Examples with TreeLikelihood dr.oldevomodel.treelikelihood.TreeLikelihood used on opensource projects

Example 6 with TreeLikelihood

use of dr.oldevomodel.treelikelihood.TreeLikelihood in project beast-mcmc by beast-dev.

the class LikelihoodTest method testLikelihoodHKY85I.

public void testLikelihoodHKY85I() {
    System.out.println("\nTest Likelihood using HKY85I:");
    // Sub model
    Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
    Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 38.564672, 0, 100);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    //siteModel
    Parameter mu = new Parameter.Default(GammaSiteModelParser.MUTATION_RATE, 1.0, 0, Double.POSITIVE_INFINITY);
    Parameter invar = new Parameter.Default(GammaSiteModelParser.PROPORTION_INVARIANT, 0.701211, 0, 1.0);
    GammaSiteModel siteModel = new GammaSiteModel(hky, mu, null, 4, invar);
    //treeLikelihood
    SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
    TreeLikelihood treeLikelihood = new TreeLikelihood(patterns, treeModel, siteModel, null, null, false, false, true, false, false);
    assertEquals("treeLikelihoodHKY85I", format.format(-1789.91240), format.format(treeLikelihood.getLogLikelihood()));
}

Example 7 with TreeLikelihood

use of dr.oldevomodel.treelikelihood.TreeLikelihood in project beast-mcmc by beast-dev.

the class LikelihoodTest method testLikelihoodJC69.

public void testLikelihoodJC69() {
    System.out.println("\nTest Likelihood using JC69:");
    // Sub model
    Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
    Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 1.0, 0, 100);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    //siteModel
    GammaSiteModel siteModel = new GammaSiteModel(hky);
    Parameter mu = new Parameter.Default(GammaSiteModelParser.MUTATION_RATE, 1.0, 0, Double.POSITIVE_INFINITY);
    siteModel.setMutationRateParameter(mu);
    //treeLikelihood
    SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
    TreeLikelihood treeLikelihood = new TreeLikelihood(patterns, treeModel, siteModel, null, null, false, false, true, false, false);
    assertEquals("treeLikelihoodJC69", format.format(-1992.20564), format.format(treeLikelihood.getLogLikelihood()));
}

Example 8 with TreeLikelihood

use of dr.oldevomodel.treelikelihood.TreeLikelihood in project beast-mcmc by beast-dev.

the class Coevolve method runModel2.

private void runModel2(PatternList patternList, PrintWriter pw, Tree tree, SubstitutionModel substModel, final Parameter betaParameter) {
    final Parameter muParameter = new Parameter.Default(1.0);
    muParameter.setId("mu");
    SiteModel siteModel = new GammaSiteModel(substModel, muParameter, null, 1, null);
    TreeModel treeModel = new TreeModel(tree);
    final TreeLikelihood treeLikelihood = new TreeLikelihood(patternList, treeModel, siteModel, null, null, false, false, true, false, false);
    treeLikelihood.setId("likelihood");
    MultivariateFunction function = new MultivariateFunction() {

        public double evaluate(double[] argument) {
            betaParameter.setParameterValue(0, argument[0]);
            betaParameter.setParameterValue(1, argument[1]);
            muParameter.setParameterValue(0, argument[2]);
            double lnL = -treeLikelihood.getLogLikelihood();
            // System.err.println("" + argument[0] + "\t" + argument[1] + "\t" + argument[2] + "\t" + lnL);
            return lnL;
        }

        public int getNumArguments() {
            return 3;
        }

        public double getLowerBound(int n) {
            return 0.0;
        }

        public double getUpperBound(int n) {
            return 100.0;
        }
    };
    MultivariateMinimum optimizer = new ConjugateGradientSearch();
    double lnL = optimizer.findMinimum(function, new double[] { 1.0, 1.0, 1.0 }, 6, 6);
    pw.write(betaParameter.getParameterValue(0) + "\t");
    pw.write(betaParameter.getParameterValue(1) + "\t");
    pw.write(muParameter.getParameterValue(0) + "\t");
    pw.write(lnL + "\n");
    pw.flush();
    System.out.println("" + betaParameter.getParameterValue(0) + "\t" + betaParameter.getParameterValue(1) + "\t" + muParameter.getParameterValue(0) + "\t" + lnL);
}

Example 9 with TreeLikelihood

use of dr.oldevomodel.treelikelihood.TreeLikelihood in project beast-mcmc by beast-dev.

the class RandomLocalClockTestProblem method testRandomLocalClock.

public void testRandomLocalClock() throws Exception {
    Parameter popSize = new Parameter.Default(ConstantPopulationModelParser.POPULATION_SIZE, 0.077, 0, Double.POSITIVE_INFINITY);
    ConstantPopulationModel constantModel = createRandomInitialTree(popSize);
    CoalescentLikelihood coalescent = new CoalescentLikelihood(treeModel, null, new ArrayList<TaxonList>(), constantModel);
    coalescent.setId("coalescent");
    // clock model
    Parameter ratesParameter = new Parameter.Default(RandomLocalClockModelParser.RATES, 10, 1);
    Parameter rateIndicatorParameter = new Parameter.Default(RandomLocalClockModelParser.RATE_INDICATORS, 10, 1);
    Parameter meanRateParameter = new Parameter.Default(RandomLocalClockModelParser.CLOCK_RATE, 1, 1.0);
    RandomLocalClockModel branchRateModel = new RandomLocalClockModel(treeModel, meanRateParameter, rateIndicatorParameter, ratesParameter, false, 0.5);
    SumStatistic rateChanges = new SumStatistic("rateChangeCount", true);
    rateChanges.addStatistic(rateIndicatorParameter);
    RateStatistic meanRate = new RateStatistic("meanRate", treeModel, branchRateModel, true, true, RateStatisticParser.MEAN);
    RateStatistic coefficientOfVariation = new RateStatistic(RateStatisticParser.COEFFICIENT_OF_VARIATION, treeModel, branchRateModel, true, true, RateStatisticParser.COEFFICIENT_OF_VARIATION);
    RateCovarianceStatistic covariance = new RateCovarianceStatistic("covariance", treeModel, branchRateModel);
    // Sub model
    Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
    Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 1.0, 0, Double.POSITIVE_INFINITY);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    //siteModel
    GammaSiteModel siteModel = new GammaSiteModel(hky);
    Parameter mu = new Parameter.Default(GammaSiteModelParser.MUTATION_RATE, 1.0, 0, Double.POSITIVE_INFINITY);
    siteModel.setMutationRateParameter(mu);
    //treeLikelihood
    SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
    TreeLikelihood treeLikelihood = new TreeLikelihood(patterns, treeModel, siteModel, branchRateModel, null, false, false, true, false, false);
    treeLikelihood.setId(TreeLikelihoodParser.TREE_LIKELIHOOD);
    // Operators
    OperatorSchedule schedule = new SimpleOperatorSchedule();
    MCMCOperator operator = new ScaleOperator(kappa, 0.75);
    operator.setWeight(1.0);
    schedule.addOperator(operator);
    operator = new ScaleOperator(ratesParameter, 0.75);
    operator.setWeight(10.0);
    schedule.addOperator(operator);
    operator = new BitFlipOperator(rateIndicatorParameter, 15.0, true);
    schedule.addOperator(operator);
    operator = new ScaleOperator(popSize, 0.75);
    operator.setWeight(3.0);
    schedule.addOperator(operator);
    Parameter rootHeight = treeModel.getRootHeightParameter();
    rootHeight.setId(TREE_HEIGHT);
    operator = new ScaleOperator(rootHeight, 0.75);
    operator.setWeight(3.0);
    schedule.addOperator(operator);
    Parameter internalHeights = treeModel.createNodeHeightsParameter(false, true, false);
    operator = new UniformOperator(internalHeights, 30.0);
    schedule.addOperator(operator);
    operator = new SubtreeSlideOperator(treeModel, 15.0, 0.0077, true, false, false, false, CoercionMode.COERCION_ON);
    schedule.addOperator(operator);
    operator = new ExchangeOperator(ExchangeOperator.NARROW, treeModel, 15.0);
    //        operator.doOperation();
    schedule.addOperator(operator);
    operator = new ExchangeOperator(ExchangeOperator.WIDE, treeModel, 3.0);
    //        operator.doOperation();
    schedule.addOperator(operator);
    operator = new WilsonBalding(treeModel, 3.0);
    //        operator.doOperation();
    schedule.addOperator(operator);
    //CompoundLikelihood
    OneOnXPrior likelihood1 = new OneOnXPrior();
    likelihood1.addData(popSize);
    OneOnXPrior likelihood2 = new OneOnXPrior();
    likelihood2.addData(kappa);
    DistributionLikelihood likelihood3 = new DistributionLikelihood(new GammaDistribution(0.5, 2.0), 0.0);
    likelihood3.addData(ratesParameter);
    DistributionLikelihood likelihood4 = new DistributionLikelihood(new PoissonDistribution(1.0), 0.0);
    likelihood4.addData(rateChanges);
    List<Likelihood> likelihoods = new ArrayList<Likelihood>();
    likelihoods.add(likelihood1);
    likelihoods.add(likelihood2);
    likelihoods.add(likelihood3);
    likelihoods.add(likelihood4);
    likelihoods.add(coalescent);
    Likelihood prior = new CompoundLikelihood(0, likelihoods);
    prior.setId(CompoundLikelihoodParser.PRIOR);
    likelihoods.clear();
    likelihoods.add(treeLikelihood);
    Likelihood likelihood = new CompoundLikelihood(-1, likelihoods);
    likelihoods.clear();
    likelihoods.add(prior);
    likelihoods.add(likelihood);
    Likelihood posterior = new CompoundLikelihood(0, likelihoods);
    posterior.setId(CompoundLikelihoodParser.POSTERIOR);
    // Log
    ArrayLogFormatter formatter = new ArrayLogFormatter(false);
    MCLogger[] loggers = new MCLogger[2];
    loggers[0] = new MCLogger(formatter, 1000, false);
    loggers[0].add(posterior);
    loggers[0].add(prior);
    loggers[0].add(treeLikelihood);
    loggers[0].add(rootHeight);
    loggers[0].add(kappa);
    //        loggers[0].add(meanRate);
    loggers[0].add(rateChanges);
    loggers[0].add(coefficientOfVariation);
    loggers[0].add(covariance);
    loggers[0].add(popSize);
    loggers[0].add(coalescent);
    loggers[1] = new MCLogger(new TabDelimitedFormatter(System.out), 10000, false);
    loggers[1].add(posterior);
    loggers[1].add(treeLikelihood);
    loggers[1].add(rootHeight);
    loggers[1].add(meanRate);
    loggers[1].add(rateChanges);
    // MCMC
    MCMC mcmc = new MCMC("mcmc1");
    MCMCOptions options = new MCMCOptions(1000000);
    mcmc.setShowOperatorAnalysis(true);
    mcmc.init(options, posterior, schedule, loggers);
    mcmc.run();
    // time
    System.out.println(mcmc.getTimer().toString());
    // Tracer
    List<Trace> traces = formatter.getTraces();
    ArrayTraceList traceList = new ArrayTraceList("RandomLocalClockTest", traces, 0);
    for (int i = 1; i < traces.size(); i++) {
        traceList.analyseTrace(i);
    }
    //        <expectation name="posterior" value="-1818.26"/>
    //        <expectation name="prior" value="-2.70143"/>
    //        <expectation name="likelihood" value="-1815.56"/>
    //        <expectation name="treeModel.rootHeight" value="6.363E-2"/>
    //        <expectation name="constant.popSize" value="9.67405E-2"/>
    //        <expectation name="hky.kappa" value="30.0394"/>
    //        <expectation name="coefficientOfVariation" value="7.02408E-2"/>
    //        covariance 0.47952
    //        <expectation name="rateChangeCount" value="0.40786"/>
    //        <expectation name="coalescent" value="7.29521"/>
    TraceCorrelation likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(CompoundLikelihoodParser.POSTERIOR));
    assertExpectation(CompoundLikelihoodParser.POSTERIOR, likelihoodStats, -1818.26);
    likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(CompoundLikelihoodParser.PRIOR));
    assertExpectation(CompoundLikelihoodParser.PRIOR, likelihoodStats, -2.70143);
    likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TreeLikelihoodParser.TREE_LIKELIHOOD));
    assertExpectation(TreeLikelihoodParser.TREE_LIKELIHOOD, likelihoodStats, -1815.56);
    TraceCorrelation treeHeightStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TREE_HEIGHT));
    assertExpectation(TREE_HEIGHT, treeHeightStats, 6.363E-2);
    TraceCorrelation kappaStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(HKYParser.KAPPA));
    assertExpectation(HKYParser.KAPPA, kappaStats, 30.0394);
    TraceCorrelation rateChangeStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("rateChangeCount"));
    assertExpectation("rateChangeCount", rateChangeStats, 0.40786);
    TraceCorrelation coefficientOfVariationStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(RateStatisticParser.COEFFICIENT_OF_VARIATION));
    assertExpectation(RateStatisticParser.COEFFICIENT_OF_VARIATION, coefficientOfVariationStats, 7.02408E-2);
    TraceCorrelation covarianceStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("covariance"));
    assertExpectation("covariance", covarianceStats, 0.47952);
    TraceCorrelation popStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(ConstantPopulationModelParser.POPULATION_SIZE));
    assertExpectation(ConstantPopulationModelParser.POPULATION_SIZE, popStats, 9.67405E-2);
    TraceCorrelation coalescentStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("coalescent"));
    assertExpectation("coalescent", coalescentStats, 7.29521);
}

Example 10 with TreeLikelihood

use of dr.oldevomodel.treelikelihood.TreeLikelihood in project beast-mcmc by beast-dev.

the class TreeLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    boolean useAmbiguities = xo.getAttribute(USE_AMBIGUITIES, false);
    boolean allowMissingTaxa = xo.getAttribute(ALLOW_MISSING_TAXA, false);
    boolean storePartials = xo.getAttribute(STORE_PARTIALS, true);
    boolean forceJavaCore = xo.getAttribute(FORCE_JAVA_CORE, false);
    if (Boolean.valueOf(System.getProperty("java.only"))) {
        forceJavaCore = true;
    }
    PatternList patternList = (PatternList) xo.getChild(PatternList.class);
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    SiteModel siteModel = (SiteModel) xo.getChild(SiteModel.class);
    BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    TipStatesModel tipStatesModel = (TipStatesModel) xo.getChild(TipStatesModel.class);
    if (tipStatesModel != null && tipStatesModel.getPatternList() != null) {
        throw new XMLParseException("The same sequence error model cannot be used for multiple partitions");
    }
    if (tipStatesModel != null && tipStatesModel.getModelType() == TipStatesModel.Type.STATES) {
        throw new XMLParseException("The state emitting TipStateModel requires BEAGLE");
    }
    boolean forceRescaling = xo.getAttribute(FORCE_RESCALING, false);
    return new TreeLikelihood(patternList, treeModel, siteModel, branchRateModel, tipStatesModel, useAmbiguities, allowMissingTaxa, storePartials, forceJavaCore, forceRescaling);
}