Examples with GammaSiteModel dr.oldevomodel.sitemodel.GammaSiteModel used on opensource projects

Example 26 with GammaSiteModel

use of dr.oldevomodel.sitemodel.GammaSiteModel 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 27 with GammaSiteModel

use of dr.oldevomodel.sitemodel.GammaSiteModel 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 28 with GammaSiteModel

use of dr.oldevomodel.sitemodel.GammaSiteModel 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()));
}