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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()));
}
Also used : FrequencyModel(dr.oldevomodel.substmodel.FrequencyModel) SitePatterns(dr.evolution.alignment.SitePatterns) GammaSiteModel(dr.oldevomodel.sitemodel.GammaSiteModel) HKY(dr.oldevomodel.substmodel.HKY) TreeLikelihood(dr.oldevomodel.treelikelihood.TreeLikelihood) Parameter(dr.inference.model.Parameter)

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()));
}
Also used : FrequencyModel(dr.oldevomodel.substmodel.FrequencyModel) SitePatterns(dr.evolution.alignment.SitePatterns) GammaSiteModel(dr.oldevomodel.sitemodel.GammaSiteModel) GTR(dr.oldevomodel.substmodel.GTR) TreeLikelihood(dr.oldevomodel.treelikelihood.TreeLikelihood) Parameter(dr.inference.model.Parameter)

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()));
}
Also used : FrequencyModel(dr.oldevomodel.substmodel.FrequencyModel) SitePatterns(dr.evolution.alignment.SitePatterns) GammaSiteModel(dr.oldevomodel.sitemodel.GammaSiteModel) HKY(dr.oldevomodel.substmodel.HKY) TreeLikelihood(dr.oldevomodel.treelikelihood.TreeLikelihood) Parameter(dr.inference.model.Parameter)

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()));
}
Also used : FrequencyModel(dr.oldevomodel.substmodel.FrequencyModel) SitePatterns(dr.evolution.alignment.SitePatterns) GammaSiteModel(dr.oldevomodel.sitemodel.GammaSiteModel) HKY(dr.oldevomodel.substmodel.HKY) TreeLikelihood(dr.oldevomodel.treelikelihood.TreeLikelihood) Parameter(dr.inference.model.Parameter)

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()));
}
Also used : FrequencyModel(dr.oldevomodel.substmodel.FrequencyModel) SitePatterns(dr.evolution.alignment.SitePatterns) GammaSiteModel(dr.oldevomodel.sitemodel.GammaSiteModel) HKY(dr.oldevomodel.substmodel.HKY) TreeLikelihood(dr.oldevomodel.treelikelihood.TreeLikelihood) Parameter(dr.inference.model.Parameter)

Aggregations

SitePatterns (dr.evolution.alignment.SitePatterns)30 Parameter (dr.inference.model.Parameter)20 FrequencyModel (dr.oldevomodel.substmodel.FrequencyModel)16 GammaSiteModel (dr.oldevomodel.sitemodel.GammaSiteModel)15 TreeLikelihood (dr.oldevomodel.treelikelihood.TreeLikelihood)15 HKY (dr.oldevomodel.substmodel.HKY)11 ArrayList (java.util.ArrayList)7 BranchRateModel (dr.evomodel.branchratemodel.BranchRateModel)6 GammaSiteRateModel (dr.evomodel.siteratemodel.GammaSiteRateModel)6 TaxonList (dr.evolution.util.TaxonList)5 BranchModel (dr.evomodel.branchmodel.BranchModel)5 ExchangeOperator (dr.evomodel.operators.ExchangeOperator)5 SubtreeSlideOperator (dr.evomodel.operators.SubtreeSlideOperator)5 WilsonBalding (dr.evomodel.operators.WilsonBalding)5 TreeModel (dr.evomodel.tree.TreeModel)5 ArrayLogFormatter (dr.inference.loggers.ArrayLogFormatter)5 MCLogger (dr.inference.loggers.MCLogger)5 TabDelimitedFormatter (dr.inference.loggers.TabDelimitedFormatter)5 MCMC (dr.inference.mcmc.MCMC)5 MCMCOptions (dr.inference.mcmc.MCMCOptions)5