Examples with IntegerParameter beast.core.parameter.IntegerParameter used on opensource projects

Example 21 with IntegerParameter

use of beast.core.parameter.IntegerParameter in project MultiTypeTree by tgvaughan.

the class TWB_TS_Test method test1.

@Test
public void test1() throws Exception {
    System.out.println("TWB_test 1");
    // Fix seed.
    Randomizer.setSeed(42);
    // Assemble initial MultiTypeTree
    String newickStr = "((1[&deme=0]:1,2[&deme=0]:1)[&deme=0]:1," + "3[&deme=0]:2)[&deme=0]:0;";
    MultiTypeTreeFromNewick mtTree = new MultiTypeTreeFromNewick();
    mtTree.initByName("value", newickStr, "typeLabel", "deme");
    // Assemble migration model:
    RealParameter rateMatrix = new RealParameter("0.1 0.1");
    RealParameter popSizes = new RealParameter("7.0 7.0");
    SCMigrationModel migModel = new SCMigrationModel();
    migModel.initByName("rateMatrix", rateMatrix, "popSizes", popSizes, "typeSet", new TypeSet("A", "B"));
    // Assemble distribution:
    StructuredCoalescentTreeDensity distribution = new StructuredCoalescentTreeDensity();
    distribution.initByName("migrationModel", migModel, "multiTypeTree", mtTree);
    // Set up state:
    State state = new State();
    state.initByName("stateNode", mtTree);
    // Set up operator:
    TypedWilsonBalding operatorTWB = new TypedWilsonBalding();
    operatorTWB.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel, "alpha", 0.2);
    Operator operatorMTTS = new MultiTypeTreeScale();
    operatorMTTS.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel, "scaleFactor", 0.8, "useOldTreeScaler", false);
    // Set up stat analysis logger:
    MultiTypeTreeStatLogger logger = new MultiTypeTreeStatLogger();
    logger.initByName("multiTypeTree", mtTree, "burninFrac", 0.2, "logEvery", 1000);
    // Set up MCMC:
    MCMC mcmc = new MCMC();
    mcmc.initByName("chainLength", "1000000", "state", state, "distribution", distribution, "operator", operatorTWB, "operator", operatorMTTS, "logger", logger);
    // Run MCMC:
    mcmc.run();
    System.out.format("height mean = %s\n", logger.getHeightMean());
    System.out.format("height var = %s\n", logger.getHeightVar());
    System.out.format("height ESS = %s\n", logger.getHeightESS());
    // Direct simulation:
    double[] heights = UtilMethods.getSimulatedHeights(migModel, new IntegerParameter("0 0 0"));
    double simHeightMean = DiscreteStatistics.mean(heights);
    double simHeightVar = DiscreteStatistics.variance(heights);
    // Compare results with simulation results:
    boolean withinTol = (logger.getHeightESS() > 400) && (Math.abs(logger.getHeightMean() - simHeightMean) < 1.0) && (Math.abs(logger.getHeightVar() - simHeightVar) < 30);
    Assert.assertTrue(withinTol);
}

Example 22 with IntegerParameter

use of beast.core.parameter.IntegerParameter in project MultiTypeTree by tgvaughan.

the class TWB_TS_Test method testTWB2.

@Test
public void testTWB2() throws Exception {
    System.out.println("TWB_test 2");
    // Fix seed.
    Randomizer.setSeed(42);
    // Assemble initial MultiTypeTree
    String newickStr = "((1[&deme=1]:1,2[&deme=0]:1)[&deme=0]:1," + "3[&deme=0]:2)[&deme=0]:0;";
    MultiTypeTreeFromNewick mtTree = new MultiTypeTreeFromNewick();
    mtTree.initByName("value", newickStr, "typeLabel", "deme");
    // Assemble migration model:
    RealParameter rateMatrix = new RealParameter("0.1 0.1");
    RealParameter popSizes = new RealParameter("7.0 7.0");
    SCMigrationModel migModel = new SCMigrationModel();
    migModel.initByName("rateMatrix", rateMatrix, "popSizes", popSizes, "typeSet", new TypeSet("A", "B"));
    // Assemble distribution:
    StructuredCoalescentTreeDensity distribution = new StructuredCoalescentTreeDensity();
    distribution.initByName("migrationModel", migModel, "multiTypeTree", mtTree);
    // Set up state:
    State state = new State();
    state.initByName("stateNode", mtTree);
    // Set up operator:
    TypedWilsonBalding operatorTWB = new TypedWilsonBalding();
    operatorTWB.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel, "alpha", 0.2);
    Operator operatorMTTS = new MultiTypeTreeScale();
    operatorMTTS.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel, "scaleFactor", 0.8, "useOldTreeScaler", false);
    // Set up stat analysis logger:
    MultiTypeTreeStatLogger logger = new MultiTypeTreeStatLogger();
    logger.initByName("multiTypeTree", mtTree, "burninFrac", 0.1, "logEvery", 1000);
    // Set up MCMC:
    MCMC mcmc = new MCMC();
    mcmc.initByName("chainLength", "1000000", "state", state, "distribution", distribution, "operator", operatorTWB, "logger", logger);
    // Run MCMC:
    mcmc.run();
    System.out.format("height mean = %s\n", logger.getHeightMean());
    System.out.format("height var = %s\n", logger.getHeightVar());
    System.out.format("height ESS = %s\n", logger.getHeightESS());
    // Direct simulation:
    double[] heights = UtilMethods.getSimulatedHeights(migModel, new IntegerParameter("1 0 0"));
    double simHeightMean = DiscreteStatistics.mean(heights);
    double simHeightVar = DiscreteStatistics.variance(heights);
    // Compare analysis results with truth:
    boolean withinTol = (logger.getHeightESS() > 400) && (Math.abs(logger.getHeightMean() - simHeightMean) < 1.0) && (Math.abs(logger.getHeightVar() - simHeightVar) < 30);
    Assert.assertTrue(withinTol);
}

Example 23 with IntegerParameter

use of beast.core.parameter.IntegerParameter in project MultiTypeTree by tgvaughan.

the class SCSimTest method test.

@Test
public void test() throws Exception {
    System.out.println("SCSim test");
    Randomizer.setSeed(42);
    // Set up migration model.
    RealParameter rateMatrix = new RealParameter();
    rateMatrix.initByName("dimension", 2, "value", "0.1 0.1");
    RealParameter popSizes = new RealParameter();
    popSizes.initByName("value", "7.0 7.0");
    SCMigrationModel migrationModel = new SCMigrationModel();
    migrationModel.initByName("rateMatrix", rateMatrix, "popSizes", popSizes, "typeSet", new TypeSet("A", "B"));
    // Specify leaf types:
    IntegerParameter leafTypes = new IntegerParameter();
    leafTypes.initByName("value", "0 0 0");
    // Generate ensemble:
    int reps = 100000;
    double[] heights = new double[reps];
    for (int i = 0; i < reps; i++) {
        beast.evolution.tree.StructuredCoalescentMultiTypeTree sctree;
        sctree = new beast.evolution.tree.StructuredCoalescentMultiTypeTree();
        sctree.initByName("migrationModel", migrationModel, "leafTypes", leafTypes);
        heights[i] = sctree.getRoot().getHeight();
    }
    double meanHeights = DiscreteStatistics.mean(heights);
    double varHeights = DiscreteStatistics.variance(heights);
    boolean withinTol = (Math.abs(meanHeights - 19.2) < 0.2) && (Math.abs(varHeights - 310) < 20);
    Assert.assertTrue(withinTol);
}

Example 24 with IntegerParameter

use of beast.core.parameter.IntegerParameter in project beast2 by CompEvol.

the class BayesianSkyline method initAndValidate.

// /**
// * This pseudo-constructor is only used for junit tests
// *
// * @param populationSize
// * @param groupSizes
// * @param tree
// */
// public void init(RealParameter populationSize, IntegerParameter
// groupSizes, Tree tree) {
// super.init(populationSize, groupSizes, tree);
// }
@Override
public void initAndValidate() {
    if (treeInput.get() != null) {
        throw new IllegalArgumentException("only tree intervals (not tree) should not be specified");
    }
    intervals = treeIntervalsInput.get();
    groupSizes = groupSizeParamInput.get();
    popSizes = popSizeParamInput.get();
    // make sure that the sum of groupsizes == number of coalescent events
    int events = intervals.treeInput.get().getInternalNodeCount();
    if (groupSizes.getDimension() > events) {
        throw new IllegalArgumentException("There are more groups than coalescent nodes in the tree.");
    }
    int paramDim2 = groupSizes.getDimension();
    int eventsCovered = 0;
    for (int i = 0; i < groupSizes.getDimension(); i++) {
        eventsCovered += groupSizes.getValue(i);
    }
    if (eventsCovered != events) {
        if (eventsCovered == 0 || eventsCovered == paramDim2) {
            // double[] uppers = new double[paramDim2];
            // double[] lowers = new double[paramDim2];
            // For these special cases we assume that the XML has not
            // specified initial group sizes
            // or has set all to 1 and we set them here automatically...
            int eventsEach = events / paramDim2;
            int eventsExtras = events % paramDim2;
            Integer[] values = new Integer[paramDim2];
            for (int i = 0; i < paramDim2; i++) {
                if (i < eventsExtras) {
                    values[i] = eventsEach + 1;
                } else {
                    values[i] = eventsEach;
                }
            // uppers[i] = Double.MAX_VALUE;
            // lowers[i] = 1.0;
            }
            // if (type == EXPONENTIAL_TYPE || type == LINEAR_TYPE) {
            // lowers[0] = 2.0;
            // }
            IntegerParameter parameter = new IntegerParameter(values);
            parameter.setBounds(1, Integer.MAX_VALUE);
            groupSizes.assignFromWithoutID(parameter);
        } else {
            // initial group sizes.
            throw new IllegalArgumentException("The sum of the initial group sizes does not match the number of coalescent events in the tree.");
        }
    }
    prepare();
}

Example 25 with IntegerParameter

use of beast.core.parameter.IntegerParameter in project beast2 by CompEvol.

the class IntegerParameterListTest method test1.

@Test
public void test1() throws Exception {
    IntegerParameterList parameterList = new IntegerParameterList();
    // Parameters with which to initialise list
    IntegerParameter param1 = new IntegerParameter();
    param1.initByName("value", "2");
    IntegerParameter param2 = new IntegerParameter();
    param2.initByName("value", "3");
    // Initialise parameter list
    parameterList.initByName("initialParam", param1, "initialParam", param2);
    // Create dummy state to allow statenode editing
    State state = new State();
    state.initByName("stateNode", parameterList);
    state.initialise();
    // Test parameter value modification
    parameterList.get(0).setValue(20);
    // Test parameter creation and modification
    Parameter<Integer> newParam = parameterList.addNewParam();
    newParam.setValue(53);
    assertTrue(parameterList.get(0).getValue() == 20);
    assertTrue(parameterList.get(0).getKey() == 0);
    assertTrue(parameterList.get(1).getValue() == 3);
    assertTrue(parameterList.get(1).getKey() == 1);
    assertTrue(parameterList.get(2).getValue() == 53);
    assertTrue(parameterList.get(2).getKey() == 2);
    assertTrue(parameterList.size() == 3);
    parameterList.remove(1);
    newParam = parameterList.addNewParam();
    newParam.setValue(42);
    assertTrue(parameterList.get(0).getValue() == 20);
    assertTrue(parameterList.get(0).getKey() == 0);
    assertTrue(parameterList.get(1).getValue() == 53);
    assertTrue(parameterList.get(1).getKey() == 2);
    assertTrue(parameterList.get(2).getValue() == 42);
    assertTrue(parameterList.get(2).getKey() == 1);
    assertTrue(parameterList.size() == 3);
    // Test state restore
    parameterList.restore();
    assertTrue(parameterList.get(0).getValue() == 2);
    assertTrue(parameterList.get(0).getKey() == 0);
    assertTrue(parameterList.get(1).getValue() == 3);
    assertTrue(parameterList.get(1).getKey() == 1);
    assertTrue(parameterList.size() == 2);
    // Test serialization
    String xmlStr = parameterList.toXML();
    assertEquals(xmlStr, "<statenode id='null'>" + "Dimension: [1, 1], " + "Bounds: [-2147483647,2147483646], " + "AvailableKeys: [], " + "NextKey: 2, " + "Parameters: [[2],[3]], " + "ParameterKeys: [0,1]" + "</statenode>\n");
    // Test deserialization
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    Document doc = factory.newDocumentBuilder().parse(new ByteArrayInputStream(xmlStr.getBytes()));
    doc.normalize();
    NodeList nodes = doc.getElementsByTagName("*");
    org.w3c.dom.Node docNode = nodes.item(0);
    IntegerParameterList newParameterList = new IntegerParameterList();
    newParameterList.initAndValidate();
    newParameterList.fromXML(docNode);
    assertTrue(newParameterList.get(0).getValue() == 2);
    assertTrue(newParameterList.get(0).getKey() == 0);
    assertTrue(newParameterList.get(1).getValue() == 3);
    assertTrue(newParameterList.get(1).getKey() == 1);
    assertTrue(newParameterList.size() == 2);
}