Examples with RealParameter beast.core.parameter.RealParameter used on opensource projects

Example 66 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class UnorderedAlignmentsTest method getTree.

public static Tree getTree(TaxonSet taxa) throws Exception {
    Tree tree = new RandomTree();
    TraitSet dates = getDates(taxa);
    ConstantPopulation constant = new ConstantPopulation();
    constant.initByName("popSize", new RealParameter("5.0"));
    tree.initByName("taxonset", taxa, "populationModel", constant, "trait", dates);
    return tree;
}

Example 67 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class DeltaExchangeOperatorTest method testKeepsSum.

@Test
public void testKeepsSum() {
    DeltaExchangeOperator operator = new DeltaExchangeOperator();
    RealParameter parameter = new RealParameter(new Double[] { 1., 1., 1., 1. });
    register(operator, "parameter", parameter);
    for (int i = 0; i < 100; ++i) {
        operator.proposal();
    }
    double i = 0;
    for (Double p : parameter.getValues()) {
        i += p;
    }
    assertEquals("The DeltaExchangeOperator should not change the sum of a parameter", i, 4, 0.00001);
}

Example 68 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class DeltaExchangeOperatorTest method testCanOperate.

@Test
public void testCanOperate() {
    // Test whether a validly initialised operator may make proposals
    State state = new State();
    RealParameter parameter = new RealParameter(new Double[] { 1., 1., 1., 1. });
    state.initByName("stateNode", parameter);
    state.initialise();
    DeltaExchangeOperator d = new DeltaExchangeOperator();
    // proposals
    try {
        d.initByName("parameter", parameter);
    } catch (RuntimeException e) {
        return;
    }
    d.proposal();
}

Example 69 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class DeltaExchangeOperatorTest method testKeepsWeightedSum.

@Test
public void testKeepsWeightedSum() {
    RealParameter parameter = new RealParameter(new Double[] { 1., 1., 1., 1. });
    register(new DeltaExchangeOperator(), "weightvector", new IntegerParameter(new Integer[] { 0, 1, 2, 1 }), "parameter", parameter);
    Double[] p = parameter.getValues();
    assertEquals("The DeltaExchangeOperator should not change the sum of a parameter", 0 * p[1] + 1 * p[1] + 2 * p[2] + 1 * p[3], 4, 0.00001);
}

Example 70 with RealParameter

use of beast.core.parameter.RealParameter 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]));
        }
    }
}