def profileSimulate(self):
startDate, endDate, recordStep, printStep, M, targetGraph = HIVModelUtils.realSimulationParams()
meanTheta, sigmaTheta = HIVModelUtils.estimatedRealTheta()
meanTheta = numpy.array([337, 1.4319, 0.211, 0.0048, 0.0032, 0.5229, 0.042, 0.0281, 0.0076, 0.0293])
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+100)
model.setRecordStep(recordStep)
model.setPrintStep(printStep)
model.setParams(meanTheta)
logging.debug("MeanTheta=" + str(meanTheta))
ProfileUtils.profile('model.simulate()', globals(), locals())
from exp.viroscopy.model.HIVModelUtils import HIVModelUtils
import matplotlib.pyplot as plt
"""
This is the epidemic model for the HIV spread in cuba. We try to get more bisexual
contacts
"""
assert False, "Must run with -O flag"
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
numpy.seterr(all='raise')
numpy.random.seed(24)
numpy.set_printoptions(suppress=True, precision=4, linewidth=100)
startDate, endDate, recordStep, M, targetGraph = HIVModelUtils.realSimulationParams()
endDate = startDate + 10000
meanTheta, sigmaTheta = HIVModelUtils.estimatedRealTheta()
meanTheta = numpy.array([ 50, 0.5131, 0.3242, 0.1, 0.0001, 0.0, 325, 0.34, 0.001, 0.1, 0.1, 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)