Examples with Parameter dr.inference.model.Parameter used on opensource projects

Example 16 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class SelectorOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final Parameter parameter = (Parameter) xo.getChild(Parameter.class);
    final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    final SelectorOperator op = new SelectorOperator(parameter);
    op.setWeight(weight);
    return op;
}

Example 17 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class SetOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    double[] values = xo.getDoubleArrayAttribute(SET);
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    Parameter parameter = (Parameter) xo.getChild(Parameter.class);
    System.out.println("Creating set operator for parameter " + parameter.getParameterName());
    System.out.print("  set = {" + values[0]);
    for (int i = 1; i < values.length; i++) {
        System.out.print(", " + values[i]);
    }
    System.out.println("}");
    SetOperator operator = new SetOperator(parameter, values);
    operator.setWeight(weight);
    return operator;
}

Example 18 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class CompleteHistorySimulatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    int nReplications = xo.getIntegerAttribute(REPLICATIONS);
    Tree tree = (Tree) xo.getChild(Tree.class);
    GammaSiteRateModel siteModel = (GammaSiteRateModel) xo.getChild(GammaSiteRateModel.class);
    BranchRateModel rateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    if (rateModel == null)
        rateModel = new DefaultBranchRateModel();
    DataType dataType = siteModel.getSubstitutionModel().getDataType();
    String jumpTag = xo.getAttribute(JUMP_TAG_NAME, JUMP_TAG);
    boolean sumAcrossSites = xo.getAttribute(SUM_SITES, false);
    Parameter branchSpecificParameter = null;
    Parameter variableValueParameter = null;
    if (xo.hasChildNamed(BRANCH_SPECIFIC_SPECIFICATION)) {
        XMLObject cxo = xo.getChild(BRANCH_SPECIFIC_SPECIFICATION);
        branchSpecificParameter = (Parameter) cxo.getChild(BRANCH_VARIABLE_PARAMETER).getChild(Parameter.class);
        variableValueParameter = (Parameter) cxo.getChild(VARIABLE_VALUE_PARAMETER).getChild(Parameter.class);
    }
    CompleteHistorySimulator history = new CompleteHistorySimulator(tree, siteModel, rateModel, nReplications, sumAcrossSites, branchSpecificParameter, variableValueParameter);
    XMLObject cxo = xo.getChild(COUNTS);
    if (cxo != null) {
        MarkovJumpsTreeLikelihoodParser.parseAllChildren(cxo, history, dataType.getStateCount(), jumpTag, MarkovJumpsType.COUNTS, false);
    }
    cxo = xo.getChild(REWARDS);
    if (cxo != null) {
        MarkovJumpsTreeLikelihoodParser.parseAllChildren(cxo, history, dataType.getStateCount(), jumpTag, MarkovJumpsType.REWARDS, false);
    }
    if (dataType instanceof Codons) {
        Codons codons = (Codons) dataType;
        if (xo.getAttribute(SYN_JUMPS, false)) {
            // use base 61
            double[] synRegMatrix = CodonLabeling.getRegisterMatrix(CodonLabeling.SYN, codons, false);
            Parameter registerParameter = new Parameter.Default(synRegMatrix);
            registerParameter.setId("S");
            history.addRegister(registerParameter, MarkovJumpsType.COUNTS, false);
        }
        if (xo.getAttribute(NON_SYN_JUMPS, false)) {
            // use base 61
            double[] nonSynRegMatrix = CodonLabeling.getRegisterMatrix(CodonLabeling.NON_SYN, codons, false);
            Parameter registerParameter = new Parameter.Default(nonSynRegMatrix);
            registerParameter.setId("N");
            history.addRegister(registerParameter, MarkovJumpsType.COUNTS, false);
        }
    }
    if (xo.getAttribute(ANNOTATE_WITH_ALIGNMENT, false)) {
        history.addAlignmentTrait();
    }
    boolean alignmentOnly = xo.getAttribute(ALIGNMENT_ONLY, false);
    if (dataType instanceof Codons && !alignmentOnly) {
        System.out.println("Codon models give exception when count statistics are done on them. " + "You can supress this by setting alignmentOnly to true.");
    }
    if (alignmentOnly) {
        history.setAlignmentOnly();
    }
    history.simulate();
    return history;
}

Example 19 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class AncestralSequenceAnnotator method loadSiteModel.

/*
     * This method is equivalent to the SubstitutionModelLoader without having to
     * be object orientated and can be much more flexible.
     */
private GammaSiteRateModel loadSiteModel(Tree tree) {
    String modelType = (String) tree.getAttribute(SUBST_MODEL);
    /* Identify the datatype and substitution model. Load the model */
    SubstitutionModelLoader sml = null;
    String substModelName = modelType.replaceFirst("\\*.+", "").replaceFirst("\\+.+", "").trim();
    System.out.println("Basic Substitution Model is " + substModelName);
    for (int i = 0; i < GENERAL_MODELS_LIST.length; i++) {
        if (substModelName.matches(GENERAL_MODELS_LIST[i])) {
            sml = new GeneralSubstitutionModelLoader(tree, modelType);
        }
    }
    for (int i = 0; i < NUCLEOTIDE_MODELS_LIST.length; i++) {
        if (substModelName.matches(NUCLEOTIDE_MODELS_LIST[i])) {
            sml = new NucleotideSubstitutionModelLoader(tree, modelType);
        }
    }
    for (int i = 0; i < AMINO_ACID_MODELS_LIST.length; i++) {
        if (substModelName.matches(AMINO_ACID_MODELS_LIST[i])) {
            sml = new AminoAcidSubstitutionModelLoader(tree, modelType);
        }
    }
    for (int i = 0; i < TRIPLET_MODELS_LIST.length; i++) {
        if (substModelName.matches(TRIPLET_MODELS_LIST[i])) {
            sml = new TripletSubstitutionModelLoader(tree, modelType);
        }
    }
    for (int i = 0; i < CODON_MODELS_LIST.length; i++) {
        if (substModelName.matches(CODON_MODELS_LIST[i])) {
            sml = new CodonSubstitutionModelLoader(tree, modelType);
        }
    }
    if (sml.getSubstitutionModel() == null) {
        System.err.println("Substitution model type '" + modelType + "' not implemented");
        System.exit(-1);
    }
    //SiteModel siteModel = new GammaSiteModel(sml.getSubstitutionModel(), new Parameter.Default(1.0), null, 0, null);
    //SiteModel siteModel = new GammaSiteModel(sml.getSubstitutionModel(), null, null, 0, null);
    String siteRatesModels = modelType.substring(modelType.indexOf("+") + 1, modelType.length());
    //String[] siteRatesModels = siteRatesParameters.split(" + ");
    System.out.println("Site rate models: " + siteRatesModels);
    if (sml.getSubstitutionModel().getDataType().getClass().equals(Codons.class) && siteRatesModels.length() > 0) {
        if (siteRatesModels.indexOf("+M2") >= 0) {
            /* M2 */
            System.out.println("Site model - M2 Codon site model used");
            Parameter m2FrequencyAAInv = new Parameter.Default(Double.parseDouble(tree.getAttribute("M2_f[AA INV]").toString()));
            Parameter m2FrequencyNeutral = new Parameter.Default(Double.parseDouble(tree.getAttribute("M2_f[Neutral]").toString()));
            Parameter m2FrequencySelected = new Parameter.Default(Double.parseDouble(tree.getAttribute("M2_f[Selected]").toString()));
            Parameter m2Omega = new Parameter.Default(Double.parseDouble(tree.getAttribute("M2_omega").toString()));
            //Parameter m2FrequencyAAInv = new Parameter.Default((Double) tree.getAttribute("M2_f[AA INV]"));
            //Parameter m2FrequencyNeutral = new Parameter.Default((Double) tree.getAttribute("M2_f[Neutral]"));
            //Parameter m2FrequencySelected = new Parameter.Default((Double) tree.getAttribute("M2_f[Selected]"));
            //Parameter m2Omega = new Parameter.Default((Double) tree.getAttribute("M2_omega"));
            System.err.println("Sorry, M2 substitution model is not yet implemented in BEAST");
            System.exit(0);
        } else if (siteRatesModels.indexOf("+M3") >= 0) {
            /* M3 */
            System.out.println("Site model - M3 Codon site model used");
            int numberOfBins = Integer.parseInt(siteRatesModels.replaceFirst(".+M3\\[", "").replaceFirst("\\].+", ""));
            System.out.println(" + M3 n value: " + numberOfBins);
            Parameter[] m3Frequencies = new Parameter[numberOfBins];
            Parameter[] m3Omegas = new Parameter[numberOfBins];
            for (int i = 1; i <= numberOfBins; i++) {
                m3Frequencies[i - 1] = new Parameter.Default(Double.parseDouble(tree.getAttribute("M3_f" + i).toString()));
                m3Omegas[i - 1] = new Parameter.Default(Double.parseDouble(tree.getAttribute("M3_omega" + i).toString()));
            //m3Frequencies[i-1] = new Parameter.Default((Double) tree.getAttribute("M3_f"+i));
            //m3Omegas[i-1] = new Parameter.Default((Double) tree.getAttribute("M3_omega"+i));
            }
            System.err.println("Sorry, M3 substitution model is not yet implemented in BEAST");
            System.exit(0);
        } else if (siteRatesModels.indexOf("+M0_omega~Beta(") >= 0) {
            /* M7 */
            System.out.println("Site model - M7 Codon site model used");
            int numberOfBins = Integer.parseInt(siteRatesModels.replaceFirst("M0_omega~Beta\\(", "").replaceFirst("\\)", ""));
            System.out.println(" + M7 n value: " + numberOfBins);
            Parameter m7BetaMu = new Parameter.Default(Double.parseDouble(tree.getAttribute("beta_mu").toString()));
            Parameter m7BetaVarMu = new Parameter.Default(Double.parseDouble(tree.getAttribute("beta_Var/mu").toString()));
            //Parameter m7BetaMu = new Parameter.Default((Double) tree.getAttribute("beta_mu"));
            //Parameter m7BetaVarMu = new Parameter.Default((Double) tree.getAttribute("beta_Var/mu"));
            System.err.println("Sorry, M7 substitution model is not yet implemented in BEAST");
            System.exit(0);
        }
    } else if (siteRatesModels.length() > 0) {
        /* i.e. for other data types. */
        /* Do gamma/lognormal + pinv */
        Parameter pInvParameter = null;
        int categories = -1;
        Parameter alphaParameter = null;
        if (siteRatesModels.indexOf("+INV") >= 0) {
            System.out.println("Site model -  proportion of invariable sites used");
            //pInvParameter = new Parameter.Default(((Double) tree.getAttribute("INV_p")).doubleValue());
            pInvParameter = new Parameter.Default(Double.parseDouble(tree.getAttribute("INV_p").toString()));
        }
        if (siteRatesModels.indexOf("+rate~Gamma(") >= 0) {
            System.out.println("Site model - gamma site rate heterogeneity used");
            categories = Integer.parseInt(siteRatesModels.replaceFirst(".+rate~Gamma\\(", "").replaceFirst("\\).*", ""));
            //double sigmaMu = (Double) tree.getAttribute("gamma_sigma/mu");
            double sigmaMu = Double.parseDouble(tree.getAttribute("gamma_sigma/mu").toString());
            sigmaMu = (1.0 / sigmaMu) * (1.0 / sigmaMu);
            /* BAli-Phy is parameterised by sigma/mu instead of alpha */
            alphaParameter = new Parameter.Default(sigmaMu);
        } else if (siteRatesModels.indexOf("+rate~LogNormal(") >= 0) {
            // TODO implement lognormal site model
            System.out.println("Site model - lognormal site rate heterogeneity used");
            System.err.println("Sorry, lognormal site rates are not yet implemented in BEAST");
            System.exit(0);
            categories = Integer.parseInt(siteRatesModels.replaceFirst(".+rate~LogNormal\\(", "").replaceFirst("\\).*", ""));
            //double sigmaMu = (Double) tree.getAttribute("log-normal_sigma/mu");
            double sigmaMu = Double.parseDouble(tree.getAttribute("log-normal_sigma/mu").toString());
            sigmaMu = (1.0 / sigmaMu) * (1.0 / sigmaMu);
            /* BAli-Phy is parameterised by sigma/mu instead of alpha */
            alphaParameter = new Parameter.Default(sigmaMu);
        } else if (siteRatesModels.indexOf("+GAMMA(") >= 0) {
            /* For BEAST output */
            System.out.println("Site model - gamma site rate heterogeneity used");
            categories = Integer.parseInt(siteRatesModels.replaceFirst(".+GAMMA\\(", "").replaceFirst("\\).*", ""));
            //double sigmaMu = (Double) tree.getAttribute("gamma_sigma/mu");
            double alpha = Double.parseDouble(tree.getAttribute("alpha").toString());
            alphaParameter = new Parameter.Default(alpha);
        }
        //System.out.println("alpha and pinv parameters: " + alphaParameter.getParameterValue(0) + "\t" + pInvParameter.getParameterValue(0));
        //GammaSiteRateModel siteModel = new GammaSiteRateModel(sml.getSubstitutionModel(), new Parameter.Default(1.0), alphaParameter, categories, pInvParameter);
        GammaSiteRateModel siteModel = new GammaSiteRateModel(GammaSiteModelParser.SITE_MODEL, new Parameter.Default(1.0), alphaParameter, categories, pInvParameter);
        siteModel.setSubstitutionModel(sml.getSubstitutionModel());
        //SiteModel siteModel = new GammaSiteModel(sml.getSubstitutionModel(), null, null, 0, null);
        return siteModel;
    }
    /* Default with no gamma or pinv */
    //SiteRateModel siteModel = new GammaSiteRateModel(sml.getSubstitutionModel());
    GammaSiteRateModel siteModel = new GammaSiteRateModel(GammaSiteModelParser.SITE_MODEL);
    siteModel.setSubstitutionModel(sml.getSubstitutionModel());
    return siteModel;
}

Example 20 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class RecomboGen method main.

public static void main(String[] argv) {
    // Simulate sequences on this tree to generate sequences at the top of the
    // recombination process.
    Parameter kappa = new Parameter.Default(1, 2);
    Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
    FrequencyModel freqModel = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, freqModel);
    // create site model
    SiteModel siteModel = new GammaSiteModel(hky);
    // create branch rate model
    Parameter rate = new Parameter.Default(1, 1.0E-4);
    BranchRateModel branchRateModel = new StrictClockBranchRates(rate);
//        RecomboGen recomboGen = new RecomboGen(8.0E-2, 100, 1000, 1.0E-4,
//                new String[] { "taxon1_0", "taxon2_0", "taxon3_10", "taxon4_10", "taxon5_20", "taxon6_20"},
//                new double[] { 0, 0, 10, 10, 20, 20} );
//
//        recomboGen.generate();
}