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Example 1 with ARGLogger

use of dr.evomodel.arg.ARGLogger in project beast-mcmc by beast-dev.

the class ARGAddRemoveOperatorTest method flatPriorTester.

private void flatPriorTester(ARGModel arg, int chainLength, int sampleTreeEvery, double nodeCountSetting, double rootHeightAlpha, double rootHeightBeta, int maxCount) throws IOException, Importer.ImportException {
    MCMC mcmc = new MCMC("mcmc1");
    MCMCOptions options = new MCMCOptions(chainLength);
    //        double nodeCountSetting = 2.0;
    //        double rootHeightAlpha = 100;
    //        double rootHeightBeta = 0.5;
    OperatorSchedule schedule = getSchedule(arg);
    ARGUniformPrior uniformPrior = new ARGUniformPrior(arg, maxCount, arg.getExternalNodeCount());
    PoissonDistribution poisson = new PoissonDistribution(nodeCountSetting);
    DistributionLikelihood nodeCountPrior = new DistributionLikelihood(poisson, 0.0);
    ARGReassortmentNodeCountStatistic nodeCountStatistic = new ARGReassortmentNodeCountStatistic("nodeCount", arg);
    nodeCountPrior.addData(nodeCountStatistic);
    DistributionLikelihood rootPrior = new DistributionLikelihood(new GammaDistribution(rootHeightAlpha, rootHeightBeta), 0.0);
    CompoundParameter rootHeight = (CompoundParameter) arg.createNodeHeightsParameter(true, false, false);
    rootPrior.addData(rootHeight);
    List<Likelihood> likelihoods = new ArrayList<Likelihood>();
    likelihoods.add(uniformPrior);
    likelihoods.add(rootPrior);
    likelihoods.add(nodeCountPrior);
    CompoundLikelihood compoundLikelihood = new CompoundLikelihood(1, likelihoods);
    compoundLikelihood.setId("likelihood1");
    MCLogger[] loggers = new MCLogger[3];
    loggers[0] = new MCLogger(new TabDelimitedFormatter(System.out), 10000, false);
    loggers[0].add(compoundLikelihood);
    loggers[0].add(arg);
    File file = new File("test.args");
    file.deleteOnExit();
    FileOutputStream out = new FileOutputStream(file);
    loggers[1] = new ARGLogger(arg, new TabDelimitedFormatter(out), sampleTreeEvery, "test");
    ArrayLogFormatter formatter = new ArrayLogFormatter(false);
    loggers[2] = new MCLogger(formatter, sampleTreeEvery, false);
    loggers[2].add(arg);
    arg.getRootHeightParameter().setId("root");
    loggers[2].add(arg.getRootHeightParameter());
    mcmc.setShowOperatorAnalysis(true);
    mcmc.init(options, compoundLikelihood, schedule, loggers);
    mcmc.run();
    out.flush();
    out.close();
    List<Trace> traces = formatter.getTraces();
    //        Set<String> uniqueTrees = new HashSet<String>();
    //
    //        NexusImporter importer = new NexusImporter(new FileReader(file));
    //        while (importer.hasTree()) {
    //            Tree t = importer.importNextTree();
    //            uniqueTrees.add(Tree.Utils.uniqueNewick(t, t.getRoot()));
    //        }
    //
    //        TestCase.assertEquals(numTopologies, uniqueTrees.size());            List<Trace> traces = formatter.getTraces();
    ArrayTraceList traceList = new ArrayTraceList("ARGTest", traces, 0);
    for (int i = 1; i < traces.size(); i++) {
        traceList.analyseTrace(i);
    }
    TraceCorrelation nodeCountStats = traceList.getCorrelationStatistics(1);
    TraceCorrelation rootHeightStats = traceList.getCorrelationStatistics(4);
    assertExpectation("nodeCount", nodeCountStats, poisson.truncatedMean(maxCount));
    assertExpectation(TreeModelParser.ROOT_HEIGHT, rootHeightStats, rootHeightAlpha * rootHeightBeta);
}
Also used : PoissonDistribution(dr.math.distributions.PoissonDistribution) CompoundLikelihood(dr.inference.model.CompoundLikelihood) Likelihood(dr.inference.model.Likelihood) DistributionLikelihood(dr.inference.distribution.DistributionLikelihood) MCMC(dr.inference.mcmc.MCMC) ArrayList(java.util.ArrayList) ARGUniformPrior(dr.evomodel.arg.coalescent.ARGUniformPrior) CompoundParameter(dr.inference.model.CompoundParameter) MCMCOptions(dr.inference.mcmc.MCMCOptions) ArrayLogFormatter(dr.inference.loggers.ArrayLogFormatter) ARGReassortmentNodeCountStatistic(dr.evomodel.arg.ARGReassortmentNodeCountStatistic) GammaDistribution(dr.math.distributions.GammaDistribution) TraceCorrelation(dr.inference.trace.TraceCorrelation) OperatorSchedule(dr.inference.operators.OperatorSchedule) SimpleOperatorSchedule(dr.inference.operators.SimpleOperatorSchedule) CompoundLikelihood(dr.inference.model.CompoundLikelihood) TabDelimitedFormatter(dr.inference.loggers.TabDelimitedFormatter) Trace(dr.inference.trace.Trace) ARGLogger(dr.evomodel.arg.ARGLogger) ArrayTraceList(dr.inference.trace.ArrayTraceList) FileOutputStream(java.io.FileOutputStream) DistributionLikelihood(dr.inference.distribution.DistributionLikelihood) File(java.io.File) MCLogger(dr.inference.loggers.MCLogger)

Aggregations

ARGLogger (dr.evomodel.arg.ARGLogger)1 ARGReassortmentNodeCountStatistic (dr.evomodel.arg.ARGReassortmentNodeCountStatistic)1 ARGUniformPrior (dr.evomodel.arg.coalescent.ARGUniformPrior)1 DistributionLikelihood (dr.inference.distribution.DistributionLikelihood)1 ArrayLogFormatter (dr.inference.loggers.ArrayLogFormatter)1 MCLogger (dr.inference.loggers.MCLogger)1 TabDelimitedFormatter (dr.inference.loggers.TabDelimitedFormatter)1 MCMC (dr.inference.mcmc.MCMC)1 MCMCOptions (dr.inference.mcmc.MCMCOptions)1 CompoundLikelihood (dr.inference.model.CompoundLikelihood)1 CompoundParameter (dr.inference.model.CompoundParameter)1 Likelihood (dr.inference.model.Likelihood)1 OperatorSchedule (dr.inference.operators.OperatorSchedule)1 SimpleOperatorSchedule (dr.inference.operators.SimpleOperatorSchedule)1 ArrayTraceList (dr.inference.trace.ArrayTraceList)1 Trace (dr.inference.trace.Trace)1 TraceCorrelation (dr.inference.trace.TraceCorrelation)1 GammaDistribution (dr.math.distributions.GammaDistribution)1 PoissonDistribution (dr.math.distributions.PoissonDistribution)1 File (java.io.File)1