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

Example 21 with Frequencies

use of beast.evolution.substitutionmodel.Frequencies 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);
    }
}