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 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]))
Ejemplo n.º 3
0
 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)