Examples with TreeModel dr.evomodel.tree.TreeModel used on opensource projects

Example 16 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class NarrowExchangeTest method testNarrow.

/**
	 * Test method for {@link dr.evomodel.operators.ExchangeOperator#narrow()}.
	 */
public void testNarrow() throws IOException, ImportException {
    // probability of picking B node is 1/(2n-4) = 1/6
    // probability of swapping it with C is 1/1
    // total = 1/6
    System.out.println("Test 1: Forward");
    String treeMatch = "((((A,C),B),D),E);";
    int count = 0;
    int reps = 100000;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5);
        ExchangeOperator operator = new ExchangeOperator(ExchangeOperator.NARROW, treeModel, 1);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_1 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_1);
    System.out.println("Number of expected ratio:\t" + 1.0 / 6.0);
    assertExpectation(1.0 / 6.0, p_1, reps);
}

Example 17 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class OperatorAssert method irreducibilityTester.

private void irreducibilityTester(Tree tree, int numLabelledTopologies, int chainLength, int sampleTreeEvery) throws IOException, Importer.ImportException {
    MCMC mcmc = new MCMC("mcmc1");
    MCMCOptions options = new MCMCOptions(chainLength);
    TreeModel treeModel = new TreeModel("treeModel", tree);
    TreeLengthStatistic tls = new TreeLengthStatistic(TL, treeModel);
    TreeHeightStatistic rootHeight = new TreeHeightStatistic(TREE_HEIGHT, treeModel);
    OperatorSchedule schedule = getOperatorSchedule(treeModel);
    Parameter b = new Parameter.Default("b", 2.0, 0.0, Double.MAX_VALUE);
    Parameter d = new Parameter.Default("d", 0.0, 0.0, Double.MAX_VALUE);
    SpeciationModel speciationModel = new BirthDeathGernhard08Model(b, d, null, BirthDeathGernhard08Model.TreeType.UNSCALED, Units.Type.YEARS);
    Likelihood likelihood = new SpeciationLikelihood(treeModel, speciationModel, "yule.like");
    MCLogger[] loggers = new MCLogger[2];
    //        loggers[0] = new MCLogger(new ArrayLogFormatter(false), 100, false);
    //        loggers[0].add(likelihood);
    //        loggers[0].add(rootHeight);
    //        loggers[0].add(tls);
    loggers[0] = new MCLogger(new TabDelimitedFormatter(System.out), 10000, false);
    loggers[0].add(likelihood);
    loggers[0].add(rootHeight);
    loggers[0].add(tls);
    File file = new File("yule.trees");
    file.deleteOnExit();
    FileOutputStream out = new FileOutputStream(file);
    loggers[1] = new TreeLogger(treeModel, new TabDelimitedFormatter(out), sampleTreeEvery, true, true, false);
    mcmc.setShowOperatorAnalysis(true);
    mcmc.init(options, likelihood, schedule, loggers);
    mcmc.run();
    out.flush();
    out.close();
    Set<String> uniqueTrees = new HashSet<String>();
    HashMap<String, Integer> topologies = new HashMap<String, Integer>();
    HashMap<String, HashMap<String, Integer>> treeCounts = new HashMap<String, HashMap<String, Integer>>();
    NexusImporter importer = new NexusImporter(new FileReader(file));
    int sampleSize = 0;
    while (importer.hasTree()) {
        sampleSize++;
        Tree t = importer.importNextTree();
        String uniqueNewick = TreeUtils.uniqueNewick(t, t.getRoot());
        String topology = uniqueNewick.replaceAll("\\w+", "X");
        if (!uniqueTrees.contains(uniqueNewick)) {
            uniqueTrees.add(uniqueNewick);
        }
        HashMap<String, Integer> counts;
        if (topologies.containsKey(topology)) {
            topologies.put(topology, topologies.get(topology) + 1);
            counts = treeCounts.get(topology);
        } else {
            topologies.put(topology, 1);
            counts = new HashMap<String, Integer>();
            treeCounts.put(topology, counts);
        }
        if (counts.containsKey(uniqueNewick)) {
            counts.put(uniqueNewick, counts.get(uniqueNewick) + 1);
        } else {
            counts.put(uniqueNewick, 1);
        }
    }
    TestCase.assertEquals(numLabelledTopologies, uniqueTrees.size());
    TestCase.assertEquals(sampleSize, chainLength / sampleTreeEvery + 1);
    Set<String> keys = topologies.keySet();
    double ep = 1.0 / topologies.size();
    for (String topology : keys) {
        double ap = ((double) topologies.get(topology)) / (sampleSize);
        //          	assertExpectation(ep, ap, sampleSize);
        HashMap<String, Integer> counts = treeCounts.get(topology);
        Set<String> trees = counts.keySet();
        double MSE = 0;
        double ep1 = 1.0 / counts.size();
        for (String t : trees) {
            double ap1 = ((double) counts.get(t)) / (topologies.get(topology));
            //              	assertExpectation(ep1, ap1, topologies.get(topology));
            MSE += (ep1 - ap1) * (ep1 - ap1);
        }
        MSE /= counts.size();
        System.out.println("The Mean Square Error for the topolgy " + topology + " is " + MSE);
    }
}

Example 18 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class ImportancePruneAndRegraftTestProblem method testDoOperation.

/**
	 * Test method for {@link SimpleMCMCOperator#doOperation()}.
	 * @throws ImportException 
	 * @throws IOException 
	 */
public void testDoOperation() throws IOException, ImportException {
    // probability of picking (A,B) node is 1/(2n-3) = 1/7
    // probability of swapping with D is 1/2
    // total = 1/14
    //probability of picking {D} node is 1/(2n-3) = 1/7
    //probability of picking {A,B} is 1/5
    // total = 1/35
    //total = 1/14 + 1/35 = 7/70 = 0.1
    System.out.println("Test 1: Forward");
    String treeMatch = "(((D,C),(A,B)),E);";
    int count = 0;
    int reps = 1000000;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5);
        ImportancePruneAndRegraft operator = new ImportancePruneAndRegraft(treeModel, 1.0, 0);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_1 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_1);
    System.out.println("Number of expected ratio:\t" + 0.1);
    assertExpectation(0.1, p_1, reps);
    // lets see what the backward probability is for the hastings ratio
    // (((D:2.0,C:2.0):1.0,(A:1.0,B:1.0):2.0):1.0,E:4.0) -> ((((A,B),C),D),E)
    // probability of picking (A,B) node is 1/(2n-3) = 1/7
    // probability of swapping with D is 1/3
    // total = 1/21
    //probability of picking {D} node is 1/(2n-2) = 1/7
    //probability of picking {A,B} is 1/4
    // total = 1/28
    //total = 1/21 + 1/28 = 7/84 = 0.08333333
    System.out.println("Test 2: Backward");
    treeMatch = "((((A,B),C),D),E);";
    NewickImporter importer = new NewickImporter("(((D:2.0,C:2.0):1.0,(A:1.0,B:1.0):2.0):1.0,E:4.0);");
    FlexibleTree tree5_2 = (FlexibleTree) importer.importTree(null);
    count = 0;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5_2);
        ImportancePruneAndRegraft operator = new ImportancePruneAndRegraft(treeModel, 1.0, 1);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_2 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_2);
    System.out.println("Number of expected ratio:\t" + 0.0833333);
    assertExpectation(0.0833333, p_2, reps);
}

Example 19 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class ImportanceSubtreeSwapTestProblem method testDoOperation.

/**
	 * Test method for {@link SimpleMCMCOperator#doOperation()}.
	 * @throws ImportException 
	 * @throws IOException 
	 */
public void testDoOperation() throws IOException, ImportException {
    // probability of picking (A,B) node is 1/(2n-3) = 1/7
    // probability of swapping with D is 1/2
    // total = 1/14
    //probability of picking {D} node is 1/(2n-3) = 1/7
    //probability of picking {A,B} is 1/5
    // total = 1/35
    //total = 1/14 + 1/35 = 7/70 = 0.1
    System.out.println("Test 1: Forward");
    String treeMatch = "(((D,C),(A,B)),E);";
    int count = 0;
    int reps = 100000;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5);
        ImportanceSubtreeSwap operator = new ImportanceSubtreeSwap(treeModel, 1.0, 0);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_1 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_1);
    System.out.println("Number of expected ratio:\t" + 0.1);
    assertExpectation(0.1, p_1, reps);
    // lets see what the backward probability is for the hastings ratio
    // (((D:2.0,C:2.0):1.0,(A:1.0,B:1.0):2.0):1.0,E:4.0) -> ((((A,B),C),D),E)
    // probability of picking (A,B) node is 1/(2n-3) = 1/7
    // probability of swapping with D is 1/3
    // total = 1/21
    //probability of picking {D} node is 1/(2n-2) = 1/7
    //probability of picking {A,B} is 1/4
    // total = 1/28
    //total = 1/21 + 1/28 = 7/84 = 0.08333333
    System.out.println("Test 2: Backward");
    treeMatch = "((((A,B),C),D),E);";
    NewickImporter importer = new NewickImporter("(((D:2.0,C:2.0):1.0,(A:1.0,B:1.0):2.0):1.0,E:4.0);");
    FlexibleTree tree5_2 = (FlexibleTree) importer.importTree(null);
    count = 0;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5_2);
        ImportanceSubtreeSwap operator = new ImportanceSubtreeSwap(treeModel, 1.0, 0);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_2 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_2);
    System.out.println("Number of expected ratio:\t" + 0.0833333);
    assertExpectation(0.0833333, p_2, reps);
}

Example 20 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class BeagleSeqSimTest method simulateTwoPartitions.

// END: simulateOnePartition
static void simulateTwoPartitions() {
    try {
        System.out.println("Test case 3: simulateTwoPartitions");
        MathUtils.setSeed(666);
        int sequenceLength = 11;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        // create tree
        NewickImporter importer = new NewickImporter("(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981);");
        Tree tree = importer.importTree(null);
        TreeModel treeModel = new TreeModel(tree);
        // create Frequency Model
        Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
        FrequencyModel freqModel = new FrequencyModel(Nucleotides.INSTANCE, freqs);
        // create substitution model
        Parameter kappa = new Parameter.Default(1, 10);
        HKY hky = new HKY(kappa, freqModel);
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(hky);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        0, // to
        3, // every
        1);
        // create partition
        Partition Partition = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        4, // to
        sequenceLength - 1, // every
        1);
        Sequence ancestralSequence = new Sequence();
        ancestralSequence.appendSequenceString("TCAAGTG");
        Partition.setRootSequence(ancestralSequence);
        partitionsList.add(partition1);
        partitionsList.add(Partition);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        System.out.println(simulator.simulate(simulateInPar, false).toString());
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch block
}