Ejemplo n.º 1
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) 
Ejemplo n.º 2
0
 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)