Example 1 with NNI
use of dr.evomodel.operators.NNI in project beast-mcmc by beast-dev.
the class NNITest method getOperatorSchedule.
public OperatorSchedule getOperatorSchedule(TreeModel treeModel) {
Parameter rootParameter = treeModel.createNodeHeightsParameter(true, false, false);
Parameter internalHeights = treeModel.createNodeHeightsParameter(false, true, false);
NNI operator = new NNI(treeModel, 1.0);
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);
return schedule;
}Example 2 with NNI
use of dr.evomodel.operators.NNI in project beast-mcmc by beast-dev.
the class NNIParser method parseXMLObject.
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
return new NNI(treeModel, weight);
}Example 3 with NNI
use of dr.evomodel.operators.NNI in project beast-mcmc by beast-dev.
the class NNITest method testDoOperation.
/**
* Test method for {@link SimpleMCMCOperator#doOperation()}.
* @throws ImportException
* @throws IOException
*/
public void testDoOperation() 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);
NNI operator = new NNI(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);
}