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utils.py
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import random
import pandas as pd
from Types import *
import const
df = pd.read_csv('population2020.csv')
age_array = df.values
def set_incubation_time():
"""
Sets the incubation time for the person
The incubation time is between 2 and 14 days
The mean of incubation time is between 3 and 5 days
source from: https://www.worldometers.info/coronavirus/coronavirus-incubation-period/
date collected: 28.09.2020
----------
Return:
int - a weighted random between 2 and 14 with higher weight on 3 and 5
"""
weight = [1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1]
days = range(2, 15)
return int(random.choices(days, weights=weight, k=1)[0])
def set_age():
"""
Sets a random weighted age for the person
Data collected from ssb.no to get realistic ages
collected from: https://www.ssb.no/statbank/table/07459/
date: (21.09.2020)
----------
Return:
age - int, the age of the person
"""
weight = []
ages = []
for group in age_array:
weight.append(group[1])
ages.append(group[0])
age = int(random.choices(ages, weights=weight, k=1)[0])
return age
def get_age_group(age):
"""
:param age: int - the age of a Person
:return: AgeGroup enum - the age group of a Person
"""
if age in AgeGroup.INFANT.value:
return AgeGroup.INFANT
elif age in AgeGroup.CHILD.value:
return AgeGroup.CHILD
elif age in AgeGroup.YOUNG_ADULT.value:
return AgeGroup.YOUNG_ADULT
elif age in AgeGroup.ADULT.value:
return AgeGroup.ADULT
elif age in AgeGroup.MIDDLE_AGE.value:
return AgeGroup.MIDDLE_AGE
elif age in AgeGroup.AGED.value:
return AgeGroup.AGED
elif age in AgeGroup.OLD.value:
return AgeGroup.OLD
def get_background_sickness(age):
"""
Gets background sickness depending on age
Realistic background sickness
The probability from background_sickness2019.csv is collected from
source: https://www.ssb.no/statbank/table/11190/tableViewLayout1/
date: 29.09.2020
:param age: int - the age of a person
:return: BackgroundSickness.YES or NO - Enum, if the person should have a background sickness
"""
sickness = pd.read_csv('./background_sickness2019.csv').values
if age in range(0, 16):
return BackgroundSickness.NO
for i in range(len(sickness)):
if age in range(sickness[i][0], sickness[i][1]):
return BackgroundSickness.YES if random.randint(0, 100) < sickness[i][2] else BackgroundSickness.NO
def get_adherence(age):
"""
Gets the adherence(following protocols) depending on age
source: https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.37.2001607#figuresntables
date: 12.10.2020
:param age: age - int, the age of a person
:return: float - the percentage of adherence
"""
if age in range(18, 30):
return 0.90
elif age in range(30, 50):
return 0.40
elif age in range(50, 70):
return 0.10
elif age in range(70, 90):
return 0.15
else:
return 1
def get_smoking(age):
"""
Gets the smoking depending on age
source: https://www.ssb.no/statbank/table/05307/tableViewLayout1/
date: 12.10.2020
:param age: int - the age of a Person
:return: int - 1 or 0, if the person smokes or not
"""
if age in range(0, 16):
return 0
elif age in range(16, 25):
return 1 if random.uniform(0, 1) < 0.02 else 0
elif age in range(25, 35):
return 1 if random.uniform(0, 1) < 0.04 else 0
elif age in range(35, 45):
return 1 if random.uniform(0, 1) < 0.10 else 0
elif age in range(45, 55):
return 1 if random.uniform(0, 1) < 0.12 else 0
elif age in range(55, 65):
return 1 if random.uniform(0, 1) < 0.13 else 0
else:
return 1 if random.uniform(0, 1) < 0.12 else 0
def get_obesity(age):
"""
Gets the obesity depending on age
The first value is bmi 30-35, second value bmi > 35
source: https://www.ssb.no/statbank/table/06181/tableViewLayout1/
date: 12.10.2020
----------
Parameters:
age - int, the age of a person
----------
Return:
int - it the person is obese or not
"""
if age in range(0, 16):
return 0
elif age in range(16, 25):
return 1 if random.uniform(0, 1) < 0.06 + 0.01 else 0
elif age in range(25, 45):
return 1 if random.uniform(0, 1) < 0.13 + 0.03 else 0
elif age in range(45, 67):
return 1 if random.uniform(0, 1) < 0.17 + 0.04 else 0
elif age in range(67, 80):
return 1 if random.uniform(0, 1) < 0.15 + 0.02 else 0
else:
return 1 if random.uniform(0, 1) < 0.09 + 0.01 else 0
def fitness_function(brief_statistic):
"""
Calculates a fitness score based on the states of Persons in a GroupOfPeople.
:param brief_statistic: dict - {key(state of each person):value(number of person in that state)}
:return: int - the calculated fitness score
"""
return brief_statistic['healthy'] * 5 + brief_statistic['infectious'] * 4 + brief_statistic['sick'] * 3 + \
brief_statistic['recovered'] * 2 + brief_statistic['dead'] * 1
def fitness_function_with_cost(brief_statistic, healthcare, hygiene, mask, distancing, curfew, test_rate,
quarantine_rules, isolation_rules):
"""
Calculates a fitness score based on the states of Persons in a GroupOfPeople minus a cost of having higher
restriction values.
:param brief_statistic: dict - {key(state of each person):value(number of person in that state)}
:param healthcare: float 0-1
:param hygiene: float 0-1
:param mask: float 0-1
:param distancing: float 0-1
:param curfew: float 0-1
:param test_rate: float 0-1
:param quarantine_rules: int 0-4
:param isolation_rules: int 0-4
:return: int - the calculated fitness score
"""
state_scores = brief_statistic['healthy'] * 5 + brief_statistic['infectious'] * 4 + brief_statistic['sick'] * 3 + \
brief_statistic['recovered'] * 2 + brief_statistic['dead'] * 1
size = const.X * const.Y
costs = (((healthcare + hygiene + mask + distancing + curfew + test_rate)/6) + ((isolation_rules.value + quarantine_rules.value)/20)) * (size/4)
fitness = state_scores - costs
return fitness
def mutate_parameter(value, variation):
"""
Mutates a value with a random number between -variation to +variation.
:param value: float 0-1
:param variation: float 0-1
:return: float 0-1 - the mutated parameter
"""
mutated_parameter = random.uniform(value - variation, value + variation)
if mutated_parameter <= 0:
return 0
elif mutated_parameter >= 1:
return 1
return mutated_parameter
def mutate_quarantine_isolation(value, variation):
"""
Mutates a value with a random number between -variation to +variation.
:param value: int 0-4
:param variation: int 0-4
:return: int 0-4 - the mutated parameter
"""
mutated_parameter = random.randint(value - variation, value + variation)
if mutated_parameter <= 0:
mutated_parameter = 0
elif mutated_parameter >= 4:
mutated_parameter = 4
return mutated_parameter