def testInfectionProbability(self): undirected = True numVertices = 10 graph = HIVGraph(numVertices, undirected) hiddenDegSeq = self.gen.rvs(size=graph.getNumVertices()) rates = HIVRates(graph, hiddenDegSeq) t = 0.1 graph.getVertex(0)[HIVVertices.stateIndex] = HIVVertices.infected graph.getVertex(1)[HIVVertices.stateIndex] = HIVVertices.removed graph.getVertex(2)[HIVVertices.stateIndex] = HIVVertices.infected for vertexInd1 in range(numVertices): for vertexInd2 in range(numVertices): vertex1 = graph.getVertex(vertexInd1) vertex2 = graph.getVertex(vertexInd2) if vertex1[HIVVertices.stateIndex]!=HIVVertices.infected or vertex2[HIVVertices.stateIndex]!=HIVVertices.susceptible: self.assertEquals(rates.infectionProbability(vertexInd1, vertexInd2, t), 0.0) elif vertex1[HIVVertices.genderIndex] == HIVVertices.female and vertex2[HIVVertices.genderIndex] == HIVVertices.male: self.assertEquals(rates.infectionProbability(vertexInd1, vertexInd2, t), rates.infectProb) elif vertex1[HIVVertices.genderIndex] == HIVVertices.male and vertex2[HIVVertices.genderIndex] == HIVVertices.female: self.assertEquals(rates.infectionProbability(vertexInd1, vertexInd2, t), rates.infectProb) elif vertex1[HIVVertices.genderIndex] == HIVVertices.male and vertex2[HIVVertices.orientationIndex]==HIVVertices.bi: self.assertEquals(rates.infectionProbability(vertexInd1, vertexInd2, t), rates.infectProb) else: self.assertEquals(rates.infectionProbability(vertexInd1, vertexInd2, t), 0.0)
def testUpperDetectionRates(self): """ See if the upper bound on detection rates is correct """ 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) graph.getVertexList().setInfected(1, t) graph.getVertexList().setInfected(8, t) t = 0.2 rates.removeEvent(8, HIVVertices.randomDetect, t) rates.infectionProbability = 1.0 infectedList = graph.infectedIndsAt(t) removedList = graph.removedIndsAt(t) n = graph.size-removedList self.assertEquals(rates.upperDetectionRates(infectedList, n), rates.randomDetectionRates(infectedList, n, seed=21).sum()) t = 0.3 rates.contactEvent(0, 2, t) graph.vlist.setInfected(2, t) t = 0.4 rates.removeEvent(0, HIVVertices.randomDetect, t) infectedList = graph.infectedIndsAt(t) removedSet = graph.removedIndsAt(t) removedSet = set(removedSet.tolist()) nptst.assert_array_almost_equal(rates.contactTracingRates(infectedList, removedSet, t + rates.ctStartTime + 1), numpy.array([0, rates.ctRatePerPerson])) upperDetectionRates = rates.ctRatePerPerson + rates.randomDetectionRates(infectedList, n, seed=21).sum() self.assertEquals(rates.upperDetectionRates(infectedList, n), upperDetectionRates)