Examples with ImportancePruneAndRegraft dr.evomodel.operators.ImportancePruneAndRegraft used on opensource projects

Example 1 with ImportancePruneAndRegraft

use of dr.evomodel.operators.ImportancePruneAndRegraft 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 2 with ImportancePruneAndRegraft

use of dr.evomodel.operators.ImportancePruneAndRegraft in project beast-mcmc by beast-dev.

the class ImportancePruneAndRegraftParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    int samples = xo.getIntegerAttribute("samples");
    return new ImportancePruneAndRegraft(treeModel, weight, samples);
}

Example 3 with ImportancePruneAndRegraft

use of dr.evomodel.operators.ImportancePruneAndRegraft in project beast-mcmc by beast-dev.

the class ImportancePruneAndRegraftTestProblem method getOperatorSchedule.

public OperatorSchedule getOperatorSchedule(TreeModel treeModel) {
    Parameter rootParameter = treeModel.createNodeHeightsParameter(true, false, false);
    Parameter internalHeights = treeModel.createNodeHeightsParameter(false, true, false);
    ImportancePruneAndRegraft operator = new ImportancePruneAndRegraft(treeModel, 1.0, 1);
    ScaleOperator scaleOperator = new ScaleOperator(rootParameter, 0.75, CoercionMode.COERCION_ON, 1.0);
    UniformOperator uniformOperator = new UniformOperator(internalHeights, 1.0);
    OperatorSchedule schedule = new SimpleOperatorSchedule();
    schedule.addOperator(operator);
    schedule.addOperator(scaleOperator);
    schedule.addOperator(uniformOperator);
    return schedule;
}