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

Example 1 with TreeLikelihood

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

the class StrictClockTest method testStrictClock.

public void testStrictClock() throws Exception {
    Parameter popSize = new Parameter.Default(ConstantPopulationModelParser.POPULATION_SIZE, 380.0, 0, 38000.0);
    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, 2.3E-5, 0, 100.0);
    StrictClockBranchRates branchRateModel = new StrictClockBranchRates(rateParameter);
    // Sub model
    Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
    Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 1.0, 0, 100.0);
    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(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);
    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, 1.0, 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
    List<Likelihood> likelihoods = new ArrayList<Likelihood>();
    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, 500, false);
    loggers[0].add(posterior);
    loggers[0].add(treeLikelihood);
    loggers[0].add(rootHeight);
    loggers[0].add(rateParameter);
    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);
    loggers[1].add(coalescent);
    // 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="-3928.71"/>
    //        <expectation name="clock.rate" value="8.04835E-4"/>
    //        <expectation name="constant.popSize" value="37.3762"/>
    //        <expectation name="hky.kappa" value="18.2782"/>
    //        <expectation name="treeModel.rootHeight" value="69.0580"/>
    //        <expectation name="treeLikelihood" value="-3856.59"/>
    //        <expectation name="coalescent" value="-72.1285"/>
    TraceCorrelation likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(CompoundLikelihoodParser.POSTERIOR));
    assertExpectation(CompoundLikelihoodParser.POSTERIOR, likelihoodStats, -3928.71);
    likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TreeLikelihoodParser.TREE_LIKELIHOOD));
    assertExpectation(TreeLikelihoodParser.TREE_LIKELIHOOD, likelihoodStats, -3856.59);
    TraceCorrelation treeHeightStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TREE_HEIGHT));
    assertExpectation(TREE_HEIGHT, treeHeightStats, 69.0580);
    TraceCorrelation kappaStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(HKYParser.KAPPA));
    assertExpectation(HKYParser.KAPPA, kappaStats, 18.2782);
    TraceCorrelation rateStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(StrictClockBranchRates.RATE));
    assertExpectation(StrictClockBranchRates.RATE, rateStats, 8.04835E-4);
    TraceCorrelation popStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(ConstantPopulationModelParser.POPULATION_SIZE));
    assertExpectation(ConstantPopulationModelParser.POPULATION_SIZE, popStats, 37.3762);
    TraceCorrelation coalescentStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("coalescent"));
    assertExpectation("coalescent", coalescentStats, -72.1285);
}

Example 2 with TreeLikelihood

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

the class MsatFullLikelihoodTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    //taxa
    ArrayList<Taxon> taxonList1 = new ArrayList<Taxon>();
    Collections.addAll(taxonList1, new Taxon("taxon1"), new Taxon("taxon2"), new Taxon("taxon3"));
    Taxa taxa1 = new Taxa(taxonList1);
    //msat datatype
    Microsatellite msat = new Microsatellite(1, 3);
    Patterns msatPatterns = new Patterns(msat, taxa1);
    //pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 1, 2 });
    //create tree
    NewickImporter importer = new NewickImporter("(taxon1:7.5,(taxon2:5.3,taxon3:5.3):2.2);");
    Tree tree = importer.importTree(null);
    //treeModel
    TreeModel treeModel = new TreeModel(tree);
    //msatsubstModel
    AsymmetricQuadraticModel aqm1 = new AsymmetricQuadraticModel(msat, null);
    //siteModel
    GammaSiteModel siteModel = new GammaSiteModel(aqm1);
    //treeLikelihood
    treeLikelihood1 = new TreeLikelihood(msatPatterns, treeModel, siteModel, null, null, false, false, true, false, false);
    setUpExample2();
    setUpExample3();
}

Example 3 with TreeLikelihood

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

the class MsatFullLikelihoodTest method setUpExample2.

private void setUpExample2() throws Exception {
    //taxa
    ArrayList<Taxon> taxonList2 = new ArrayList<Taxon>();
    Collections.addAll(taxonList2, new Taxon("taxon1"), new Taxon("taxon2"), new Taxon("taxon3"), new Taxon("taxon4"), new Taxon("taxon5"));
    Taxa taxa2 = new Taxa(taxonList2);
    //msat datatype
    Microsatellite msat = new Microsatellite(1, 3);
    Patterns msatPatterns = new Patterns(msat, taxa2);
    //pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 1, 2, 1, 2 });
    //create tree
    NewickImporter importer = new NewickImporter("(((taxon1:1.5,taxon2:1.5):1.5,(taxon3:2.1,taxon4:2.1):0.9):0.7,taxon5:3.7);");
    Tree tree = importer.importTree(null);
    //treeModel
    TreeModel treeModel = new TreeModel(tree);
    //msatsubstModel
    AsymmetricQuadraticModel aqm2 = new AsymmetricQuadraticModel(msat, null);
    //siteModel
    GammaSiteModel siteModel = new GammaSiteModel(aqm2);
    //treeLikelihood
    treeLikelihood2 = new TreeLikelihood(msatPatterns, treeModel, siteModel, null, null, false, false, true, false, false);
}

Example 4 with TreeLikelihood

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

the class GeneralSubstitutionModelTest method testGeneralSubstitutionModel.

public void testGeneralSubstitutionModel() {
    // Sub model
    FrequencyModel freqModel = new FrequencyModel(dataType, alignment.getStateFrequencies());
    // dimension="5" value="1.0"
    Parameter ratesPara = new Parameter.Default(GeneralSubstitutionModelParser.RATES, 5, 1.0);
    // relativeTo="5"
    GeneralSubstitutionModel generalSubstitutionModel = new GeneralSubstitutionModel(dataType, freqModel, ratesPara, 4);
    //siteModel
    GammaSiteModel siteModel = new GammaSiteModel(generalSubstitutionModel);
    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);
    treeLikelihood.setId(TreeLikelihoodParser.TREE_LIKELIHOOD);
    // Operators
    OperatorSchedule schedule = new SimpleOperatorSchedule();
    MCMCOperator operator = new ScaleOperator(ratesPara, 0.5);
    operator.setWeight(1.0);
    schedule.addOperator(operator);
    Parameter rootHeight = treeModel.getRootHeightParameter();
    rootHeight.setId(TREE_HEIGHT);
    operator = new ScaleOperator(rootHeight, 0.5);
    operator.setWeight(1.0);
    schedule.addOperator(operator);
    Parameter internalHeights = treeModel.createNodeHeightsParameter(false, true, false);
    operator = new UniformOperator(internalHeights, 10.0);
    schedule.addOperator(operator);
    operator = new SubtreeSlideOperator(treeModel, 1, 1, true, false, false, false, CoercionMode.COERCION_ON);
    schedule.addOperator(operator);
    operator = new ExchangeOperator(ExchangeOperator.NARROW, treeModel, 1.0);
    //        operator.doOperation();
    schedule.addOperator(operator);
    operator = new ExchangeOperator(ExchangeOperator.WIDE, treeModel, 1.0);
    //        operator.doOperation();
    schedule.addOperator(operator);
    operator = new WilsonBalding(treeModel, 1.0);
    //        operator.doOperation();
    schedule.addOperator(operator);
    // Log
    ArrayLogFormatter formatter = new ArrayLogFormatter(false);
    MCLogger[] loggers = new MCLogger[2];
    loggers[0] = new MCLogger(formatter, 1000, false);
    loggers[0].add(treeLikelihood);
    loggers[0].add(rootHeight);
    loggers[0].add(ratesPara);
    loggers[1] = new MCLogger(new TabDelimitedFormatter(System.out), 100000, false);
    loggers[1].add(treeLikelihood);
    loggers[1].add(rootHeight);
    loggers[1].add(ratesPara);
    // MCMC
    MCMC mcmc = new MCMC("mcmc1");
    MCMCOptions options = new MCMCOptions(10000000);
    mcmc.setShowOperatorAnalysis(true);
    mcmc.init(options, treeLikelihood, schedule, loggers);
    mcmc.run();
    // time
    System.out.println(mcmc.getTimer().toString());
    // Tracer
    List<Trace> traces = formatter.getTraces();
    ArrayTraceList traceList = new ArrayTraceList("GeneralSubstitutionModelTest", traces, 0);
    for (int i = 1; i < traces.size(); i++) {
        traceList.analyseTrace(i);
    }
    //      <expectation name="likelihood" value="-1815.75"/>
    //		<expectation name="treeModel.rootHeight" value="6.42048E-2"/>
    //		<expectation name="rateAC" value="6.08986E-2"/>
    TraceCorrelation likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TreeLikelihoodParser.TREE_LIKELIHOOD));
    assertExpectation(TreeLikelihoodParser.TREE_LIKELIHOOD, likelihoodStats, -1815.75);
    TraceCorrelation treeHeightStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TREE_HEIGHT));
    assertExpectation(TREE_HEIGHT, treeHeightStats, 0.0640787258170083);
    TraceCorrelation rateACStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(GeneralSubstitutionModelParser.RATES + "1"));
    assertExpectation(GeneralSubstitutionModelParser.RATES + "1", rateACStats, 0.061071756742081366);
}

Example 5 with TreeLikelihood

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

the class LikelihoodTest method testLikelihoodGTR.

public void testLikelihoodGTR() {
    System.out.println("\nTest Likelihood using GTR:");
    // Sub model
    Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    Variable<Double> rateACValue = new Parameter.Default(GTRParser.A_TO_C, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateAGValue = new Parameter.Default(GTRParser.A_TO_G, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateATValue = new Parameter.Default(GTRParser.A_TO_T, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateCGValue = new Parameter.Default(GTRParser.C_TO_G, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateCTValue = new Parameter.Default(GTRParser.C_TO_T, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateGTValue = new Parameter.Default(GTRParser.G_TO_T, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    GTR gtr = new GTR(rateACValue, rateAGValue, rateATValue, rateCGValue, rateCTValue, rateGTValue, f);
    //siteModel
    Parameter mu = new Parameter.Default(GammaSiteModelParser.MUTATION_RATE, 1.0, 0, Double.POSITIVE_INFINITY);
    GammaSiteModel siteModel = new GammaSiteModel(gtr, mu, null, 4, null);
    //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("treeLikelihoodGTR", format.format(-1969.14584), format.format(treeLikelihood.getLogLikelihood()));
}