def testContactRates(self):
undirected = True
numVertices = 10
graph = HIVGraph(numVertices, undirected)
t = 0.2
contactList = range(numVertices)
hiddenDegSeq = self.gen.rvs(size=graph.getNumVertices())
rates = HIVRates(graph, hiddenDegSeq)
contactRateInds, contactRates = rates.contactRates([0, 5, 7], contactList, t)
self.assertEquals(contactRates.shape[0], 3)
#Now we have that 0 had contact with another
rates.contactEvent(0, 3, 0.2)
rates.contactEvent(1, 9, 0.1)
infectedInds = numpy.arange(numVertices)
contactRateInds, contactRates = rates.contactRates(infectedInds, contactList, t)
#Note that in some cases an infected has no contacted as the persons do not match
for i in range(infectedInds.shape[0]):
if contactRateInds[i] != -1:
if graph.getVertex(infectedInds[i])[HIVVertices.genderIndex]==graph.getVertex(contactRateInds[i])[HIVVertices.genderIndex]:
self.assertEquals(contactRates[i], rates.heteroContactRate)
elif graph.getVertex(infectedInds[i])[HIVVertices.genderIndex]!=graph.getVertex(contactRateInds[1])[HIVVertices.genderIndex] and graph.getVertex(infectedInds[i])[HIVVertices.orientationIndex]==HIVVertices.bi and graph.getVertex(contactRateInds[i])[HIVVertices.orientationIndex]==HIVVertices.bi:
self.assertEquals(contactRates[i],rates.biContactRate)
def testContactRates3(self):
#Figure out why infection does not explode when we set infection probability
#to a high value and do not detect
undirected = True
numVertices = 20
graph = HIVGraph(numVertices, undirected)
hiddenDegSeq = self.gen.rvs(size=graph.getNumVertices())
rates = HIVRates(graph, hiddenDegSeq)
t = 0.1
for i in range(10):
graph.getVertexList().setInfected(i, t)
t = 0.2
infectedList = graph.infectedIndsAt(t)
contactList = range(0, numVertices)
contactRateInds, contactRates = rates.contactRates(infectedList, contactList, t)
print(contactRateInds, contactRates)
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)
