Python HIVModelUtils.realSimulationParams示例

示例#1

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#2

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#3

文件： ModelRealExp.py 项目： pierrebo/wallhack

    numProcesses = multiprocessing.cpu_count()

if len(sys.argv) > 2:
    i = int(sys.argv[2])
else: 
    i = 0 

FORMAT = "%(levelname)s:root:%(process)d:%(message)s"
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG, format=FORMAT)
logging.debug("Number of processes: " + str(numProcesses))
logging.debug("Epidemic period index " + str(i))
numpy.set_printoptions(suppress=True, precision=4, linewidth=150)
numpy.seterr(invalid='raise')

resultsDir = PathDefaults.getOutputDir() + "viroscopy/real/" 
startDate, endDate, recordStep, M, targetGraph, numInds = HIVModelUtils.realSimulationParams(ind=i)
N, matchAlpha, breakScale, numEpsilons, epsilon, minEpsilon, matchAlg, abcMaxRuns, batchSize, pertScale = HIVModelUtils.realABCParams(i)

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. 
    """

示例#4

文件： RunEpidemicModel.py 项目： pierrebo/wallhack

matplotlib.use("GTK3Agg")
import matplotlib.pyplot as plt 

"""
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())

示例#5

文件： ModelRealExp2.py 项目： pierrebo/wallhack

assert False, "Must run with -O flag"

if len(sys.argv) > 1:
    numProcesses = int(sys.argv[1])
else: 
    numProcesses = multiprocessing.cpu_count()

FORMAT = "%(levelname)s:root:%(process)d:%(message)s"
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG, format=FORMAT)
logging.debug("Number of processes: " + str(numProcesses))
numpy.set_printoptions(suppress=True, precision=4, linewidth=150)
numpy.seterr(invalid='raise')

resultsDir = PathDefaults.getOutputDir() + "viroscopy/real/" 
startDates, endDates, numRecordSteps, M, targetGraph = HIVModelUtils.realSimulationParams()
N, matchAlpha, breakScale, numEpsilons, epsilon, minEpsilon, matchAlg, abcMaxRuns, batchSize = HIVModelUtils.realABCParams()

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

alpha = 2
zeroVal = 0.9

for i, endDate in enumerate(endDates): 
    startDate = startDates[i]
    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 * breakScale
    logging.debug("Largest acceptable graph is " + str(breakSize))