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)