Examples with BinaryCovarion beast.evolution.substitutionmodel.BinaryCovarion used on opensource projects

Example 1 with BinaryCovarion

use of beast.evolution.substitutionmodel.BinaryCovarion in project beast2 by CompEvol.

the class BinaryCovarionModelTest method doWithUnEqualHFreqs.

private void doWithUnEqualHFreqs(String mode) {
    Frequencies dummyFreqs = new Frequencies();
    dummyFreqs.initByName("frequencies", "0.25 0.25 0.25 0.25", "estimate", false);
    BinaryCovarion substModel;
    double d = 0.05 + Randomizer.nextDouble() * 0.9;
    RealParameter hfrequencies = new RealParameter(new Double[] { d, 1.0 - d });
    d = 0.05 + Randomizer.nextDouble() * 0.9;
    RealParameter vfrequencies = new RealParameter(new Double[] { d, 1.0 - d });
    substModel = new BinaryCovarion();
    substModel.initByName("frequencies", dummyFreqs, "hfrequencies", hfrequencies, /* [f0, f1] */
    "vfrequencies", vfrequencies, /* [p0, p1] */
    "alpha", "0.01", "switchRate", "0.1", // "eigenSystem", "beast.evolution.substitutionmodel.RobustEigenSystem",
    "mode", mode);
    double[] matrix = new double[16];
    substModel.getTransitionProbabilities(null, 1000, 0, 1.0, matrix);
    double[] baseFreqs = new double[] { (vfrequencies.getValue(0) * hfrequencies.getValue(0)), (vfrequencies.getValue(1) * hfrequencies.getValue(0)), (vfrequencies.getValue(0) * hfrequencies.getValue(1)), (vfrequencies.getValue(1) * hfrequencies.getValue(1)) };
    System.err.println("Expected: " + Arrays.toString(baseFreqs));
    System.err.println("Calculat: " + Arrays.toString(matrix));
    for (int j = 0; j < 4; j++) {
        assertEquals(baseFreqs[j], matrix[j], 1e-3);
    }
}

Example 2 with BinaryCovarion

use of beast.evolution.substitutionmodel.BinaryCovarion in project beast2 by CompEvol.

the class TreeLikelihoodTest method testBinaryCovarionLikelihood.

@Test
public void testBinaryCovarionLikelihood() throws Exception {
    Alignment data = BEASTTestCase.getCovarionAlignment();
    Tree tree = BEASTTestCase.getTree(data, "((English_ST:0.22743347188019544,(German_ST:0.10557648379843088,Dutch_List:0.10557648379843088):0.12185698808176457):1.5793160946109988,(Spanish:0.11078392189606047,(Italian:0.10119772534558173,French:0.10119772534558173):0.009586196550478737):1.6959656445951337)");
    RealParameter alpha = new RealParameter("0.284");
    RealParameter switchRate = new RealParameter("0.829");
    RealParameter frequencies = new RealParameter("0.683 0.317");
    RealParameter hfrequencies = new RealParameter("0.5 0.5");
    BinaryCovarion covarion = new BinaryCovarion();
    covarion.initByName("alpha", alpha, "switchRate", switchRate, "vfrequencies", frequencies, "hfrequencies", hfrequencies);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", covarion);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    likelihood.initByName("useAmbiguities", true, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    // beast1 xml gives -1730.5363
    assertEquals(logP, -1730.53631739, BEASTTestCase.PRECISION);
}

Example 3 with BinaryCovarion

use of beast.evolution.substitutionmodel.BinaryCovarion in project beast2 by CompEvol.

the class BinaryCovarionModelTest method doWithEqualHFreqs.

private void doWithEqualHFreqs(String mode) {
    Frequencies dummyFreqs = new Frequencies();
    dummyFreqs.initByName("frequencies", "0.25 0.25 0.25 0.25", "estimate", false);
    BinaryCovarion substModel;
    RealParameter hfrequencies = new RealParameter(new Double[] { 0.5, 0.5 });
    double d = Randomizer.nextDouble();
    RealParameter vfrequencies = new RealParameter(new Double[] { d, 1.0 - d });
    substModel = new BinaryCovarion();
    substModel.initByName("frequencies", dummyFreqs, "hfrequencies", hfrequencies, /* [f0, f1] */
    "vfrequencies", vfrequencies, /* [p0, p1] */
    "alpha", "0.01", "switchRate", "0.1", "mode", mode);
    double[] matrix = new double[16];
    substModel.getTransitionProbabilities(null, 100, 0, 1.0, matrix);
    double EPSILON = 1e-10;
    assertEquals(vfrequencies.getValue(0) * hfrequencies.getValue(0), matrix[0], EPSILON);
    assertEquals(vfrequencies.getValue(1) * hfrequencies.getValue(0), matrix[1], EPSILON);
    assertEquals(vfrequencies.getValue(0) * hfrequencies.getValue(1), matrix[2], EPSILON);
    assertEquals(vfrequencies.getValue(1) * hfrequencies.getValue(1), matrix[3], EPSILON);
}

Example 4 with BinaryCovarion

use of beast.evolution.substitutionmodel.BinaryCovarion in project beast2 by CompEvol.

the class BinaryCovarionModelTest method doWithTufflySteel.

private void doWithTufflySteel() {
    Frequencies dummyFreqs = new Frequencies();
    dummyFreqs.initByName("frequencies", "0.25 0.25 0.25 0.25", "estimate", false);
    BinaryCovarion substModel;
    double d = 0.05 + Randomizer.nextDouble() * 0.9;
    RealParameter vfrequencies = new RealParameter(new Double[] { d, 1.0 - d });
    RealParameter switchrate = new RealParameter(new Double[] { Randomizer.nextDouble(), Randomizer.nextDouble() });
    substModel = new BinaryCovarion();
    substModel.initByName("frequencies", dummyFreqs, "vfrequencies", vfrequencies, /* [p0, p1] */
    "alpha", "0.01", "switchRate", switchrate, // "eigenSystem", "beast.evolution.substitutionmodel.RobustEigenSystem",
    "mode", "TUFFLEYSTEEL");
    double[] matrix = new double[16];
    substModel.getTransitionProbabilities(null, 1000, 0, 1.0, matrix);
    double h0 = switchrate.getValue(1) / (switchrate.getValue(0) + switchrate.getValue(1));
    double h1 = switchrate.getValue(0) / (switchrate.getValue(0) + switchrate.getValue(1));
    double[] baseFreqs = new double[] { vfrequencies.getValue(0) * h0, vfrequencies.getValue(1) * h0, vfrequencies.getValue(0) * h1, vfrequencies.getValue(1) * h1 };
    System.err.println("Expected: " + Arrays.toString(baseFreqs));
    System.err.println("Calculat: " + Arrays.toString(matrix));
    for (int j = 0; j < 4; j++) {
        assertEquals(baseFreqs[j], matrix[j], 1e-3);
    }
}