Examples with HKY dr.evomodel.substmodel.nucleotide.HKY used on opensource projects

Example 21 with HKY

use of dr.evomodel.substmodel.nucleotide.HKY in project beast-mcmc by beast-dev.

the class VariableBranchCompleteHistorySimulatorTest method testHKYVariableSimulation.

public void testHKYVariableSimulation() {
    System.out.println("Starting HKY variable branch simulation");
    Parameter kappa = new Parameter.Default(1, 2.0);
    double[] pi = { 0.45, 0.05, 0.25, 0.25 };
    Parameter freqs = new Parameter.Default(pi);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    int stateCount = hky.getDataType().getStateCount();
    Parameter mu = new Parameter.Default(1, 0.5);
    Parameter alpha = new Parameter.Default(1, 0.5);
    GammaSiteRateModel siteModel = new GammaSiteRateModel("gammaModel", mu, alpha, 4, null);
    siteModel.setSubstitutionModel(hky);
    BranchRateModel branchRateModel = new DefaultBranchRateModel();
    double analyticResult = TreeUtils.getTreeLength(tree, tree.getRoot()) * mu.getParameterValue(0);
    int nSites = 200;
    double[] register1 = new double[stateCount * stateCount];
    double[] register2 = new double[stateCount * stateCount];
    // Count all jumps
    MarkovJumpsCore.fillRegistrationMatrix(register1, stateCount);
    // Move some jumps from 1 to 2
    register1[1 * stateCount + 2] = 0;
    register2[1 * stateCount + 2] = 1;
    register1[1 * stateCount + 3] = 0;
    register2[1 * stateCount + 3] = 1;
    register1[2 * stateCount + 3] = 0;
    register2[2 * stateCount + 3] = 1;
    double[] branchValues = { 10.0, 10.0, 10.0, 10.0, 10.0 };
    Parameter branchValuesParam = new Parameter.Default(branchValues);
    runSimulation(N, tree, siteModel, branchRateModel, nSites, new double[][] { register1, register2 }, analyticResult, kappa, branchValuesParam);
}

Example 22 with HKY

use of dr.evomodel.substmodel.nucleotide.HKY in project beast-mcmc by beast-dev.

the class UniformizedStateHistoryTest method setUp.

public void setUp() {
    MathUtils.setSeed(666);
    Parameter kappa = new Parameter.Default(1, 2.0);
    double[] pi = { 0.45, 0.05, 0.30, 0.20 };
    Parameter freqs = new Parameter.Default(pi);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    hky = new HKY(kappa, f);
    stateCount = hky.getDataType().getStateCount();
    double[] lambda = new double[stateCount * stateCount];
    hky.getInfinitesimalMatrix(lambda);
    process = new SubordinatedProcess(lambda, stateCount);
}