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()));
}
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()));
}
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()));
}
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()));
}
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()));
}
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