numRemoved = numpy.zeros(numRepetitions)
for j in range(numRepetitions):
graph = HIVGraph(M, undirected)
logging.debug("Created graph: " + str(graph))
alpha = 2
zeroVal = 0.9
p = Util.powerLawProbs(alpha, zeroVal)
hiddenDegSeq = Util.randomChoice(p, graph.getNumVertices())
rates = HIVRates(graph, hiddenDegSeq)
model = HIVEpidemicModel(graph, rates)
model.setT(endDate)
model.setRecordStep(recordStep)
model.setParams(theta)
logging.debug("Theta = " + str(theta))
times, infectedIndices, removedIndices, graph = model.simulate(True)
graphFileName = outputDir + "ToyEpidemicGraph" + str(j)
graph.save(graphFileName)
graphList.append(graph)
numInfected[j] = len(graph.getInfectedSet())
numRemoved[j] = len(graph.getRemovedSet())
logging.debug("Infected (mean, std): " + str((numpy.mean(numInfected), numpy.std(numInfected))))
logging.debug("Removed (mean, std): " + str((numpy.mean(numRemoved), numpy.std(numRemoved))))
logging.debug("All done.")
def testSimulate(self):
T = 1.0
self.graph.getVertexList().setInfected(0, 0.0)
self.model.setT(T)
times, infectedIndices, removedIndices, graph = self.model.simulate(verboseOut=True)
numInfects = 0
for i in range(graph.getNumVertices()):
if graph.getVertex(i)[HIVVertices.stateIndex] == HIVVertices==infected:
numInfects += 1
self.assertTrue(numInfects == 0 or times[len(times)-1] >= T)
#Test with a larger population as there seems to be an error when the
#number of infectives becomes zero.
M = 100
undirected = True
graph = HIVGraph(M, undirected)
graph.setRandomInfected(10)
self.graph.removeAllEdges()
T = 21.0
hiddenDegSeq = self.gen.rvs(size=self.graph.getNumVertices())
rates = HIVRates(self.graph, hiddenDegSeq)
model = HIVEpidemicModel(self.graph, rates)
model.setRecordStep(10)
model.setT(T)
#Test detection rates
print("Starting test")
T = 1000.0
graph = HIVGraph(M, undirected)
graph.setRandomInfected(10)
rates = HIVRates(graph, hiddenDegSeq)
rates.contactRate = 0
rates.randDetectRate = 0.1
model = HIVEpidemicModel(graph, rates)
model.setT(T)
times, infectedIndices, removedIndices, graph = model.simulate(verboseOut=True)
print(times)
self.assertEquals(len(infectedIndices[0]), 10)
self.assertEquals(len(removedIndices[0]), 0)
T = 10.0
graph.removeAllEdges()
graph = HIVGraph(M, undirected)
graph.setRandomInfected(10)
rates = HIVRates(graph, hiddenDegSeq)
rates.randDetectRate = 0.0
model = HIVEpidemicModel(graph, rates)
model.setT(T)
times, infectedIndices, removedIndices, graph = model.simulate(verboseOut=True)
self.assertEquals(len(removedIndices[-1]), 0)
T = 100.0
graph.removeAllEdges()
graph = HIVGraph(M, undirected)
graph.setRandomInfected(10)
rates = HIVRates(graph, hiddenDegSeq)
rates.randDetectRate = 10.0
model = HIVEpidemicModel(graph, rates)
model.setT(T)
times, infectedIndices, removedIndices, graph = model.simulate(verboseOut=True)
self.assertEquals(len(removedIndices[-1]), 10)
#Test contact tracing
T = 1000.0
graph = HIVGraph(M, undirected)
graph.setRandomInfected(10)
rates = HIVRates(graph, hiddenDegSeq)
rates.randDetectRate = 0.01
rates.ctRatePerPerson = 0.5
model = HIVEpidemicModel(graph, rates)
model.setT(T)
times, infectedIndices, removedIndices, graph = model.simulate(verboseOut=True)
self.assertTrue((graph.vlist.V[:, HIVVertices.detectionTypeIndex] == HIVVertices.contactTrace).sum() > 0)
#Test contact rate
print("Testing contact rate")
contactRates = [0.5, 1, 2, 4]
numContacts = numpy.zeros(len(contactRates))
for i, contactRate in enumerate(contactRates):
T = 100.0
graph = HIVGraph(M, undirected)
graph.setRandomInfected(1)
print(i, graph.vlist.V[graph.getInfectedSet().pop(), :])
rates = HIVRates(graph, hiddenDegSeq)
rates.contactRate = contactRate
rates.infectProb = 0.0
model = HIVEpidemicModel(graph, rates)
model.setT(T)
times, infectedIndices, removedIndices, graph = model.simulate(verboseOut=True)
numContacts[i] = model.numContacts
lastN = -1
for i, n in enumerate(numContacts):
#This is an odd case in which we have a bisexual woman, there are no contacts
#since they are not modelled
if n != 0:
self.assertTrue(n > lastN)
#Test infection rate
print("Testing infection probability")
infectProbs = [0.01, 0.1, 0.2, 0.5]
numInfects = numpy.zeros(len(contactRates))
for i, infectProb in enumerate(infectProbs):
T = 100.0
graph = HIVGraph(M, undirected)
graph.setRandomInfected(10)
rates = HIVRates(graph, hiddenDegSeq)
rates.contactRate = 0.5
rates.infectProb = infectProb
model = HIVEpidemicModel(graph, rates)
model.setT(T)
times, infectedIndices, removedIndices, graph = model.simulate(verboseOut=True)
numInfects[i] = len(graph.getInfectedSet())
for n in numInfects:
self.assertTrue(n > lastN)
print("Testing contact paramters")
alphas = 1-numpy.array([0.01, 0.1, 0.2, 0.5, 0.99])
edges = numpy.zeros(len(alphas))
for i, alpha in enumerate(alphas):
T = 100.0
graph = HIVGraph(M, undirected)
graph.setRandomInfected(1)
rates = HIVRates(graph, hiddenDegSeq)
rates.setAlpha(alpha)
rates.infectProb = 0
model = HIVEpidemicModel(graph, rates)
model.setT(T)
times, infectedIndices, removedIndices, graph = model.simulate(verboseOut=True)
edges[i] = graph.getNumEdges()
self.assertEquals(edges[0], 1)
self.assertTrue((numpy.diff(edges) > 0).all())