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

Example 11 with Frequencies

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

the class TreeLikelihoodTest method testGTRGLikelihood.

@Test
public void testGTRGLikelihood() throws Exception {
    // Set up GTR model: 4 gamma categories, gamma shape = 0.5
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data);
    GeneralSubstitutionModel gsm = new GeneralSubstitutionModel();
    gsm.initByName("rates", "1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0", "frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 4, "shape", "0.5", "substModel", gsm);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1949.0360143622, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", false, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1949.0360143622, BEASTTestCase.PRECISION);
}

Example 12 with Frequencies

use of beast.evolution.substitutionmodel.Frequencies 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 13 with Frequencies

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

the class HKYTest method testHKY.

public void testHKY() throws Exception {
    for (Instance test : all) {
        RealParameter f = new RealParameter(test.getPi());
        Frequencies freqs = new Frequencies();
        freqs.initByName("frequencies", f, "estimate", false);
        HKY hky = new HKY();
        hky.initByName("kappa", test.getKappa().toString(), "frequencies", freqs);
        double distance = test.getDistance();
        double[] mat = new double[4 * 4];
        hky.getTransitionProbabilities(null, distance, 0, 1, mat);
        final double[] result = test.getExpectedResult();
        for (int k = 0; k < mat.length; ++k) {
            assertEquals(mat[k], result[k], 1e-10);
            System.out.println(k + " : " + (mat[k] - result[k]));
        }
    }
}

Example 14 with Frequencies

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

the class GTRTest method testGTR.

public void testGTR() throws Exception {
    for (Instance test : all) {
        RealParameter f = new RealParameter(test.getPi());
        Frequencies freqs = new Frequencies();
        freqs.initByName("frequencies", f, "estimate", false);
        GTR gtr = new GTR();
        Double[] rates = test.getRates();
        gtr.initByName("rateAC", new RealParameter(rates[0] + ""), "rateAG", new RealParameter(rates[1] + ""), "rateAT", new RealParameter(rates[2] + ""), "rateCG", new RealParameter(rates[3] + ""), "rateCT", new RealParameter(rates[4] + ""), "rateGT", new RealParameter(rates[5] + ""), "frequencies", freqs);
        double distance = test.getDistance();
        double[] mat = new double[4 * 4];
        gtr.getTransitionProbabilities(null, distance, 0, 1, mat);
        final double[] result = test.getExpectedResult();
        for (int k = 0; k < mat.length; ++k) {
            assertEquals(mat[k], result[k], 1e-10);
            System.out.println(k + " : " + (mat[k] - result[k]));
        }
    }
}

Example 15 with Frequencies

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

the class FrequenciesInputEditor method addComboBox.

// init
@Override
protected /**
 * suppress combobox *
 */
void addComboBox(JComponent box, Input<?> input, BEASTInterface beastObject) {
    Frequencies freqs = (Frequencies) input.get();
    JComboBox<String> comboBox = new JComboBox<>(new String[] { "Estimated", "Empirical", "All equal" });
    if (freqs.frequenciesInput.get() != null) {
        comboBox.setSelectedIndex(0);
        freqsParameter = freqs.frequenciesInput.get();
        alignment = (Alignment) getCandidate(freqs.dataInput, freqs);
    } else if (freqs.estimateInput.get()) {
        comboBox.setSelectedIndex(1);
        alignment = freqs.dataInput.get();
        freqsParameter = (RealParameter) getCandidate(freqs.frequenciesInput, freqs);
    } else {
        comboBox.setSelectedIndex(2);
        alignment = freqs.dataInput.get();
        freqsParameter = (RealParameter) getCandidate(freqs.frequenciesInput, freqs);
    }
    comboBox.addActionListener(e -> {
        // @SuppressWarnings("unchecked")
        // JComboBox<String> comboBox = (JComboBox<String>) e.getSource();
        int selected = comboBox.getSelectedIndex();
        // Frequencies freqs = (Frequencies) m_input.get();
        try {
            switch(selected) {
                case 0:
                    freqs.frequenciesInput.setValue(freqsParameter, freqs);
                    freqs.dataInput.setValue(null, freqs);
                    break;
                case 1:
                    freqs.frequenciesInput.setValue(null, freqs);
                    freqs.dataInput.setValue(alignment, freqs);
                    freqs.estimateInput.setValue(true, freqs);
                    break;
                case 2:
                    freqs.frequenciesInput.setValue(null, freqs);
                    freqs.dataInput.setValue(alignment, freqs);
                    freqs.estimateInput.setValue(false, freqs);
                    break;
            }
        } catch (Exception e2) {
            e2.printStackTrace();
        }
    // System.err.println(freqs.frequencies.get() + " " + freqs.m_data.get() + " " + freqs.m_bEstimate.get());
    });
    box.add(comboBox);
}