Python HIVModelUtils.estimatedRealTheta示例

示例#1

文件： HIVEpidemicModelProfile.py 项目： pierrebo/wallhack

    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())

示例#2

文件： ProcessResults.py 项目： charanpald/wallhack

def loadParams(ind): 
    if processReal: 
        resultsDir = PathDefaults.getOutputDir() + "viroscopy/real/theta" + str(ind) + "/"
        outputDir = resultsDir + "stats/"
        
        N, matchAlpha, breakScale, numEpsilons, epsilon, minEpsilon, matchAlg, abcMaxRuns, batchSize, pertScale = HIVModelUtils.realABCParams(True)
        startDate, endDate, recordStep, M, targetGraph, numInds = HIVModelUtils.realSimulationParams(test=True, ind=ind)
        realTheta, sigmaTheta, pertTheta = HIVModelUtils.estimatedRealTheta(ind)
        numInds=2
        prefix = "Real"
    else: 
        resultsDir = PathDefaults.getOutputDir() + "viroscopy/toy/theta/"
        outputDir = resultsDir + "stats/"        
        
        N, matchAlpha, breakScale, numEpsilons, epsilon, minEpsilon, matchAlg, abcMaxRuns, batchSize, pertScale = HIVModelUtils.toyABCParams()
        startDate, endDate, recordStep, M, targetGraph = HIVModelUtils.toySimulationParams(test=True)
        realTheta, sigmaTheta, pertTheta = HIVModelUtils.toyTheta()
        prefix = "Toy"
        numInds = 1

    breakSize = (targetGraph.subgraph(targetGraph.removedIndsAt(endDate)).size - targetGraph.subgraph(targetGraph.removedIndsAt(startDate)).size)  * breakScale       
        
    return N, resultsDir, outputDir, recordStep, startDate, endDate, prefix, targetGraph, breakSize, numEpsilons, M, matchAlpha, matchAlg, numInds

示例#3

文件： ModelRealExp.py 项目： pierrebo/wallhack

logging.debug("Posterior sample size " + str(N))
logging.debug("Matching algorithm " + str(matchAlg))

logging.debug("="*10 + "Starting new simulation batch with index " + str(i) + "="*10) 
logging.debug("Total time of simulation is " + str(endDate-startDate))    

breakSize = (targetGraph.subgraph(targetGraph.removedIndsAt(endDate)).size - targetGraph.subgraph(targetGraph.removedIndsAt(startDate)).size)  * breakScale
logging.debug("Largest acceptable graph is " + str(breakSize))

def createModel(t):
    """
    The parameter t is the particle index. 
    """
    return HIVModelUtils.createModel(targetGraph, startDate, endDate, recordStep, M, matchAlpha, breakSize, matchAlg)

meanTheta, stdTheta, pertTheta = HIVModelUtils.estimatedRealTheta(i)

logging.debug("Using mean theta of " + str(meanTheta))
logging.debug("Using std theta of " + str(stdTheta))
logging.debug("Using perturbation std theta of " + str(pertTheta))
    
abcParams = HIVABCParameters(meanTheta, stdTheta, pertTheta)
thetaDir = resultsDir + "theta" + str(i) + "/"

if not os.path.exists(thetaDir): 
    os.mkdir(thetaDir)

#Now get something more precise 
epsilonArray = numpy.ones(numEpsilons)*epsilon    
abcSMC = ABCSMC(epsilonArray, createModel, abcParams, thetaDir, True, minEpsilon=minEpsilon, thetaUniformChoice=False)
abcSMC.setPosteriorSampleSize(N)

示例#4

文件： RunEpidemicModel.py 项目： pierrebo/wallhack

"""
This is the epidemic model for the HIV spread in cuba. Let's try to get an 
exponential infection. 
"""

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()
M = 100
endDate = startDate + 1000
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)