Examples with MCMCCriterion dr.inference.mcmc.MCMCCriterion used on opensource projects

Example 1 with MCMCCriterion

use of dr.inference.mcmc.MCMCCriterion in project beast-mcmc by beast-dev.

the class MCMCMC method swapChainTemperatures.

private int swapChainTemperatures() {
    if (DEBUG) {
        System.out.print("Current scores: ");
        for (int i = 0; i < chains.length; i++) {
            System.out.print("\t");
            if (i == coldChain) {
                System.out.print("[");
            }
            System.out.print(chains[i].getCurrentScore());
            if (i == coldChain) {
                System.out.print("]");
            }
        }
        System.out.println();
    }
    int newColdChain = coldChain;
    int index1 = MathUtils.nextInt(chains.length);
    int index2 = MathUtils.nextInt(chains.length);
    while (index1 == index2) {
        index2 = MathUtils.nextInt(chains.length);
    }
    double score1 = chains[index1].getCurrentScore();
    MCMCCriterion acceptor1 = ((MCMCCriterion) chains[index1].getAcceptor());
    double temperature1 = acceptor1.getTemperature();
    double score2 = chains[index2].getCurrentScore();
    MCMCCriterion acceptor2 = ((MCMCCriterion) chains[index2].getAcceptor());
    double temperature2 = acceptor2.getTemperature();
    double logRatio = ((score2 - score1) * temperature1) + ((score1 - score2) * temperature2);
    boolean swap = (Math.log(MathUtils.nextDouble()) < logRatio);
    if (swap) {
        if (DEBUG) {
            System.out.println("Swapping chain " + index1 + " and chain " + index2);
        }
        acceptor1.setTemperature(temperature2);
        acceptor2.setTemperature(temperature1);
        OperatorSchedule schedule1 = schedules[index1];
        OperatorSchedule schedule2 = schedules[index2];
        for (int i = 0; i < schedule1.getOperatorCount(); i++) {
            MCMCOperator operator1 = schedule1.getOperator(i);
            MCMCOperator operator2 = schedule2.getOperator(i);
            long tmp = operator1.getAcceptCount();
            operator1.setAcceptCount(operator2.getAcceptCount());
            operator2.setAcceptCount(tmp);
            tmp = operator1.getRejectCount();
            operator1.setRejectCount(operator2.getRejectCount());
            operator2.setRejectCount(tmp);
            double tmp2 = operator1.getSumDeviation();
            operator1.setSumDeviation(operator2.getSumDeviation());
            operator2.setSumDeviation(tmp2);
            if (operator1 instanceof CoercableMCMCOperator) {
                tmp2 = ((CoercableMCMCOperator) operator1).getCoercableParameter();
                ((CoercableMCMCOperator) operator1).setCoercableParameter(((CoercableMCMCOperator) operator2).getCoercableParameter());
                ((CoercableMCMCOperator) operator2).setCoercableParameter(tmp2);
            }
        }
        if (index1 == coldChain) {
            newColdChain = index2;
        } else if (index2 == coldChain) {
            newColdChain = index1;
        }
    }
    return newColdChain;
}