Examples with SitePatterns dr.evolution.alignment.SitePatterns used on opensource projects

Example 26 with SitePatterns

use of dr.evolution.alignment.SitePatterns in project beast-mcmc by beast-dev.

the class LikelihoodTest method testLikelihoodHKY85GI.

public void testLikelihoodHKY85GI() {
    System.out.println("\nTest Likelihood using HKY85GI:");
    // Sub model
    Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
    Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 39.464538, 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, 0.587649, 0, 1000.0);
    Parameter invar = new Parameter.Default(GammaSiteModelParser.PROPORTION_INVARIANT, 0.486548, 0, 1.0);
    GammaSiteModel siteModel = new GammaSiteModel(hky, mu, shape, 4, invar);
    //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("treeLikelihoodHKY85GI", format.format(-1789.63923), format.format(treeLikelihood.getLogLikelihood()));
}

Example 27 with SitePatterns

use of dr.evolution.alignment.SitePatterns in project beast-mcmc by beast-dev.

the class LikelihoodTest method testLikelihoodGTRGI.

public void testLikelihoodGTRGI() {
    System.out.println("\nTest Likelihood using GTRGI:");
    // Sub model
    Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    Variable<Double> rateACValue = new Parameter.Default(GTRParser.A_TO_C, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateAGValue = new Parameter.Default(GTRParser.A_TO_G, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateATValue = new Parameter.Default(GTRParser.A_TO_T, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateCGValue = new Parameter.Default(GTRParser.C_TO_G, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateCTValue = new Parameter.Default(GTRParser.C_TO_T, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    Variable<Double> rateGTValue = new Parameter.Default(GTRParser.G_TO_T, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    GTR gtr = new GTR(rateACValue, rateAGValue, rateATValue, rateCGValue, rateCTValue, rateGTValue, f);
    //siteModel
    Parameter mu = new Parameter.Default(GammaSiteModelParser.MUTATION_RATE, 1.0, 0, Double.POSITIVE_INFINITY);
    Parameter shape = new Parameter.Default(GammaSiteModelParser.GAMMA_SHAPE, 0.5, 0, 100.0);
    Parameter invar = new Parameter.Default(GammaSiteModelParser.PROPORTION_INVARIANT, 0.5, 0, 1.0);
    GammaSiteModel siteModel = new GammaSiteModel(gtr, mu, shape, 4, invar);
    //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("treeLikelihoodGTRGI", format.format(-1947.58294), format.format(treeLikelihood.getLogLikelihood()));
}

Example 28 with SitePatterns

use of dr.evolution.alignment.SitePatterns 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 29 with SitePatterns

use of dr.evolution.alignment.SitePatterns 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 30 with SitePatterns

use of dr.evolution.alignment.SitePatterns 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()));
}