Examples with FrequencyModel dr.oldevomodel.substmodel.FrequencyModel used on opensource projects

Example 46 with FrequencyModel

use of dr.oldevomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class PMDTestProblem method testPMD.

public void testPMD() throws Exception {
    Parameter popSize = new Parameter.Default(ConstantPopulationModelParser.POPULATION_SIZE, 496432.69917113904, 0, Double.POSITIVE_INFINITY);
    ConstantPopulationModel constantModel = createRandomInitialTree(popSize);
    CoalescentLikelihood coalescent = new CoalescentLikelihood(treeModel, null, new ArrayList<TaxonList>(), constantModel);
    coalescent.setId("coalescent");
    // clock model
    Parameter rateParameter = new Parameter.Default(StrictClockBranchRates.RATE, 4.0E-7, 0, 100.0);
    StrictClockBranchRates branchRateModel = new StrictClockBranchRates(rateParameter);
    // 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, 1.0E-8, 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);
    // SequenceErrorModel
    Parameter ageRelatedRateParameter = new Parameter.Default(SequenceErrorModelParser.AGE_RELATED_RATE, 4.0E-7, 0, 100.0);
    TipStatesModel aDNADamageModel = new SequenceErrorModel(null, null, SequenceErrorModel.ErrorType.TRANSITIONS_ONLY, null, ageRelatedRateParameter, null);
    //treeLikelihood
    SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
    TreeLikelihood treeLikelihood = new TreeLikelihood(patterns, treeModel, siteModel, branchRateModel, aDNADamageModel, 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(rateParameter, 0.75);
    operator.setWeight(3.0);
    schedule.addOperator(operator);
    Parameter allInternalHeights = treeModel.createNodeHeightsParameter(true, true, false);
    operator = new UpDownOperator(new Scalable[] { new Scalable.Default(rateParameter) }, new Scalable[] { new Scalable.Default(allInternalHeights) }, 0.75, 3.0, CoercionMode.COERCION_ON);
    schedule.addOperator(operator);
    operator = new ScaleOperator(popSize, 0.75);
    operator.setWeight(3.0);
    schedule.addOperator(operator);
    operator = new ScaleOperator(ageRelatedRateParameter, 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, 49643.2699171139, 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);
    // ??? correct?
    operator = new DeltaExchangeOperator(freqs, new int[] { 1, 1, 1, 1 }, 0.01, 1.0, false, CoercionMode.COERCION_ON);
    schedule.addOperator(operator);
    //CompoundLikelihood
    OneOnXPrior likelihood1 = new OneOnXPrior();
    likelihood1.addData(popSize);
    OneOnXPrior likelihood2 = new OneOnXPrior();
    likelihood2.addData(kappa);
    List<Likelihood> likelihoods = new ArrayList<Likelihood>();
    likelihoods.add(likelihood1);
    likelihoods.add(likelihood2);
    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(treeLikelihood);
    loggers[0].add(rootHeight);
    loggers[0].add(rateParameter);
    loggers[0].add(ageRelatedRateParameter);
    loggers[0].add(popSize);
    loggers[0].add(kappa);
    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(rateParameter);
    // 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("PMDTest", traces, 0);
    for (int i = 1; i < traces.size(); i++) {
        traceList.analyseTrace(i);
    }
    //        <expectation name="clock.rate" value="1.5E-7"/>
    //        <expectation name="errorModel.ageRate" value="0.7E-7"/>
    //        <expectation name="hky.kappa" value="10"/>
    TraceCorrelation kappaStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(HKYParser.KAPPA));
    assertExpectation(HKYParser.KAPPA, kappaStats, 10);
    TraceCorrelation rateStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(StrictClockBranchRates.RATE));
    assertExpectation(StrictClockBranchRates.RATE, rateStats, 1.5E-7);
    TraceCorrelation ageRateStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(SequenceErrorModelParser.AGE_RELATED_RATE));
    assertExpectation(SequenceErrorModelParser.AGE_RELATED_RATE, ageRateStats, 0.7E-7);
}

Example 47 with FrequencyModel

use of dr.oldevomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class TimeIrreversibleTest method testComplexSubstitutionModel.

private double[] testComplexSubstitutionModel(Original test, double[] rates) {
    System.out.println("\n*** Complex Substitution Model Test: " + test + " ***");
    Parameter ratesP = new Parameter.Default(rates);
    DataType dataType = test.getDataType();
    FrequencyModel freqModel = new FrequencyModel(dataType, new Parameter.Default(test.getFrequencies()));
    ComplexSubstitutionModel substModel = new ComplexSubstitutionModel("Complex Substitution Model Test", dataType, freqModel, ratesP);
    double logL = substModel.getLogLikelihood();
    System.out.println("Prior = " + logL);
    double[] finiteTimeProbs = null;
    if (!Double.isInfinite(logL)) {
        finiteTimeProbs = new double[substModel.getDataType().getStateCount() * substModel.getDataType().getStateCount()];
        substModel.getTransitionProbabilities(time, finiteTimeProbs);
        System.out.println("Probs = ");
        printRateMatrix(finiteTimeProbs, substModel.getDataType().getStateCount());
    }
    //            assertEquals(1, 1, 1e-10);
    return finiteTimeProbs;
}

Example 48 with FrequencyModel

use of dr.oldevomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class TimeIrreversibleTest method testSVSComplexSubstitutionModel.

private double[] testSVSComplexSubstitutionModel(Original test, double[] rates) {
    System.out.println("\n*** SVS Complex Substitution Model Test: " + test + " ***");
    double[] indicators = test.getIndicators();
    Parameter ratesP = new Parameter.Default(rates);
    Parameter indicatorsP = new Parameter.Default(indicators);
    DataType dataType = test.getDataType();
    FrequencyModel freqModel = new FrequencyModel(dataType, new Parameter.Default(test.getFrequencies()));
    SVSComplexSubstitutionModel substModel = new SVSComplexSubstitutionModel("SVS Complex Substitution Model Test", dataType, freqModel, ratesP, indicatorsP);
    double logL = substModel.getLogLikelihood();
    System.out.println("Prior = " + logL);
    double[] finiteTimeProbs = null;
    if (!Double.isInfinite(logL)) {
        finiteTimeProbs = new double[substModel.getDataType().getStateCount() * substModel.getDataType().getStateCount()];
        substModel.getTransitionProbabilities(time, finiteTimeProbs);
        System.out.println("Probs = ");
        printRateMatrix(finiteTimeProbs, substModel.getDataType().getStateCount());
    }
    //            assertEquals(1, 1, 1e-10);
    return finiteTimeProbs;
}

Example 49 with FrequencyModel

use of dr.oldevomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class TwoStateCovarionModelTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    frequencies = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
    alpha = new Parameter.Default(0.0);
    switchingRate = new Parameter.Default(1.0);
    FrequencyModel freqModel = new FrequencyModel(TwoStateCovarion.INSTANCE, frequencies);
    model = new TwoStateCovarionModel(TwoStateCovarion.INSTANCE, freqModel, alpha, switchingRate);
    dataType = model.getDataType();
}

Example 50 with FrequencyModel

use of dr.oldevomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class testNtdBMA method testNtdBMA.

public void testNtdBMA() {
    for (Instance test : all) {
        Parameter logKappa = new Parameter.Default(1, test.getLogKappa());
        Parameter logTN = new Parameter.Default(1, test.getLogTN());
        Parameter logAC = new Parameter.Default(1, test.getLogAC());
        Parameter logAT = new Parameter.Default(1, test.getLogAT());
        Parameter logGC = new Parameter.Default(1, test.getLogGC());
        Parameter logGT = new Parameter.Default(1, test.getLogGT());
        Variable<Integer> modelChoose = test.getModelChoose();
        double[] pi = test.getPi();
        Parameter freqs = new Parameter.Default(pi);
        FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
        NtdBMA ntdBMA = new NtdBMA(logKappa, logTN, logAC, logAT, logGC, logGT, modelChoose, f);
        double distance = test.getDistance();
        double[] mat = new double[4 * 4];
        ntdBMA.getTransitionProbabilities(distance, mat);
        final double[] result = test.getExpectedResult();
        for (int k = 0; k < mat.length; ++k) {
            assertEquals(mat[k], result[k], 5e-10);
        // System.out.print(" " + (mat[k] - result[k]));
        }
    }
}