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

Example 26 with IntegerParameter

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

the class DeltaExchangeOperatorTest method testKeepsWeightedSum.

@Test
public void testKeepsWeightedSum() {
    RealParameter parameter = new RealParameter(new Double[] { 1., 1., 1., 1. });
    register(new DeltaExchangeOperator(), "weightvector", new IntegerParameter(new Integer[] { 0, 1, 2, 1 }), "parameter", parameter);
    Double[] p = parameter.getValues();
    assertEquals("The DeltaExchangeOperator should not change the sum of a parameter", 0 * p[1] + 1 * p[1] + 2 * p[2] + 1 * p[3], 4, 0.00001);
}

Example 27 with IntegerParameter

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

the class IntRandomWalkOperatorTest method instantiate.

public void instantiate(int dimension, int upper, int runs, Integer[] windowSizes) {
    for (int r = 0; r < runs; r++) {
        for (Integer windowSize : windowSizes) {
            try {
                int[][] count = new int[dimension][upper + 1];
                Integer[] init = new Integer[dimension];
                Arrays.fill(init, 0);
                IntegerParameter parameter = new IntegerParameter(init);
                parameter.setLower(0);
                parameter.setUpper(upper);
                State state = new State();
                state.initByName("stateNode", parameter);
                state.initialise();
                IntRandomWalkOperator operator = new IntRandomWalkOperator();
                operator.initByName("parameter", parameter, "windowSize", windowSize, "weight", 1.0);
                for (int i = 0; i < 1000000 * (upper + 1); i++) {
                    operator.proposal();
                    Integer[] values = parameter.getValues();
                    for (int k = 0; k < values.length; k++) {
                        int j = values[k];
                        count[k][j] += 1;
                    }
                }
                System.out.print("Distribution lower = 0, upper = " + upper + " windowSize = " + windowSize);
                for (int j = 0; j < count.length; j++) {
                // System.out.println("x[" +j + "] = " + Arrays.toString(count[j]));
                }
                int sum = 0;
                for (int i = 0; i < dimension; i++) {
                    for (int k = 0; k < count[i].length; k++) {
                        sum += Math.abs(count[i][k] - 1000000);
                    }
                }
                System.out.println(" Average deviation: " + sum / (dimension * (upper + 1)));
                assertTrue("average deviation (" + sum / (dimension * (upper + 1)) + ") exceeds 10000", sum / (dimension * (upper + 1)) < 10000);
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
}

Example 28 with IntegerParameter

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

the class IntUniformOperator method proposal.

/**
 * override this for proposals,
 * returns log of hastingRatio, or Double.NEGATIVE_INFINITY if proposal should not be accepted *
 */
@Override
public double proposal() {
    IntegerParameter param = parameterInput.get(this);
    int i = Randomizer.nextInt(param.getDimension());
    int newValue = Randomizer.nextInt(param.getUpper() - param.getLower() + 1) + param.getLower();
    param.setValue(i, newValue);
    return 0.0;
}

Example 29 with IntegerParameter

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

the class UCRelaxedClockModel method initAndValidate.

@Override
public void initAndValidate() {
    tree = treeInput.get();
    branchCount = tree.getNodeCount() - 1;
    categories = categoryInput.get();
    usingQuantiles = (categories == null);
    if (!usingQuantiles) {
        LATTICE_SIZE_FOR_DISCRETIZED_RATES = numberOfDiscreteRates.get();
        if (LATTICE_SIZE_FOR_DISCRETIZED_RATES <= 0)
            LATTICE_SIZE_FOR_DISCRETIZED_RATES = branchCount;
        Log.info.println("  UCRelaxedClockModel: using " + LATTICE_SIZE_FOR_DISCRETIZED_RATES + " rate " + "categories to approximate rate distribution across branches.");
    } else {
        if (numberOfDiscreteRates.get() != -1) {
            throw new RuntimeException("Can't specify both numberOfDiscreteRates and rateQuantiles inputs.");
        }
        Log.info.println("  UCRelaxedClockModel: using quantiles for rate distribution across branches.");
    }
    if (usingQuantiles) {
        quantiles = quantileInput.get();
        quantiles.setDimension(branchCount);
        Double[] initialQuantiles = new Double[branchCount];
        for (int i = 0; i < branchCount; i++) {
            initialQuantiles[i] = Randomizer.nextDouble();
        }
        RealParameter other = new RealParameter(initialQuantiles);
        quantiles.assignFromWithoutID(other);
        quantiles.setLower(0.0);
        quantiles.setUpper(1.0);
    } else {
        categories.setDimension(branchCount);
        Integer[] initialCategories = new Integer[branchCount];
        for (int i = 0; i < branchCount; i++) {
            initialCategories[i] = Randomizer.nextInt(LATTICE_SIZE_FOR_DISCRETIZED_RATES);
        }
        // set initial values of rate categories
        IntegerParameter other = new IntegerParameter(initialCategories);
        categories.assignFromWithoutID(other);
        categories.setLower(0);
        categories.setUpper(LATTICE_SIZE_FOR_DISCRETIZED_RATES - 1);
    }
    distribution = rateDistInput.get();
    if (!usingQuantiles) {
        // rates are initially zero and are computed by getRawRate(int i) as needed
        rates = new double[LATTICE_SIZE_FOR_DISCRETIZED_RATES];
        storedRates = new double[LATTICE_SIZE_FOR_DISCRETIZED_RATES];
    // System.arraycopy(rates, 0, storedRates, 0, rates.length);
    }
    normalize = normalizeInput.get();
    meanRate = meanRateInput.get();
    if (meanRate == null) {
        meanRate = new RealParameter("1.0");
    }
    try {
        double mean = rateDistInput.get().getMean();
        if (Math.abs(mean - 1.0) > 1e-6) {
            Log.warning.println("WARNING: mean of distribution for relaxed clock model is not 1.0.");
        }
    } catch (RuntimeException e) {
    // ignore
    }
}

Example 30 with IntegerParameter

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

the class IntRandomWalkOperator method proposal.

/**
 * override this for proposals,
 * returns log of hastingRatio, or Double.NEGATIVE_INFINITY if proposal should not be accepted *
 */
@Override
public double proposal() {
    final IntegerParameter param = parameterInput.get(this);
    final int i = Randomizer.nextInt(param.getDimension());
    final int value = param.getValue(i);
    final int newValue = value + Randomizer.nextInt(2 * windowSize + 1) - windowSize;
    if (newValue < param.getLower() || newValue > param.getUpper()) {
        // invalid move, can be rejected immediately
        return Double.NEGATIVE_INFINITY;
    }
    if (newValue == value) {
        // this saves calculating the posterior
        return Double.NEGATIVE_INFINITY;
    }
    param.setValue(i, newValue);
    return 0.0;
}