Examples with RealParameter beast.core.parameter.RealParameter used on opensource projects

Example 86 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class SpeciesTreePrior method initAndValidate.

@Override
public void initAndValidate() {
    popFunction = popFunctionInput.get();
    popSizesBottom = popSizesBottomInput.get();
    popSizesTop = popSizesTopInput.get();
    // set up sizes of population functions
    final int speciesCount = treeInput.get().getLeafNodeCount();
    final int nodeCount = treeInput.get().getNodeCount();
    switch(popFunction) {
        case constant:
            popSizesBottom.setDimension(nodeCount);
            break;
        case linear:
            if (popSizesTop == null) {
                throw new IllegalArgumentException("topPopSize must be specified");
            }
            popSizesBottom.setDimension(speciesCount);
            popSizesTop.setDimension(nodeCount);
            break;
        case linear_with_constant_root:
            if (popSizesTop == null) {
                throw new IllegalArgumentException("topPopSize must be specified");
            }
            popSizesBottom.setDimension(speciesCount);
            popSizesTop.setDimension(nodeCount - 1);
            break;
    }
    // bottom prior = Gamma(2,Psi)
    gamma2Prior = new Gamma();
    gamma2Prior.betaInput.setValue(gammaParameterInput.get(), gamma2Prior);
    // top prior = Gamma(4,Psi)
    gamma4Prior = new Gamma();
    final RealParameter parameter = new RealParameter(new Double[] { 4.0 });
    gamma4Prior.alphaInput.setValue(parameter, gamma4Prior);
    gamma4Prior.betaInput.setValue(gammaParameterInput.get(), gamma4Prior);
    if (popFunction != TreePopSizeFunction.constant && gamma4Prior == null) {
        throw new IllegalArgumentException("Top prior must be specified when population function is not constant");
    }
// make sure the m_taxonSet is a set of taxonsets
// HACK to make Beauti initialise: skip the check here
// for (Taxon taxon : m_taxonSet.get().m_taxonset.get()) {
// if (!(taxon instanceof TaxonSet)) {
// throw new IllegalArgumentException("taxonset should be sets of taxa only, not individual taxons");
// }
// }
}

Example 87 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class RandomLocalClockModel method initAndValidate.

@Override
public void initAndValidate() {
    m_tree = treeInput.get();
    BooleanParameter indicators = indicatorParamInput.get();
    if (indicators.getDimension() != m_tree.getNodeCount() - 1) {
        Log.warning.println("RandomLocalClockModel::Setting dimension of indicators to " + (m_tree.getNodeCount() - 1));
        indicators.setDimension(m_tree.getNodeCount() - 1);
    }
    unscaledBranchRates = new double[m_tree.getNodeCount()];
    RealParameter rates = rateParamInput.get();
    if (rates.lowerValueInput.get() == null || rates.lowerValueInput.get() < 0.0) {
        rates.setLower(0.0);
    }
    if (rates.upperValueInput.get() == null || rates.upperValueInput.get() < 0.0) {
        rates.setUpper(Double.MAX_VALUE);
    }
    if (rates.getDimension() != m_tree.getNodeCount() - 1) {
        Log.warning.println("RandomLocalClockModel::Setting dimension of rates to " + (m_tree.getNodeCount() - 1));
        rates.setDimension(m_tree.getNodeCount() - 1);
    }
    ratesAreMultipliers = ratesAreMultipliersInput.get();
    meanRate = meanRateInput.get();
    if (meanRate == null) {
        meanRate = new RealParameter("1.0");
    }
}

Example 88 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class TreeLikelihoodTest method testMarginalisationOfLikelihoodBinary.

@Test
public void testMarginalisationOfLikelihoodBinary() throws Exception {
    // test summation over all patterns adds to 1 for binary data
    Sequence German_ST = new Sequence("German_ST", "           10110010");
    Sequence Dutch_List = new Sequence("Dutch_List", "          11010100");
    Sequence English_ST = new Sequence("English_ST", "          11101000");
    Alignment data = new Alignment();
    data.initByName("sequence", German_ST, "sequence", Dutch_List, "sequence", English_ST, "dataType", "binary");
    Tree tree = BEASTTestCase.getTree(data, "(English_ST:0.22743347188019544,(German_ST:0.10557648379843088,Dutch_List:0.10557648379843088):0.12185698808176457):0.0;");
    RealParameter frequencies = new RealParameter("0.683 0.317");
    Frequencies freqs = new Frequencies();
    freqs.initByName("frequencies", frequencies);
    GeneralSubstitutionModel covarion = new GeneralSubstitutionModel();
    covarion.initByName("frequencies", freqs, "rates", new RealParameter("1.0 1.0"));
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", covarion);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    likelihood.initByName("useAmbiguities", false, "data", data, "tree", tree, "siteModel", siteModel);
    likelihood.calculateLogP();
    double[] logPs = likelihood.getPatternLogLikelihoods();
    double P = 0;
    for (double d : logPs) {
        P += Math.exp(d);
    }
    assertEquals(P, 1.0, BEASTTestCase.PRECISION);
}

Example 89 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class TreeLikelihoodTest method testSDolloLikelihood.

@Test
public void testSDolloLikelihood() throws Exception {
    UserDataType dataType = new UserDataType();
    dataType.initByName("states", 2, "codeMap", "0=1, 1=0, ?=0 1, -=0 1");
    Alignment data = new Alignment();
    Sequence German_ST = new Sequence("German_ST", BEASTTestCase.German_ST.dataInput.get());
    Sequence Dutch_List = new Sequence("Dutch_List", BEASTTestCase.Dutch_List.dataInput.get());
    ;
    Sequence English_ST = new Sequence("English_ST", BEASTTestCase.English_ST.dataInput.get());
    ;
    Sequence French = new Sequence("French", BEASTTestCase.French.dataInput.get());
    ;
    Sequence Italian = new Sequence("Italian", BEASTTestCase.Italian.dataInput.get());
    ;
    Sequence Spanish = new Sequence("Spanish", BEASTTestCase.Spanish.dataInput.get());
    ;
    data.initByName("sequence", German_ST, "sequence", Dutch_List, "sequence", English_ST, "sequence", French, "sequence", Italian, "sequence", Spanish, "userDataType", dataType);
    Tree tree = BEASTTestCase.getTree(data, "((English_ST:0.22743347188019544,(German_ST:0.10557648379843088,Dutch_List:0.10557648379843088):0.12185698808176457):1.5793160946109988,(Spanish:0.11078392189606047,(Italian:0.10119772534558173,French:0.10119772534558173):0.009586196550478737):1.6959656445951337)");
    RealParameter frequencies = new RealParameter("1 0");
    Frequencies freqs = new Frequencies();
    freqs.initByName("frequencies", frequencies);
    RealParameter deathprob = new RealParameter("1.7");
    MutationDeathModel SDollo = new MutationDeathModel();
    SDollo.initByName("deathprob", deathprob, "frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", SDollo);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel, "useAmbiguities", true);
    logP = likelihood.calculateLogP();
    // beast1 xml gives -3551.6436
    assertEquals(logP, -3551.6436270344648, BEASTTestCase.PRECISION);
}

Example 90 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class TreeLikelihoodTest method testBinaryCovarionLikelihood.

@Test
public void testBinaryCovarionLikelihood() throws Exception {
    Alignment data = BEASTTestCase.getCovarionAlignment();
    Tree tree = BEASTTestCase.getTree(data, "((English_ST:0.22743347188019544,(German_ST:0.10557648379843088,Dutch_List:0.10557648379843088):0.12185698808176457):1.5793160946109988,(Spanish:0.11078392189606047,(Italian:0.10119772534558173,French:0.10119772534558173):0.009586196550478737):1.6959656445951337)");
    RealParameter alpha = new RealParameter("0.284");
    RealParameter switchRate = new RealParameter("0.829");
    RealParameter frequencies = new RealParameter("0.683 0.317");
    RealParameter hfrequencies = new RealParameter("0.5 0.5");
    BinaryCovarion covarion = new BinaryCovarion();
    covarion.initByName("alpha", alpha, "switchRate", switchRate, "vfrequencies", frequencies, "hfrequencies", hfrequencies);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", covarion);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    likelihood.initByName("useAmbiguities", true, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    // beast1 xml gives -1730.5363
    assertEquals(logP, -1730.53631739, BEASTTestCase.PRECISION);
}