def runModel(meanTheta):
startDate, endDate, recordStep, M, targetGraph = HIVModelUtils.toySimulationParams()
endDate = 1000.0
recordStep = 50
undirected = True
logging.debug("MeanTheta=" + str(meanTheta))
numReps = 10
numInfectedIndices = []
numRemovedIndices = []
numRemovedEdges = []
numContactEdges = []
statistics = GraphStatistics()
statsTimes = numpy.arange(0, endDate, recordStep)
for i in range(numReps):
graph = HIVGraph(M, undirected)
logging.info("Created graph at index " + str(i) + ": " + 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.setT0(startDate)
model.setT(endDate)
model.setRecordStep(recordStep)
model.setParams(meanTheta)
times, infectedIndices, removedIndices, graph = model.simulate(True)
vertexArray, infectedIndices, removedIndices, contactGraphStats, removedGraphStats = HIVModelUtils.generateStatistics(
graph, statsTimes
)
numInfectedIndices.append([len(x) for x in infectedIndices])
numRemovedIndices.append([len(x) for x in removedIndices])
numContactEdges.append(contactGraphStats[:, statistics.numVerticesIndex])
numRemovedEdges.append(removedGraphStats[:, statistics.numVerticesIndex])
numInfectedIndices = numpy.array(numInfectedIndices)
numInfectedIndices = numpy.mean(numInfectedIndices, 0)
numRemovedIndices = numpy.array(numRemovedIndices)
numRemovedIndices = numpy.mean(numRemovedIndices, 0)
numContactEdges = numpy.array(numContactEdges)
numContactEdges = numpy.mean(numContactEdges, 0)
numRemovedEdges = numpy.array(numRemovedEdges)
numRemovedEdges = numpy.mean(numRemovedEdges, 0)
return statsTimes, numInfectedIndices, numRemovedIndices, numContactEdges, numRemovedEdges, vertexArray[:, 6]
def profileSimulate(self):
startDate, endDates, numRecordSteps, M, targetGraph = HIVModelUtils.realSimulationParams()
meanTheta, sigmaTheta = HIVModelUtils.estimatedRealTheta()
undirected = True
graph = HIVGraph(M, undirected)
logging.info("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.setT0(startDate)
model.setT(startDate+1000)
model.setRecordStep(10)
model.setParams(meanTheta)
logging.debug("MeanTheta=" + str(meanTheta))
ProfileUtils.profile('model.simulate()', globals(), locals())
meanTheta, sigmaTheta = HIVModelUtils.estimatedRealTheta()
meanTheta = numpy.array([ 1, 0.1, 0.0, 0.00, 0.5, 0.1])
outputDir = PathDefaults.getOutputDir() + "viroscopy/"
undirected = True
graph = HIVGraph(M, undirected)
logging.info("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.setT0(startDate)
model.setT(endDate)
model.setRecordStep(recordStep)
model.setParams(meanTheta)
logging.debug("MeanTheta=" + str(meanTheta))
times, infectedIndices, removedIndices, graph = model.simulate(True)
statistics = GraphStatistics()
vertexArray, infectedIndices, removedIndices, contactGraphStats, removedGraphStats = HIVModelUtils.generateStatistics(graph, times)
numInfectedIndices = [len(x) for x in infectedIndices]
plt.figure(0)
plt.plot(times, numInfectedIndices)
