Examples with BirthDeathGernhard08Model beast.evolution.speciation.BirthDeathGernhard08Model used on opensource projects

Example 1 with BirthDeathGernhard08Model

use of beast.evolution.speciation.BirthDeathGernhard08Model in project beast2 by CompEvol.

the class BirthDeathGernhard08ModelTest method testJC69Likelihood.

@Test
public void testJC69Likelihood() throws Exception {
    // Set up JC69 model: uniform freqs, kappa = 1, 0 gamma categories
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    RealParameter birthDiffRate = new RealParameter("1.0");
    RealParameter relativeDeathRate = new RealParameter("0.5");
    RealParameter originHeight = new RealParameter("0.1");
    BirthDeathGernhard08Model likelihood = new BirthDeathGernhard08Model();
    likelihood.initByName("type", "unscaled", "tree", tree, "birthDiffRate", birthDiffRate, "relativeDeathRate", relativeDeathRate);
    double logP = 0;
    // -3.520936119641363
    logP = likelihood.calculateLogP();
    assertEquals(logP, 2.5878899503981287, BEASTTestCase.PRECISION);
    likelihood.initByName("type", "timesonly", "tree", tree, "birthDiffRate", birthDiffRate, "relativeDeathRate", relativeDeathRate);
    logP = likelihood.calculateLogP();
    assertEquals(logP, 9.16714116240823, BEASTTestCase.PRECISION);
    likelihood.initByName("type", "oriented", "tree", tree, "birthDiffRate", birthDiffRate, "relativeDeathRate", relativeDeathRate);
    logP = likelihood.calculateLogP();
    assertEquals(logP, 4.379649419626184, BEASTTestCase.PRECISION);
    likelihood.initByName("type", "labeled", "tree", tree, "birthDiffRate", birthDiffRate, "relativeDeathRate", relativeDeathRate);
    logP = likelihood.calculateLogP();
    assertEquals(logP, 1.2661341104158121, BEASTTestCase.PRECISION);
    likelihood.initByName("type", "labeled", "tree", tree, "birthDiffRate", birthDiffRate, "relativeDeathRate", relativeDeathRate, "originHeight", originHeight);
    logP = likelihood.calculateLogP();
    assertEquals(logP, 8.41413452832378, BEASTTestCase.PRECISION);
}