def setInfection(human, area, d):
human.isInfected = True
human.infectionNumber += 1
human.infectionDate = d
human.isTested = False
illness = rd.setIllnessDevelopment()
human.incubationPeriod = illness
illness += rd.setIllnessDevelopment()
human.illnessPeriod = illness
human.evolutionState = 0
#Defining if infected humans will be symptomatic or will need treatment
auxRandom = rd.aRandom()
symptomsThreshold = vr.getSymptomsThreshold(
) * human.deathRiskFactor * vr.getDeathRiskSymptomsW()
treatmentThreshold = vr.getTreatmentThreshold(
) * human.deathRiskFactor * vr.getDeathRiskTreatmentW()
reinfectionFactor = vr.getReinfectionFactor(human.infectionNumber)
if auxRandom < symptomsThreshold * reinfectionFactor:
human.willBeSymptomatic = True
auxRandom = rd.aRandom()
if auxRandom < treatmentThreshold * reinfectionFactor:
human.willNeedTreatment = True
Simulation.increaseV("totalInfected")
Simulation.increaseV("actualInfected")
if area == "A":
Simulation.increaseV("actualAInfected")
elif area == "B":
Simulation.increaseV("actualBInfected")
def setHumanContacts(humans, density):
contacts = []
quantity = rd.setContactsQuantity(gov.getIsolationFactor(), density)
if quantity > 0:
auxRandoms = rd.aRandomIntList(0, len(humans) - 1, int(quantity))
for i in range(len(auxRandoms)):
contacts.append(
Simulation.getHumanNumber(humans, auxRandoms[i]))
return contacts
def decideInfection(infectedHuman, human, area, d):
Simulation.checkImmunity(human, d, vr.getImmunityPeriod())
if human.hasImmunity == False:
r = rd.aRandom()
c = rd.isCarefulAverage(infectedHuman, human) * gov.getInfoFactor()
s = rd.isDistancedAverage(infectedHuman,
human) * gov.getSocialDistanceFactor()
infectionP = r * rd.getInfectionThresholdVar(c, s)
if infectionP < vr.getInfectionThreshold(
) * infectedHuman.contagiousFactor:
Simulation.setInfection(human, area, d)
infectedHuman.transmission += 1
def decideDeath(human):
death = False
d = rd.aRandom()
d = d * human.deathRiskFactor * gov.treatmentColapseFactor(
infectedPopulationRatio, "polynomial")
if d < vr.getDeathThreshold():
death = True
return death
def contactTracking(family, contacts, area):
for f in range(len(family)):
Simulation.lookForContact(family[f], area)
for c in contacts:
r = rd.aRandom()
if r < gov.getActiveTrackingThreshold(infectedPopulationRatio):
if c in humansInA:
Simulation.lookForContact(c, "A")
elif c in humansInB:
Simulation.lookForContact(c, "B")
def humanExchange(areaAH, areaBH):
if gov.getLockDown() == False:
areaAExits = rd.setExchangeCount(gov.getExchangeFactor())
indexesA = rd.aRandomIntList(0, len(areaAH) - 1, areaAExits)
humanNumbersA = []
for n in range(len(indexesA)):
humanNumbersA.append(
Simulation.getHumanNumber(areaAH, indexesA[n]))
for a in range(areaAExits):
family = areaAH[Simulation.getHumanIndex(
areaAH, humanNumbersA[a])].family
for f in range(len(family)):
if Simulation.checkInTreatmentFamily(areaAH,
family) == False:
member = Simulation.getHumanIndex(areaAH, family[f])
humansInB.add(family[f])
areaBH.append(areaAH[member])
Simulation.correctStatistics("A", areaAH[member])
humansInA.discard(family[f])
del areaAH[member]
areaBExits = rd.setExchangeCount(gov.getExchangeFactor())
indexesB = rd.aRandomIntList(0, len(areaBH) - 1, areaBExits)
humanNumbersB = []
for n in range(len(indexesB)):
humanNumbersB.append(
Simulation.getHumanNumber(areaBH, indexesB[n]))
for a in range(areaBExits):
family = areaBH[Simulation.getHumanIndex(
areaBH, humanNumbersB[a])].family
for f in range(len(family)):
if Simulation.checkInTreatmentFamily(areaBH,
family) == False:
member = Simulation.getHumanIndex(areaBH, family[f])
humansInA.add(family[f])
areaAH.append(areaBH[member])
Simulation.correctStatistics("B", areaBH[member])
humansInB.discard(family[f])
del areaBH[member]
def assignAreas(humans):
#Assigning urban area
print("Assigning urban areas... ", end="\r")
p = 0
while p < len(humans):
area = rd.aRandom()
if area > 0.5:
for f in range(len(humans[p].family)):
areaAHumans.append(humans[p])
humansInA.add(humans[p].humanNumber)
p += 1
else:
for f in range(len(humans[p].family)):
areaBHumans.append(humans[p])
humansInB.add(humans[p].humanNumber)
p += 1
print("Assigning urban areas complete! ", end="\n")
def assignFamilies(humans):
hcount = 0
actualFamily = 0
print("Assigning families... ", end="\r")
while hcount < len(humans):
members = rd.setFamilySize()
for i in range(members):
if i + hcount < len(humans):
humans[i + hcount].familyNumber = actualFamily
humans[hcount].family.append(i + hcount)
if members > 1:
for i in range(members - 1):
if i + hcount + 1 < len(humans):
humans[hcount + i + 1].family = humans[hcount].family
hcount += members
actualFamily += 1
print("Assigning families complete! ", end="\n")
def decideTest(notTestedHuman, area):
r = rd.aRandom()
tested = False
if notTestedHuman.isSymptomatic == True:
if r < gov.getTestingResponseThreshold():
tested = True
elif notTestedHuman.isSymptomatic == False:
if r < gov.getTestingResponseASThreshold():
tested = True
if notTestedHuman.isInTreatment == True: #Probability of being tested in treatment is 1
tested = True
if tested == True:
Simulation.testHuman(notTestedHuman, area)
if gov.getActiveTracking() == True:
Simulation.contactTracking(notTestedHuman.family,
notTestedHuman.contactsHistory,
area)
def createHumans(population, casesCero, simulationName,
autoIsolationThreshold, startingImmunity):
#Humans initialization
humans = []
auxRandom = 0
auxRandoms = []
for p in range(population):
humans.append(hn(p))
if p % 100 == 0:
print("Creating humans: " + str(p) + " ", end="\r")
tm.sleep(0.0001)
#Human configuration
humans[p].age = rd.setAge()
humans[p].sex = rd.setSex()
humans[p].carefulFactor = rd.setCarefulFactor()
humans[p].socialDistanceFactor = rd.setSocialDistanceFactor()
humans[p].contagiousFactor = vr.getBaseASContagiousFactor()
humans[p].deathRiskFactor = vr.deathRiskFactor(
humans[p].age, "polynomial")
#Defining if human will isolate himself in case of having symptoms
auxRandom = rd.aRandom()
if auxRandom <= autoIsolationThreshold:
humans[p].autoIsolation = True
auxRandom = rd.aRandom()
if auxRandom <= startingImmunity:
humans[p].hasImmunity = True
Simulation.increaseV("actualImmunity")
Simulation.assignFamilies(humans)
Simulation.assignAreas(humans)
print("Creating humans complete! ", end="\n")
def __init__(self, populationcount, periodindays, simNumber, casesCero, simulationName, bDensity, \
govActions, govActionsList, govFailureList, autoIsolationThreshold, startingImmunity, \
behaviorB, behaviorTrigger, behaviorOff, behaviorFactor):
if simNumber > 1: #We need to clean some variables
Simulation.deleteSimulation()
global simulationStartTime
simulationStartTime = tm.time(
) #To know how much time a simulation takes
global population
population = populationcount
if simNumber == 1: #Some things will be the same in all iterations
global period
period = periodindays
global simulationName0
simulationName0 = simulationName
global areaBDensity
areaBDensity = bDensity
global govMode
govMode = govActionsList[0]
vr.startRiskVariables()
gov.startColapseVariables()
gov.setAutoActionsTrigger(govActionsList[1])
gov.setAutoActionsOff(govActionsList[2])
gov.setStartCaseCount(govActionsList[3])
gov.setActionsPeriod(govActionsList[4])
gov.setActiveIsolation(govActionsList[10])
gov.setActiveTracking(govActionsList[11])
gov.setActiveTrackingThreshold(govActionsList[12])
gov.setActiveTrackingPressureW(govActionsList[13])
gov.setTestingResponseThreshold(govActionsList[14])
gov.setTestingResponseASThreshold(govActionsList[15])
global govFailure
govFailure = govFailureList[0]
global govActionsFailurePeriod
govActionsFailurePeriod = govFailureList[2]
print("Saving starting point data...", end="\r")
gov.saveSimulationConfig(simulationName)
vr.saveSimulationConfig(simulationName)
rd.saveSimulationConfig(simulationName)
print("Starting point data saved! ", end="\n")
#Now we create the population that will suffer the outbreak
Simulation.createHumans(population, casesCero, simulationName,
autoIsolationThreshold, startingImmunity)
#We inject desire number of infected humans in area A
print("Injecting infected humans in urban area A...", end="\r")
auxRandoms = rd.aRandomIntList(0, len(areaAHumans) - 1, casesCero)
for i in range(casesCero):
Simulation.setInfection(areaAHumans[auxRandoms[i]], "A", 1)
if areaAHumans[auxRandoms[i]].hasImmunity == True:
areaAHumans[auxRandoms[i]].hasImmunity = False
Simulation.decreaseV("actualImmunity")
print("Infected humans injected! ", end="\n")
dt.savePopulationData(areaAHumans, areaBHumans, simulationName)
print("", end="\n")
#Simulating each day, one by one...
for d in range(period):
print("Simulating day " + str(d + 1) + "... ", end="\r")
Simulation.simulateDay(d + 1)
Simulation.saveDay(d + 1)
if behaviorB == True:
Simulation.checkHumansBehavior(d, behaviorTrigger, behaviorOff,
behaviorFactor)
if govActions == True:
Simulation.checkGovActions(d, govActionsList, govFailureList)
if d < period:
Simulation.humanExchange(areaAHumans, areaBHumans)
print("Simulation Complete! ", end="\n")
print("Infected: " + str(totalInfected) + ", Recovered: " +
str(totalRecovered) + ", Deaths: " + str(totalDeaths),
end="\n")
print("Time needed for this simulation: " +
Simulation.getSimulationTime(simulationStartTime, tm.time()),
end="\n")
print("", end="\n")
print("Saving simulation's data...", end="\r")
evolutionData.to_csv("SimulationData/Simulations/" + simulationName +
".csv",
index=False)
virusData.to_csv("SimulationData/Infections/" + simulationName +
"_infections.csv",
index=False)
Simulation.saveSimulationConfig(simulationName0, simNumber, casesCero, govActionsCycles, \
govActions, behaviorB, behaviorCycles)
print("Simulation's data saved! ", end="\n")