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

Example 21 with Parameter

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

the class GibbsSubtreeSwapTestProblem method getOperatorSchedule.

public OperatorSchedule getOperatorSchedule(TreeModel treeModel) {
    Parameter rootParameter = treeModel.createNodeHeightsParameter(true, false, false);
    Parameter internalHeights = treeModel.createNodeHeightsParameter(false, true, false);
    GibbsSubtreeSwap operator = new GibbsSubtreeSwap(treeModel, false, 1.0);
    ScaleOperator scaleOperator = new ScaleOperator(rootParameter, 0.75, CoercionMode.COERCION_ON, 1.0);
    UniformOperator uniformOperator = new UniformOperator(internalHeights, 1.0);
    OperatorSchedule schedule = new SimpleOperatorSchedule();
    schedule.addOperator(operator);
    schedule.addOperator(scaleOperator);
    schedule.addOperator(uniformOperator);
    return schedule;
}

Example 22 with Parameter

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

the class NNITest method getOperatorSchedule.

public OperatorSchedule getOperatorSchedule(TreeModel treeModel) {
    Parameter rootParameter = treeModel.createNodeHeightsParameter(true, false, false);
    Parameter internalHeights = treeModel.createNodeHeightsParameter(false, true, false);
    NNI operator = new NNI(treeModel, 1.0);
    ScaleOperator scaleOperator = new ScaleOperator(rootParameter, 0.75, CoercionMode.COERCION_ON, 1.0);
    UniformOperator uniformOperator = new UniformOperator(internalHeights, 1.0);
    OperatorSchedule schedule = new SimpleOperatorSchedule();
    schedule.addOperator(operator);
    return schedule;
}

Example 23 with Parameter

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

the class BeagleSeqSimTest method simulateTwoPartitions.

// END: simulateOnePartition
static void simulateTwoPartitions() {
    try {
        System.out.println("Test case 3: simulateTwoPartitions");
        MathUtils.setSeed(666);
        int sequenceLength = 11;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        // create tree
        NewickImporter importer = new NewickImporter("(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981);");
        Tree tree = importer.importTree(null);
        TreeModel treeModel = new TreeModel(tree);
        // create Frequency Model
        Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
        FrequencyModel freqModel = new FrequencyModel(Nucleotides.INSTANCE, freqs);
        // create substitution model
        Parameter kappa = new Parameter.Default(1, 10);
        HKY hky = new HKY(kappa, freqModel);
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(hky);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        0, // to
        3, // every
        1);
        // create partition
        Partition Partition = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        4, // to
        sequenceLength - 1, // every
        1);
        Sequence ancestralSequence = new Sequence();
        ancestralSequence.appendSequenceString("TCAAGTG");
        Partition.setRootSequence(ancestralSequence);
        partitionsList.add(partition1);
        partitionsList.add(Partition);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        System.out.println(simulator.simulate(simulateInPar, false).toString());
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch block
}

Example 24 with Parameter

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

the class BeagleSeqSimTest method simulateAminoAcid.

// END: simulateThreePartitions
static void simulateAminoAcid() {
    try {
        System.out.println("Test case 4: simulateAminoAcid");
        MathUtils.setSeed(666);
        int sequenceLength = 10;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        // create tree
        NewickImporter importer = new NewickImporter("(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981);");
        Tree tree = importer.importTree(null);
        TreeModel treeModel = new TreeModel(tree);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create Frequency Model
        Parameter freqs = new Parameter.Default(new double[] { 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05 });
        FrequencyModel freqModel = new FrequencyModel(AminoAcids.INSTANCE, freqs);
        // create substitution model
        EmpiricalRateMatrix rateMatrix = Blosum62.INSTANCE;
        EmpiricalAminoAcidModel empiricalAminoAcidModel = new EmpiricalAminoAcidModel(rateMatrix, freqModel);
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(empiricalAminoAcidModel);
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        0, // to
        sequenceLength - 1, // every
        1);
        partitionsList.add(partition1);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        System.out.println(simulator.simulate(simulateInPar, false).toString());
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch
}

Example 25 with Parameter

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

the class BeagleSeqSimTest method simulateRandomBranchAssignment.

// END: main
static void simulateRandomBranchAssignment() {
    try {
        System.out.println("Test case I dunno which: simulate random branch assignments");
        MathUtils.setSeed(666);
        int sequenceLength = 10;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        File treeFile = new File("/home/filip/Dropbox/BeagleSequenceSimulator/SimTree/SimTree.figtree");
        Tree tree = Utils.importTreeFromFile(treeFile);
        TreeModel treeModel = new TreeModel(tree);
        // create Frequency Model
        Parameter freqs = new Parameter.Default(Utils.UNIFORM_CODON_FREQUENCIES);
        FrequencyModel freqModel = new FrequencyModel(Codons.UNIVERSAL, freqs);
        // create base subst model
        Parameter omegaParameter = new Parameter.Default("omega", 1, 1.0);
        Parameter kappaParameter = new Parameter.Default("kappa", 1, 1.0);
        GY94CodonModel baseSubModel = new GY94CodonModel(Codons.UNIVERSAL, omegaParameter, kappaParameter, freqModel);
        RandomBranchModel substitutionModel = new RandomBranchModel(treeModel, baseSubModel, 0.25, false, -1);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        0, // to
        sequenceLength - 1, // every
        1);
        //			Sequence ancestralSequence = new Sequence();
        //			ancestralSequence.appendSequenceString("TCAAGTGAGG");
        //			partition1.setRootSequence(ancestralSequence);
        partitionsList.add(partition1);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        SimpleAlignment alignment = simulator.simulate(simulateInPar, true);
        // alignment.setOutputType(SimpleAlignment.OutputType.NEXUS);
        alignment.setOutputType(SimpleAlignment.OutputType.XML);
        System.out.println(alignment.toString());
    } catch (Exception e) {
        e.printStackTrace();
    }
// END: try-catch
}