
             for i in range(0, num_vis):
                 visitor = Person(index=visitors_ind[i], sim_obj=self, infected=True, 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={"vaccine_type": "Pfizer", "vaccine_max_efficacy": 0.913,
-                                               "vaccine_immunity_buildup_days": 14, "long_term_vaccine_eff": 0.7, "vaccine_efficacy_min_day": 180}, age=vis_age[i],
+                                 vaccine_info={"vaccine_type": vis_vaccine_type[i], "vaccine_max_efficacy": self.immunization_history_parameters.vaccine_max_efficacy[vis_vaccine_type[i]],
+                                               "vaccine_immunity_buildup_days": self.immunization_history_parameters.vaccine_immunity_buildup_days[vis_vaccine_type[i]], "long_term_vaccine_eff": self.immunization_history_parameters.long_term_vaccine_eff[vis_vaccine_type[i]], "vaccine_efficacy_min_day": self.immunization_history_parameters.vaccine_efficacy_min_day[vis_vaccine_type[i]]}, age=vis_age[i],
                                  job="Visitor", house_index=None, isolation_tendencies=0.2,
                                  case_severity='Mild', has_mask=True, virus_type="alpha")
                 self.pop.population.append(visitor)

From cf4a78a29c5be594ff0f5e9a37eb66726e790f7e Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 30 Jan 2023 18:57:34 -0500
Subject: [PATCH 11/14] updating immunization history class

---
 cv19/immunization_history.py                          |  4 ++--
 cv19/person.py                                        |  3 +--
 cv19/population.py                                    |  4 ++--
 cv19/simulation.py                                    | 11 ++++++++---
 ...eters_test.toml => immunization_history_test.toml} |  0
 test/testing_config_files/main_quarantine_1.toml      |  2 +-
 test/testing_config_files/main_quarantine_2.toml      |  2 +-
 7 files changed, 15 insertions(+), 11 deletions(-)
 rename test/testing_config_files/{immunization_history_parameters_test.toml => immunization_history_test.toml} (100%)

diff --git a/cv19/immunization_history.py b/cv19/immunization_history.py
index dcf662b..d05748d 100644
--- a/cv19/immunization_history.py
+++ b/cv19/immunization_history.py
@@ -2,7 +2,7 @@ class ImmunizationHistory:
     '''
     A class designed to keep track of a Person's vaccination history and vaccination parameters.
 
-    Holds the parameters from immunization_history_parameters.toml corresponding to the Person's vaccine type,
+    Holds the parameters from immunization_history.toml corresponding to the Person's vaccine type,
     as well as the attributes listed below.
 
     Attributes
@@ -69,7 +69,7 @@ def vaccine_efficacy(self, day):
                 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_vax_eff *= days_since_vaccination  # scale by days since vaccination
+                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
diff --git a/cv19/person.py b/cv19/person.py
index e09fe90..894b6cb 100644
--- a/cv19/person.py
+++ b/cv19/person.py
@@ -89,8 +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
-        # create immunization history object
-        self.immunization_history_obj = Immunization_History(**vaccine_info) if vaccine_info is not None else Immunization_History()
+        self.immunization_history_obj = ImmunizationHistory(**vaccine_info) if vaccine_info is not None else Immunization_History()
         self.index = index
         self.age = age
         self.job = job
diff --git a/cv19/population.py b/cv19/population.py
index af84296..48784eb 100644
--- a/cv19/population.py
+++ b/cv19/population.py
@@ -101,7 +101,7 @@ def __init__(self, sim_obj):
         
         #Prepare vaccination date array for population initialization
         vaccine_type_arr = np.random.choice(a=self.vaccine_options, p=self.vaccine_weights, size=self.nPop)
-        vaccination_date_arr = self.set_v0_parameters(self,sim_obj)
+        vaccination_date_arr = self.set_v0_parameters(sim_obj)
 
         # Initialize the house index and size for the loop
         houseIndex = 0
@@ -377,7 +377,7 @@ def set_v0_parameters(self,sim_obj):
             if v0_lower < v0_upper:  # v0_lower should be smaller (more negative) than v0_upper
                 vaccination_date_arr = np.random.uniform(low=v0_lower, high=v0_upper, size=self.v0)
                 
-            else:  # they are equal to each other:
+            else:  # they are equal to each other: everyone is vaccinated on the same day
                 vaccination_date_arr = np.ones(self.v0) * v0_lower
                 
         return vaccination_date_arr
diff --git a/cv19/simulation.py b/cv19/simulation.py
index 3ba6c86..0bd7722 100644
--- a/cv19/simulation.py
+++ b/cv19/simulation.py
@@ -404,14 +404,19 @@ def run(self, fail_on_rerun=True):
             num_vis = np.random.choice(a=self.N_VIS_OPTION, p=self.N_VIS_PROB)
             visitors_ind = [x for x in range(self.nPop, self.nPop + num_vis)]
             vis_age = np.random.choice(a=self.pop.age_options, p=self.pop.age_weights, size=num_vis)
-            vis_vaccine_type = np.random.choice(a=constants.VACCINE_OPTIONS,p=self.vaccine_type,size=num_vis)
+            vaccine_weights = np.array([self.vaccine_type[key] for key in constants.VACCINE_OPTIONS])
+            vis_vaccine_type = np.random.choice(a=constants.VACCINE_OPTIONS,p=vaccine_weights,size=num_vis)
             for i in range(0, num_vis):
                 visitor = Person(index=visitors_ind[i], sim_obj=self, infected=True, 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={"vaccine_type": vis_vaccine_type[i], "vaccine_max_efficacy": self.immunization_history_parameters.vaccine_max_efficacy[vis_vaccine_type[i]],
-                                               "vaccine_immunity_buildup_days": self.immunization_history_parameters.vaccine_immunity_buildup_days[vis_vaccine_type[i]], "long_term_vaccine_eff": self.immunization_history_parameters.long_term_vaccine_eff[vis_vaccine_type[i]], "vaccine_efficacy_min_day": self.immunization_history_parameters.vaccine_efficacy_min_day[vis_vaccine_type[i]]}, age=vis_age[i],
+                                 vaccine_info={"vaccine_type": vis_vaccine_type[i],
+                                               "vaccine_max_efficacy": self.immunization_history_parameters["vaccine_max_efficacy"][vis_vaccine_type[i]],
+                                               "vaccine_immunity_buildup_days": self.immunization_history_parameters["vaccine_immunity_buildup_days"][vis_vaccine_type[i]],
+                                               "long_term_vaccine_eff": self.immunization_history_parameters["long_term_vaccine_eff"][vis_vaccine_type[i]], 
+                                               "vaccine_efficacy_min_day": self.immunization_history_parameters["vaccine_efficacy_min_day"][vis_vaccine_type[i]]},
+                                 age=vis_age[i],
                                  job="Visitor", house_index=None, isolation_tendencies=0.2,
                                  case_severity='Mild', has_mask=True, virus_type="alpha")
                 self.pop.population.append(visitor)
diff --git a/test/testing_config_files/immunization_history_parameters_test.toml b/test/testing_config_files/immunization_history_test.toml
similarity index 100%
rename from test/testing_config_files/immunization_history_parameters_test.toml
rename to test/testing_config_files/immunization_history_test.toml
diff --git a/test/testing_config_files/main_quarantine_1.toml b/test/testing_config_files/main_quarantine_1.toml
index 291d138..e05c872 100644
--- a/test/testing_config_files/main_quarantine_1.toml
+++ b/test/testing_config_files/main_quarantine_1.toml
@@ -1,6 +1,6 @@
 [simulation_data]
 disease_config_file = "disease_quarantine_1.toml"
-immunization_history_config_file = "immunization_history_parameters_test.toml"
+immunization_history_config_file = "immunization_history_test.toml"
 nDays = 50 ## needs to be at least max infectious time (29 days) + quarantine_time (14 days)
 nPop = 10000
 vis_default_virus_type = "alpha"
diff --git a/test/testing_config_files/main_quarantine_2.toml b/test/testing_config_files/main_quarantine_2.toml
index 51d9161..5abe1b6 100644
--- a/test/testing_config_files/main_quarantine_2.toml
+++ b/test/testing_config_files/main_quarantine_2.toml
@@ -1,6 +1,6 @@
 [simulation_data]
 disease_config_file = "disease_quarantine_1.toml"
-immunization_history_config_file = "immunization_history_parameters_test.toml"
+immunization_history_config_file = "immunization_history_test.toml"
 nDays = 30
 nPop = 10000
 vis_default_virus_type = "alpha"

From d14971214680eb0fd98a43c6e66222666c5cc6b7 Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 30 Jan 2023 19:22:58 -0500
Subject: [PATCH 12/14] updating vaccine code

---
 config_files/main.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/config_files/main.toml b/config_files/main.toml
index 713a3c8..5948269 100644
--- a/config_files/main.toml
+++ b/config_files/main.toml
@@ -1,7 +1,7 @@
 [simulation_data]
 disease_config_file = "disease.toml"
 immunization_history_config_file = "immunization_history.toml"
-nDays = 100
+nDays = 50
 nPop = 10000
 vis_default_virus_type = "alpha"
 student_default_virus_type = "alpha"
@@ -13,9 +13,9 @@ vis_age_upper = 60
 vis_age_lower = 16
 inf_students_upper = 2
 inf_students_lower = 0
-num_vaccinations = 0
+num_vaccinations = 100
     [simulation_data.v0_parameters]
-    v0 = 10000
+    v0 = 1000
     v0_interval_start_day = -30
     v0_interval_end_day = 0
 

From 894165aa6d7c584c26697f092592789609dde6e7 Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 13 Feb 2023 18:02:40 -0500
Subject: [PATCH 13/14] amending immunization history class again, based on
 github errors

---
 cv19/immunization_history.py | 29 +++++++++++++---------
 cv19/interaction_sites.py    | 11 +++------
 cv19/person.py               | 47 +-----------------------------------
 cv19/population.py           | 31 +++++++++++++-----------
 cv19/simulation.py           | 15 +++++++-----
 5 files changed, 47 insertions(+), 86 deletions(-)

diff --git a/cv19/immunization_history.py b/cv19/immunization_history.py
index d05748d..f427bd3 100644
--- a/cv19/immunization_history.py
+++ b/cv19/immunization_history.py
@@ -1,5 +1,5 @@
 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,
@@ -11,12 +11,12 @@ class ImmunizationHistory:
         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()
@@ -27,16 +27,16 @@ def __init__(self, vaccine_type=None, vaccine_max_efficacy=None, vaccine_immunit
         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.
+        """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.
+        """Method to set a person to be vaccinated.
 
         Parameters
         ----------
@@ -46,19 +46,24 @@ def set_vaccinated(self, day):
         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
+        """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_vax_eff: :obj:`float`
-        '''
+        self.current_vaccine_eff: :obj:`float`
+        """
 
         if self.vaccinated:
 
@@ -71,7 +76,7 @@ def vaccine_efficacy(self, day):
                 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
+            else:  # plateau in immunity after and including min_day
                 self.current_vaccine_eff = self.long_term_vaccine_eff
 
             return self.current_vaccine_eff
diff --git a/cv19/interaction_sites.py b/cv19/interaction_sites.py
index bcac694..01e0208 100644
--- a/cv19/interaction_sites.py
+++ b/cv19/interaction_sites.py
@@ -524,15 +524,10 @@ def calc_interactions(self, site_day_pop):
                                                                    size=site_day_pop)).astype(int)
 
         return number_of_interactions
-
-<<<<<<< HEAD
+    
     def interact(self, person_1, person_2, day):
-        '''Method that models the interaction between two people.
-=======
-    def interact(self, person_1, person_2):
-        """Method that models the interaction between two people.
->>>>>>> 1f6c4b90cdb6c9bea98ba08dee7c1b6d5b383210
-
+        """
+        Method that models the interaction between two people.
         Parameters
         ----------
         person_1 : :obj:`cv19.person.Person`
diff --git a/cv19/person.py b/cv19/person.py
index e784480..8f185b3 100644
--- a/cv19/person.py
+++ b/cv19/person.py
@@ -89,7 +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.immunization_history_obj = ImmunizationHistory(**vaccine_info) if vaccine_info is not None else Immunization_History()
+        self.immunization_history_obj = ImmunizationHistory(**vaccine_info) if vaccine_info is not None else ImmunizationHistory()
         self.index = index
         self.age = age
         self.job = job
@@ -767,48 +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
-<<<<<<< HEAD
-=======
-
-    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
->>>>>>> 1f6c4b90cdb6c9bea98ba08dee7c1b6d5b383210
diff --git a/cv19/population.py b/cv19/population.py
index 76f73c0..c6c4a36 100644
--- a/cv19/population.py
+++ b/cv19/population.py
@@ -98,8 +98,7 @@ def __init__(self, sim_obj):
 
         mask_type_arr = np.random.choice(a=self.mask_options, p=self.mask_weights, size=self.nPop)
         has_mask_arr = np.random.uniform(size=self.nPop) < self.prob_has_mask
-        
-        #Prepare vaccination date array for population initialization
+        # Prepare vaccination date array for population initialization
         vaccine_type_arr = np.random.choice(a=self.vaccine_options, p=self.vaccine_weights, size=self.nPop)
         vaccination_date_arr = self.set_v0_parameters(sim_obj)
 
@@ -281,8 +280,8 @@ def __init__(self, sim_obj):
 
         # Vaccinate first v0 people
         v_indices = sample(range(self.nPop), self.v0)
-        for i,v in enumerate(v_indices):
-        # set vaccinated date based on vaccination_date_arr
+        for i, v in enumerate(v_indices):
+            # set vaccinated date based on vaccination_date_arr
             self.population[v].immunization_history_obj.set_vaccinated(day=int(vaccination_date_arr[i]))
             self.vaccinated[v] = v
 
@@ -357,29 +356,33 @@ def set_demographic_parameters(self):
 
         # Cast this so they can be used as ints
         self.house_options = [int(x) for x in constants.HOUSE_OPTIONS]
-        
-    def set_v0_parameters(self,sim_obj):
-        '''Method to set up initially vaccinated population array.
-        
+
+    def set_v0_parameters(self, sim_obj):
+        """Method to set up initially vaccinated population array.
+
+        Parameters
+        ----------
+        sim_obj : :obj:`cv19.simulation.simulation`
+            The encompassing simulation object hosting the simulation.
+
         Returns
         -------
         vaccination_date_arr: :obj:`np.array` of :obj:`int`
-        '''
-        
+        """
+
         self.v0 = sim_obj.v0_parameters["v0"]  # initial vaccinated
-        
         v0_lower = sim_obj.v0_parameters["v0_interval_start_day"]  # lower bound on v0 range
         v0_upper = sim_obj.v0_parameters["v0_interval_end_day"]  # upper bound on v0 range
         vaccination_date_arr = np.zeros(self.v0)  # initialize v0 dates array
-        
+
         if v0_lower <= 0 and v0_upper <= 0:  # v0 bounds cannot be greater than 0
 
             if v0_lower < v0_upper:  # v0_lower should be smaller (more negative) than v0_upper
                 vaccination_date_arr = np.random.uniform(low=v0_lower, high=v0_upper, size=self.v0)
-                
+
             else:  # they are equal to each other: everyone is vaccinated on the same day
                 vaccination_date_arr = np.ones(self.v0) * v0_lower
-                
+
         return vaccination_date_arr
 
     def get_population_size(self):
diff --git a/cv19/simulation.py b/cv19/simulation.py
index 96d43e6..a1c6d2a 100644
--- a/cv19/simulation.py
+++ b/cv19/simulation.py
@@ -58,12 +58,14 @@ def __init__(self, config_file, config_dir="", config_override_data=None, verbos
 
         self.config_dir = config_dir
         self.load_general_parameters(config_file)
-<<<<<<< HEAD
+
+
+<< << << < HEAD
         self.load_disease_parameters(self.disease_config_file)
         self.load_immunization_parameters(self.immunization_history_config_file)  # load immunization history files
-=======
+== == == =
         self.load_disease_parameters(self.disease_config_file, config_override_data)
->>>>>>> 1f6c4b90cdb6c9bea98ba08dee7c1b6d5b383210
+>>>>>> > 1f6c4b90cdb6c9bea98ba08dee7c1b6d5b383210
 
         self.init_classes()  # Have to initalize the classes after we have all of the parameters
 
@@ -160,7 +162,7 @@ def load_disease_parameters(self, filename, config_override_data):
                         self.disease_parameters = tomli.load(file)
 
     def load_immunization_parameters(self, config_file_name):
-        ''' Method to load in attributes from the immunization history configuration file.
+        """Method to load in attributes from the immunization history configuration file.
 
         All parameters in the file are loaded into the object, and parameter names
         are taken from dictionary keys.
@@ -169,7 +171,7 @@ def load_immunization_parameters(self, config_file_name):
         ----------
         filename : str
             Path to the immunization history configuration file.
-        '''
+        """
 
         # If path is absolute, use it.
         if Path(config_file_name).is_absolute():
@@ -381,7 +383,8 @@ def run(self, fail_on_rerun=True):
             visitors_ind = [x for x in range(self.nPop, self.nPop + num_vis)]
             vis_age = np.random.choice(a=self.pop.age_options, p=self.pop.age_weights, size=num_vis)
             vaccine_weights = np.array([self.vaccine_type[key] for key in constants.VACCINE_OPTIONS])
-            vis_vaccine_type = np.random.choice(a=constants.VACCINE_OPTIONS,p=vaccine_weights,size=num_vis)
+            vis_vaccine_type = np.random.choice(a=constants.VACCINE_OPTIONS,
+                                                p=vaccine_weights,size=num_vis)
             for i in range(0, num_vis):
                 visitor = Person(index=visitors_ind[i], sim_obj=self, infected=True, recovered=False, dead=False,
                                  hospitalized=False, ICU=False, quarantined=False, quarantined_day=None, infected_day=None,

From 42d3695afcba338894f247192e3fd214d553ec0d Mon Sep 17 00:00:00 2001
From: irina babayan <irina.babayan@gmail.com>
Date: Mon, 13 Feb 2023 20:16:50 -0500
Subject: [PATCH 14/14] fix error from merge

---
 config_files/main.toml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/config_files/main.toml b/config_files/main.toml
index 21c2c30..6d3b47f 100644
--- a/config_files/main.toml
+++ b/config_files/main.toml
@@ -1,13 +1,6 @@
 [simulation_data]
 disease_config_file = "disease.toml"
-<<<<<<< HEAD
-<<<<<<< HEAD
 immunization_history_config_file = "immunization_history.toml"
-=======
->>>>>>> 1f6c4b90cdb6c9bea98ba08dee7c1b6d5b383210
-=======
-immunization_history_config_file = "immunization_history.toml"
->>>>>>> d56b42831eb98225ce7c0db87b339d0189f3dc1d
 nDays = 50
 nPop = 10000
 vis_default_virus_type = "alpha"