Examples with IntRandomWalkOperator beast.evolution.operators.IntRandomWalkOperator used on opensource projects

Example 1 with IntRandomWalkOperator

use of beast.evolution.operators.IntRandomWalkOperator 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();
            }
        }
    }
}