Examples with SiteModel beast.evolution.sitemodel.SiteModel used on opensource projects

Example 36 with SiteModel

use of beast.evolution.sitemodel.SiteModel in project beast2 by CompEvol.

the class TreeLikelihoodTest method testSDolloLikelihood.

@Test
public void testSDolloLikelihood() throws Exception {
    UserDataType dataType = new UserDataType();
    dataType.initByName("states", 2, "codeMap", "0=1, 1=0, ?=0 1, -=0 1");
    Alignment data = new Alignment();
    Sequence German_ST = new Sequence("German_ST", BEASTTestCase.German_ST.dataInput.get());
    Sequence Dutch_List = new Sequence("Dutch_List", BEASTTestCase.Dutch_List.dataInput.get());
    ;
    Sequence English_ST = new Sequence("English_ST", BEASTTestCase.English_ST.dataInput.get());
    ;
    Sequence French = new Sequence("French", BEASTTestCase.French.dataInput.get());
    ;
    Sequence Italian = new Sequence("Italian", BEASTTestCase.Italian.dataInput.get());
    ;
    Sequence Spanish = new Sequence("Spanish", BEASTTestCase.Spanish.dataInput.get());
    ;
    data.initByName("sequence", German_ST, "sequence", Dutch_List, "sequence", English_ST, "sequence", French, "sequence", Italian, "sequence", Spanish, "userDataType", dataType);
    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 frequencies = new RealParameter("1 0");
    Frequencies freqs = new Frequencies();
    freqs.initByName("frequencies", frequencies);
    RealParameter deathprob = new RealParameter("1.7");
    MutationDeathModel SDollo = new MutationDeathModel();
    SDollo.initByName("deathprob", deathprob, "frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", SDollo);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel, "useAmbiguities", true);
    logP = likelihood.calculateLogP();
    // beast1 xml gives -3551.6436
    assertEquals(logP, -3551.6436270344648, BEASTTestCase.PRECISION);
}

Example 37 with SiteModel

use of beast.evolution.sitemodel.SiteModel in project beast2 by CompEvol.

the class TreeLikelihoodTest 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);
    JukesCantor JC = new JukesCantor();
    JC.initAndValidate();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", JC);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1992.2056440317247, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", true, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1992.2056440317247, BEASTTestCase.PRECISION);
}

Example 38 with SiteModel

use of beast.evolution.sitemodel.SiteModel in project beast2 by CompEvol.

the class TreeLikelihoodTest method testJC69Likelihood.

public double[] testJC69Likelihood(Alignment data, Tree tree) throws Exception {
    // Set up JC69 model: uniform freqs, kappa = 1, 0 gamma categories
    JukesCantor JC = new JukesCantor();
    JC.initAndValidate();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "0.6", "substModel", JC);
    // NB The rate in the JC model used here is actually alpha * 3 in the usual sense, because
    // it's divided by 3 before multiplying in the exponent (not sure why)
    System.out.println("Without tip likelihoods:");
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel, "scaling", TreeLikelihood.Scaling.none);
    double[] logP = new double[2];
    logP[0] = likelihood.calculateLogP();
    System.out.println(logP[0]);
    System.out.println("With tip likelihoods:");
    likelihood.initByName("useTipLikelihoods", true, "data", data, "tree", tree, "siteModel", siteModel, "scaling", TreeLikelihood.Scaling.none);
    logP[1] = likelihood.calculateLogP();
    System.out.println(logP[1]);
    return logP;
}

Example 39 with SiteModel

use of beast.evolution.sitemodel.SiteModel in project beast2 by CompEvol.

the class TreeLikelihoodTest method testGTRLikelihood.

@Test
public void testGTRLikelihood() throws Exception {
    // Set up GTR model: no gamma categories, no proportion invariant
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data);
    GTR gsm = new GTR();
    gsm.initByName("frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", gsm);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1969.145839307625, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", false, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1969.145839307625, BEASTTestCase.PRECISION);
}

Example 40 with SiteModel

use of beast.evolution.sitemodel.SiteModel 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);
}