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)
def testInfectedIndsAt(self): numVertices = 10 graph = HIVGraph(numVertices) self.assertTrue(graph.getRemovedSet() == set([])) graph.getVertexList().setInfected(1, 0.0) graph.getVertexList().setInfected(2, 2.0) graph.getVertexList().setInfected(7, 3.0) inds = graph.infectedIndsAt(10) nptst.assert_array_equal(inds, numpy.array([1, 2, 7])) graph.getVertexList().setInfected(5, 12.0) nptst.assert_array_equal(inds, numpy.array([1, 2, 7]))
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)