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

Example 6 with BooleanParameter

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

the class CompoundPopulationFunction method prepare.

// why do we need this additional level on top of initAndValidate - does not seem to do anything?
@Override
public void prepare() {
    getParams();
    // is that safe???
    trees = treesInput.get();
    useMid = useMiddleInput.get();
    // used to work without upper case ???
    // errors?
    type = Type.valueOf(demographicTypeInput.get().toUpperCase());
    // set lengths
    int events = 0;
    for (TreeIntervals ti : trees) {
        // number of coalescent events
        events += ti.treeInput.get().getLeafNodeCount() - 1;
    }
    // all trees share time 0, need fixing for serial data
    events += type == Type.STEPWISE ? 0 : 1;
    try {
        if (popSizeParameter.getDimension() != events) {
            final RealParameter p = new RealParameter();
            p.initByName("value", popSizeParameter.getValue() + "", "upper", popSizeParameter.getUpper(), "lower", popSizeParameter.getLower(), "dimension", events);
            p.setID(popSizeParameter.getID());
            popSizeParameter.assignFromWithoutID(p);
        }
        if (indicatorsParameter.getDimension() != events - 1) {
            final BooleanParameter p = new BooleanParameter();
            p.initByName("value", "" + indicatorsParameter.getValue(), "dimension", events - 1);
            p.setID(indicatorsParameter.getID());
            indicatorsParameter.assignFrom(p);
        }
    } catch (Exception e) {
        // what to do?
        e.printStackTrace();
    }
    initInternals();
    for (int nt = 0; nt < trees.size(); ++nt) {
        setTreeTimes(nt);
    }
    mergeTreeTimes();
    setDemographicArrays();
    shadow = new Shadow();
}

Example 7 with BooleanParameter

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

the class SampleOffValues method proposal.

@Override
public double proposal() {
    final BooleanParameter indicators = indicatorsInput.get(this);
    final RealParameter data = valuesInput.get(this);
    final ParametricDistribution distribution = distInput.get();
    final int idim = indicators.getDimension();
    final int offset = (data.getDimension() - 1) == idim ? 1 : 0;
    assert offset == 1 || data.getDimension() == idim : "" + idim + " (?+1) != " + data.getDimension();
    double hr = Double.NEGATIVE_INFINITY;
    if (scaleAll.get()) {
        for (int i = offset; i < idim; ++i) {
            if (!indicators.getValue(i - offset)) {
                try {
                    final double val = distribution.inverseCumulativeProbability(Randomizer.nextDouble());
                    hr += distribution.logDensity(data.getValue(i));
                    data.setValue(i, val);
                } catch (Exception e) {
                    // some distributions fail on extreme values - currently gamma
                    return Double.NEGATIVE_INFINITY;
                }
            }
        }
    } else {
        // available locations for direct sampling
        int[] loc = new int[idim];
        int locIndex = 0;
        for (int i = 0; i < idim; ++i) {
            if (!indicators.getValue(i)) {
                loc[locIndex] = i + offset;
                ++locIndex;
            }
        }
        if (locIndex > 0) {
            final int index = loc[Randomizer.nextInt(locIndex)];
            try {
                final double val = distribution.inverseCumulativeProbability(Randomizer.nextDouble());
                hr = distribution.logDensity(data.getValue(index));
                data.setValue(index, val);
            } catch (Exception e) {
                // some distributions fail on extreme values - currently gamma
                return Double.NEGATIVE_INFINITY;
            // throw new OperatorFailedException(e.getMessage());
            }
        } else {
        // no non-active indicators
        // return Double.NEGATIVE_INFINITY;
        }
    }
    return hr;
}

Example 8 with BooleanParameter

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

the class Sum method initAndValidate.

@Override
public void initAndValidate() {
    List<Function> valuable = functionInput.get();
    mode = Mode.integer_mode;
    for (Function v : valuable) {
        if (!(v instanceof IntegerParameter || v instanceof BooleanParameter)) {
            mode = Mode.double_mode;
        }
    }
}

Example 9 with BooleanParameter

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

the class RandomLocalClockModel method initAndValidate.

@Override
public void initAndValidate() {
    m_tree = treeInput.get();
    BooleanParameter indicators = indicatorParamInput.get();
    if (indicators.getDimension() != m_tree.getNodeCount() - 1) {
        Log.warning.println("RandomLocalClockModel::Setting dimension of indicators to " + (m_tree.getNodeCount() - 1));
        indicators.setDimension(m_tree.getNodeCount() - 1);
    }
    unscaledBranchRates = new double[m_tree.getNodeCount()];
    RealParameter rates = rateParamInput.get();
    if (rates.lowerValueInput.get() == null || rates.lowerValueInput.get() < 0.0) {
        rates.setLower(0.0);
    }
    if (rates.upperValueInput.get() == null || rates.upperValueInput.get() < 0.0) {
        rates.setUpper(Double.MAX_VALUE);
    }
    if (rates.getDimension() != m_tree.getNodeCount() - 1) {
        Log.warning.println("RandomLocalClockModel::Setting dimension of rates to " + (m_tree.getNodeCount() - 1));
        rates.setDimension(m_tree.getNodeCount() - 1);
    }
    ratesAreMultipliers = ratesAreMultipliersInput.get();
    meanRate = meanRateInput.get();
    if (meanRate == null) {
        meanRate = new RealParameter("1.0");
    }
}

Example 10 with BooleanParameter

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

the class BooleanParameterListTest method test1.

@Test
public void test1() throws Exception {
    BooleanParameterList parameterList = new BooleanParameterList();
    // Parameters with which to initialise list
    BooleanParameter param1 = new BooleanParameter();
    param1.initByName("value", "true false true");
    BooleanParameter param2 = new BooleanParameter();
    param2.initByName("value", "false true false");
    // Initialise parameter list
    parameterList.initByName("dimension", 3, "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(0, false);
    // Test parameter creation and modification
    Parameter<Boolean> newParam = parameterList.addNewParam();
    newParam.setValue(0, true);
    newParam.setValue(1, true);
    newParam.setValue(2, true);
    assertTrue(parameterList.get(0).getValue(0) == false);
    assertTrue(parameterList.get(0).getValue(1) == false);
    assertTrue(parameterList.get(0).getValue(2) == true);
    assertTrue(parameterList.get(0).getKey() == 0);
    assertTrue(parameterList.get(1).getValue(0) == false);
    assertTrue(parameterList.get(1).getValue(1) == true);
    assertTrue(parameterList.get(1).getValue(2) == false);
    assertTrue(parameterList.get(1).getKey() == 1);
    assertTrue(parameterList.get(2).getValue(0) == true);
    assertTrue(parameterList.get(2).getValue(1) == true);
    assertTrue(parameterList.get(2).getValue(2) == true);
    assertTrue(parameterList.get(2).getKey() == 2);
    assertTrue(parameterList.size() == 3);
    parameterList.remove(1);
    newParam = parameterList.addNewParam();
    newParam.setValue(0, false);
    newParam.setValue(1, false);
    newParam.setValue(2, false);
    assertTrue(parameterList.get(0).getValue(0) == false);
    assertTrue(parameterList.get(0).getValue(1) == false);
    assertTrue(parameterList.get(0).getValue(2) == true);
    assertTrue(parameterList.get(0).getKey() == 0);
    assertTrue(parameterList.get(1).getValue(0) == true);
    assertTrue(parameterList.get(1).getValue(1) == true);
    assertTrue(parameterList.get(1).getValue(2) == true);
    assertTrue(parameterList.get(1).getKey() == 2);
    assertTrue(parameterList.get(2).getValue(0) == false);
    assertTrue(parameterList.get(2).getValue(1) == false);
    assertTrue(parameterList.get(2).getValue(2) == false);
    assertTrue(parameterList.get(2).getKey() == 1);
    assertTrue(parameterList.size() == 3);
    // Test state restore
    parameterList.restore();
    assertTrue(parameterList.get(0).getValue(0) == true);
    assertTrue(parameterList.get(0).getValue(1) == false);
    assertTrue(parameterList.get(0).getValue(2) == true);
    assertTrue(parameterList.get(0).getKey() == 0);
    assertTrue(parameterList.get(1).getValue(0) == false);
    assertTrue(parameterList.get(1).getValue(1) == true);
    assertTrue(parameterList.get(1).getValue(2) == false);
    assertTrue(parameterList.get(1).getKey() == 1);
    assertTrue(parameterList.size() == 2);
    // Test serialization
    parameterList.addNewParam(newParam);
    String xmlStr = parameterList.toXML();
    assertEquals(xmlStr, "<statenode id='null'>" + "Dimension: [3, 1], " + "Bounds: [false,true], " + "AvailableKeys: [], " + "NextKey: 3, " + "Parameters: [[true,false,true],[false,true,false],[false,false,false]], " + "ParameterKeys: [0,1,2]" + "</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);
    BooleanParameterList newParameterList = new BooleanParameterList();
    newParameterList.initAndValidate();
    newParameterList.fromXML(docNode);
    assertTrue(newParameterList.get(0).getValue(0) == true);
    assertTrue(newParameterList.get(0).getValue(1) == false);
    assertTrue(newParameterList.get(0).getValue(2) == true);
    assertTrue(newParameterList.get(0).getKey() == 0);
    assertTrue(newParameterList.get(1).getValue(0) == false);
    assertTrue(newParameterList.get(1).getValue(1) == true);
    assertTrue(newParameterList.get(1).getValue(2) == false);
    assertTrue(newParameterList.get(1).getKey() == 1);
    assertTrue(newParameterList.get(2).getValue(0) == false);
    assertTrue(newParameterList.get(2).getValue(1) == false);
    assertTrue(newParameterList.get(2).getValue(2) == false);
    assertTrue(newParameterList.get(2).getKey() == 2);
    assertTrue(newParameterList.size() == 3);
}