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 testAddGraph(self): epsilon = 0.12 metrics = HIVGraphMetrics2(self.graph, epsilon) metrics.addGraph(self.graph) self.assertEquals(metrics.dists[0], 0.0) self.assertEquals(metrics.meanDistance(), 0.0) #Start a new graph #Compute distances directly matcher = GraphMatch("U") graph = HIVGraph(self.graph.size) dists = [] metrics = HIVGraphMetrics2(self.graph, epsilon) graph.vlist.setInfected(1, 0.0) graph.vlist.setDetected(1, 0.1, 0) metrics.addGraph(graph) t = graph.endTime() subgraph1 = graph.subgraph(graph.removedIndsAt(t)) subgraph2 = self.graph.subgraph(graph.removedIndsAt(t)) permutation, distance, time = matcher.match(subgraph1, subgraph2) lastDist = matcher.distance(subgraph1, subgraph2, permutation, True, True) self.assertEquals(metrics.dists[-1], lastDist) self.assertTrue(metrics.shouldBreak()) graph.vlist.setInfected(2, 2.0) graph.vlist.setDetected(2, 2.0, 0) metrics.addGraph(graph) t = graph.endTime() subgraph1 = graph.subgraph(graph.removedIndsAt(t)) subgraph2 = self.graph.subgraph(graph.removedIndsAt(t)) permutation, distance, time = matcher.match(subgraph1, subgraph2) lastDist = matcher.distance(subgraph1, subgraph2, permutation, True, True) self.assertEquals(metrics.dists[-1], lastDist) self.assertTrue(metrics.shouldBreak()) graph.vlist.setInfected(7, 3.0) graph.vlist.setDetected(7, 3.0, 0) metrics.addGraph(graph) t = graph.endTime() subgraph1 = graph.subgraph(graph.removedIndsAt(t)) subgraph2 = self.graph.subgraph(graph.removedIndsAt(t)) permutation, distance, time = matcher.match(subgraph1, subgraph2) lastDist = matcher.distance(subgraph1, subgraph2, permutation, True, True) self.assertEquals(metrics.dists[-1], lastDist) self.assertFalse(metrics.shouldBreak()) #Test case where one graph has zero size graph1 = HIVGraph(10) graph2 = HIVGraph(10) graph1.vlist[:, HIVVertices.stateIndex] = HIVVertices.removed metrics = HIVGraphMetrics2(graph2, epsilon) metrics.addGraph(graph1) #Problem is that distance is 1 when one graph is zero self.assertEquals(len(metrics.dists), 0)