def testGetInfectedSet(self):
numVertices = 10
graph = HIVGraph(numVertices)
self.assertTrue(graph.getInfectedSet() == set([]))
graph.getVertexList().setInfected(1, 0.0)
graph.getVertexList().setInfected(3, 0.0)
graph.getVertexList().setInfected(7, 0.0)
self.assertTrue(graph.getInfectedSet() == set([1, 3, 7]))
def testSetRandomInfected(self):
numVertices = 10000
graph = HIVGraph(numVertices)
graph.setRandomInfected(100)
self.assertAlmostEqual(len(graph.getInfectedSet()), 100)
graph = HIVGraph(numVertices)
graph.setRandomInfected(50, 0.5)
self.assertAlmostEqual(len(graph.getInfectedSet()), 50)
graph = HIVGraph(numVertices)
graph.setRandomInfected(20, 0.0)
self.assertAlmostEqual(len(graph.getInfectedSet()), 20)
graph = HIVGraph(numVertices)
graph.setRandomInfected(10, 1.0)
self.assertAlmostEqual(len(graph.getInfectedSet()), 10)
def testSimulate2(self):
startDate = 0.0
endDate = 100.0
M = 1000
meanTheta, sigmaTheta = HIVModelUtils.estimatedRealTheta()
undirected = True
graph = HIVGraph(M, undirected)
alpha = 2
zeroVal = 0.9
p = Util.powerLawProbs(alpha, zeroVal)
hiddenDegSeq = Util.randomChoice(p, graph.getNumVertices())
meanTheta[4] = 0.1
recordStep = 10
printStep = 10
rates = HIVRates(graph, hiddenDegSeq)
model = HIVEpidemicModel(graph, rates, endDate, startDate)
model.setRecordStep(recordStep)
model.setPrintStep(printStep)
model.setParams(meanTheta)
initialInfected = graph.getInfectedSet()
times, infectedIndices, removedIndices, graph = model.simulate(True)
#Now test the final graph
edges = graph.getAllEdges()
for i, j in edges:
if graph.vlist.V[i, HIVVertices.genderIndex] == graph.vlist.V[j, HIVVertices.genderIndex] and (graph.vlist.V[i, HIVVertices.orientationIndex] != HIVVertices.bi or graph.vlist.V[j, HIVVertices.orientationIndex] != HIVVertices.bi):
self.fail()
finalInfected = graph.getInfectedSet()
finalRemoved = graph.getRemovedSet()
self.assertEquals(numpy.intersect1d(initialInfected, finalRemoved).shape[0], len(initialInfected))
#Test case where there is no contact
meanTheta = numpy.array([100, 0.95, 1, 1, 0, 0, 0, 0, 0, 0, 0], numpy.float)
times, infectedIndices, removedIndices, graph, model = runModel(meanTheta)
self.assertEquals(len(graph.getInfectedSet()), 100)
self.assertEquals(len(graph.getRemovedSet()), 0)
self.assertEquals(graph.getNumEdges(), 0)
heteroContactRate = 0.1
meanTheta = numpy.array([100, 0.95, 1, 1, 0, 0, heteroContactRate, 0, 0, 0, 0], numpy.float)
times, infectedIndices, removedIndices, graph, model = runModel(meanTheta)
self.assertEquals(len(graph.getInfectedSet()), 100)
self.assertEquals(len(graph.getRemovedSet()), 0)
edges = graph.getAllEdges()
for i, j in edges:
self.assertNotEqual(graph.vlist.V[i, HIVVertices.genderIndex], graph.vlist.V[j, HIVVertices.genderIndex])
#Number of conacts = rate*people*time
infectedSet = graph.getInfectedSet()
numHetero = (graph.vlist.V[list(infectedSet), HIVVertices.orientationIndex] == HIVVertices.hetero).sum()
self.assertTrue(abs(numHetero*endDate*heteroContactRate- model.getNumContacts()) < 100)
heteroContactRate = 0.01
meanTheta = numpy.array([100, 0.95, 1, 1, 0, 0, heteroContactRate, 0, 0, 0, 0], numpy.float)
times, infectedIndices, removedIndices, graph, model = runModel(meanTheta)
infectedSet = graph.getInfectedSet()
numHetero = (graph.vlist.V[list(infectedSet), HIVVertices.orientationIndex] == HIVVertices.hetero).sum()
self.assertAlmostEqual(numHetero*endDate*heteroContactRate/100, model.getNumContacts()/100.0, 0)
def testContactRates2(self):
undirected = True
numVertices = 10
graph = HIVGraph(numVertices, undirected)
maleVertex = graph.getVertex(0)
maleVertex[HIVVertices.genderIndex] = HIVVertices.male
femaleVertex = maleVertex.copy()
femaleVertex[HIVVertices.genderIndex] = HIVVertices.female
for i in range(5):
graph.setVertex(i, maleVertex)
graph.setVertex(i+5, femaleVertex)
V = graph.getVertexList().getVertices()
contactList = range(numVertices)
#Test that the parameters alpha and C do the right thing
hiddenDegSeq = self.gen.rvs(size=graph.getNumVertices())
rates = HIVRates(graph, hiddenDegSeq)
t = 0.2
logging.debug("Rates with no existing contacts")
contactRateInds, contactRates = rates.contactRates(range(numVertices), contactList, t)
#When there are no contacts the choice is easy and some random new contacts
#are chosen.
#Now test differences in choice between existing and new contact.
t = 0.3
for i in range(5):
rates.contactEvent(i, i+5, t)
rates.alpha = 1.0
logging.debug("Rates with default alpha=" + str(rates.alpha))
contactRateInds, contactRates = rates.contactRates(range(numVertices), contactList, 0.4)
for i in range(5):
self.assertTrue(contactRates[i] == rates.contactRate)
self.assertTrue(contactRateInds[i] == i+5)
#Now try changing alpha
logging.debug("Rates with alpha=0.5")
rates.setAlpha(0.5)
contactRateInds, contactRates = rates.contactRates(range(numVertices), contactList, 0.4)
#Observed probabilities change as expected
#Now increase time and observe probabilities
logging.debug("Rates with t=20")
contactRateInds, contactRates = rates.contactRates(range(numVertices), contactList, 20)
#Test we don't pick from removed
graph.getVertexList().setInfected(0, t)
graph.getVertexList().setInfected(4, t)
graph.getVertexList().setInfected(7, t)
graph.getVertexList().setInfected(8, t)
#graph.getVertexList().setDetected(4, t, HIVVertices.randomDetect)
#graph.getVertexList().setDetected(7, t, HIVVertices.randomDetect)
rates.removeEvent(4, HIVVertices.randomDetect, t)
rates.removeEvent(7, HIVVertices.randomDetect, t)
infectedSet = graph.getInfectedSet()
susceptibleSet = graph.getSusceptibleSet()
removedSet = graph.getRemovedSet()
contactSet = infectedSet.union(susceptibleSet)
infectedList = list(infectedSet)
removedList = list(removedSet)
contactList = list(contactSet)
contactRateInds, contactRates = rates.contactRates(infectedList, contactList, 20)
#Contacts cannot be in removed set
self.assertTrue(numpy.intersect1d(contactRateInds, numpy.array(removedList)).shape[0]==0)
def testContactTracingRate(self):
undirected = True
numVertices = 10
graph = HIVGraph(numVertices, undirected)
hiddenDegSeq = self.gen.rvs(size=graph.getNumVertices())
rates = HIVRates(graph, hiddenDegSeq)
t = 0.1
graph.getVertexList().setInfected(0, t)
rates.contactEvent(0, 3, 0.2)
rates.contactEvent(0, 9, 0.1)
t = 0.3
graph.getVertexList().setInfected(3, t)
graph.getVertexList().setInfected(9, t)
t = 0.4
rates.removeEvent(0, HIVVertices.randomDetect, t)
removedSet = graph.getRemovedSet()
infectedList = [3, 9]
ctRates = rates.contactTracingRates(infectedList, removedSet, t)
self.assertTrue((ctRates==numpy.array([0.0, 0.0])).all())
ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctStartTime)
self.assertTrue((ctRates == numpy.array([rates.ctRatePerPerson, rates.ctRatePerPerson])).all())
#Test contact tracing is within correct time period
ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctEndTime-0.01)
self.assertTrue((ctRates == numpy.array([rates.ctRatePerPerson, rates.ctRatePerPerson])).all())
ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctEndTime+1)
self.assertTrue((ctRates == numpy.array([0, 0])).all())
rates.contactEvent(3, 5, t)
graph.getVertexList().setInfected(5, t)
rates.removeEvent(5, HIVVertices.randomDetect, t)
removedSet = graph.getRemovedSet()
ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctStartTime)
self.assertTrue((ctRates == numpy.array([rates.ctRatePerPerson, rates.ctRatePerPerson])).all())
rates.contactEvent(3, 6, t)
graph.getVertexList().setInfected(6, t)
infectedList = [3, 6, 9]
removedSet = graph.getRemovedSet()
ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctStartTime)
self.assertTrue((ctRates == numpy.array([rates.ctRatePerPerson, 0, rates.ctRatePerPerson])).all())
#Now make removedSet bigger than infectedList
graph.getVertexList().setInfected(4, t)
graph.getVertexList().setInfected(7, t)
graph.getVertexList().setInfected(8, t)
graph.getVertexList().setDetected(4, t, HIVVertices.randomDetect)
graph.getVertexList().setDetected(7, t, HIVVertices.randomDetect)
graph.getVertexList().setDetected(8, t, HIVVertices.randomDetect)
#Note: InfectedList is out of order
infectedList = list(graph.getInfectedSet())
sortInds = numpy.argsort(numpy.array(infectedList))
removedSet = graph.getRemovedSet()
ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctStartTime)
ctRates2 = numpy.array([rates.ctRatePerPerson, 0, rates.ctRatePerPerson])
self.assertTrue((ctRates[sortInds] == ctRates2).all())
#Test the case where InfectedList is out of order and removedSet is small
graph.getVertexList().setInfected(4, t)
graph.getVertex(7)[HIVVertices.stateIndex] = HIVVertices.susceptible
graph.getVertex(8)[HIVVertices.stateIndex] = HIVVertices.susceptible
infectedList = list(graph.getInfectedSet())
sortInds = numpy.argsort(numpy.array(infectedList))
removedSet = graph.getRemovedSet()
ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctStartTime)
ctRates2 = numpy.array([rates.ctRatePerPerson, 0, 0, rates.ctRatePerPerson])
self.assertTrue((ctRates[sortInds] == ctRates2).all())
class HIVRatesProfile():
def __init__(self):
#Total number of people in population
self.M = 10000
numInitialInfected = 5
#The graph is one in which edges represent a contact
undirected = True
self.graph = HIVGraph(self.M, undirected)
for i in range(self.M):
vertex = self.graph.getVertex(i)
#Set the infection time of a number of individuals to 0
if i < numInitialInfected:
vertex[HIVVertices.stateIndex] = HIVVertices.infected
outputDirectory = PathDefaults.getOutputDir()
directory = outputDirectory + "test/"
self.profileFileName = directory + "profile.cprof"
def profileContactRate(self):
susceptibleList = list(range(1, self.graph.getNumVertices()))
t = 10
s = 3
gen = scipy.stats.zipf(s)
hiddenDegSeq = gen.rvs(size=self.graph.getNumVertices())
rates = HIVRates(self.graph, hiddenDegSeq)
numContactEvents = 5000
for i in range(numContactEvents):
vertexInd1 = numpy.random.randint(0, self.graph.getNumVertices())
vertexInd2 = numpy.random.randint(0, self.graph.getNumVertices())
rates.contactEvent(vertexInd1, vertexInd2, 5)
print((self.graph.getNumEdges()))
infectedList = range(0, 100)
contactList = range(100, self.M)
t = 10
def runContactRates():
for i in range(100):
rates.contactRates(infectedList, contactList, t)
ProfileUtils.profile('runContactRates()', globals(), locals())
def profileInfectionProbability(self):
s = 3
gen = scipy.stats.zipf(s)
hiddenDegSeq = gen.rvs(size=self.graph.getNumVertices())
rates = HIVRates(self.graph, hiddenDegSeq)
t = 5
#Getting vertices and checking parameters takes the most time
def runInfectionProbs():
for i in range(10000):
vertexInd1 = numpy.random.randint(0, self.graph.getNumVertices())
vertexInd2 = numpy.random.randint(0, self.graph.getNumVertices())
rates.infectionProbability(vertexInd1, vertexInd2, t)
ProfileUtils.profile('runInfectionProbs()', globals(), locals())
def profileContactTracingRate(self):
s = 3
gen = scipy.stats.zipf(s)
hiddenDegSeq = gen.rvs(size=self.graph.getNumVertices())
rates = HIVRates(self.graph, hiddenDegSeq)
#Create a network of sexual contacts
numContactEvents = 10000
for i in range(numContactEvents):
vertexInd1 = numpy.random.randint(0, self.graph.getNumVertices())
vertexInd2 = numpy.random.randint(0, self.graph.getNumVertices())
rates.contactEvent(vertexInd1, vertexInd2, 5)
print((self.graph))
print((self.graph.degreeDistribution()))
#Choose some individuals as being infected and then detected
p = 0.3
q = 0.4
for i in range(self.graph.getNumVertices()):
if numpy.random.rand() < p and not self.graph.getVertex(i)[HIVVertices.stateIndex] == HIVVertices.infected:
self.graph.getVertexList().setInfected(i, 5.0)
if numpy.random.rand() < q:
self.graph.getVertexList().setDetected(i, 6.0, HIVVertices.randomDetect)
infectedSet = self.graph.getInfectedSet()
print((len(infectedSet)))
print((len(self.graph.getRemovedSet())))
removedSet = self.graph.getRemovedSet()
t = 200
def runContactTracingRate():
for j in range(2000):
rates.contactTracingRates(list(infectedSet), removedSet, t)
ProfileUtils.profile('runContactTracingRate()', globals(), locals())