Examples with FrequencyModel dr.oldevomodel.substmodel.FrequencyModel used on opensource projects

Example 56 with FrequencyModel

use of dr.oldevomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class LikelihoodTest method testLikelihoodHKY85.

public void testLikelihoodHKY85() {
    System.out.println("\nTest Likelihood using HKY85:");
    // Sub model
    Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
    Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 29.739445, 0, 100);
    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, null, null, false, false, true, false, false);
    assertEquals("treeLikelihoodHKY85", format.format(-1825.21317), format.format(treeLikelihood.getLogLikelihood()));
}

Example 57 with FrequencyModel

use of dr.oldevomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class LikelihoodTest method testLikelihoodHKY85G.

public void testLikelihoodHKY85G() {
    System.out.println("\nTest Likelihood using HKY85G:");
    // Sub model
    Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
    Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 38.829740, 0, 100);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    //siteModel
    Parameter mu = new Parameter.Default(GammaSiteModelParser.MUTATION_RATE, 1.0, 0, Double.POSITIVE_INFINITY);
    Parameter shape = new Parameter.Default(GammaSiteModelParser.GAMMA_SHAPE, 0.137064, 0, 1000.0);
    GammaSiteModel siteModel = new GammaSiteModel(hky, mu, shape, 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("treeLikelihoodHKY85G", format.format(-1789.75936), format.format(treeLikelihood.getLogLikelihood()));
}

Example 58 with FrequencyModel

use of dr.oldevomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class LikelihoodTest method testLikelihoodK80.

public void testLikelihoodK80() {
    System.out.println("\nTest Likelihood using K80:");
    // Sub model
    Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
    Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 27.402591, 0, 100);
    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, null, null, false, false, true, false, false);
    assertEquals("treeLikelihoodK80", format.format(-1856.30305), format.format(treeLikelihood.getLogLikelihood()));
}

Example 59 with FrequencyModel

use of dr.oldevomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class TN93Test method testTN93.

public void testTN93() {
    for (Instance test : all) {
        Parameter kappa1 = new Parameter.Default(1, test.getKappa1());
        Parameter kappa2 = new Parameter.Default(1, test.getKappa2());
        double[] pi = test.getPi();
        Parameter freqs = new Parameter.Default(pi);
        FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
        TN93 tn93 = new TN93(kappa1, kappa2, f);
        double distance = test.getDistance();
        double[] mat = new double[4 * 4];
        tn93.getTransitionProbabilities(distance, mat);
        final double[] result = test.getExpectedResult();
        for (int k = 0; k < mat.length; ++k) {
            assertEquals(mat[k], result[k], 1e-10);
        // System.out.print(" " + (mat[k] - result[k]));
        }
    }
}