Package common

Examples of common.FragmentPenalty

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    output += "Initial partition in array representation:\n"+Arrays.toString(initArrayPartition)+"\n";
    output += "Initial partition in list representation:\n"+dclong.util.Arrays.splitArray(initArrayPartition)+"\n";
    output += "burn-in="+warmupStep+", draws="+numberOfDraws+"\n";
    //define partition prior
//    FragmentPenalty fragmentPenalty = new PowerFragmentPenalty(0.5,3);//seems good
    FragmentPenalty fragmentPenalty = new PowerFragmentPenalty(power,powerCoefficient);
    //define partition prior
    FragmentPartitionPrior fragPrior = new FragmentPartitionPrior(fragmentPenalty);
    //define tuning distribution
    RandomGenerator rg = new Well44497b();
    RandomDataImpl rng = new RandomDataImpl(rg);
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    String iapFile = "/home/adu/Dropbox/research/vardeman/mc-on-partition/data/jdata/tap.bin";
    double[][] locs = dclong.io.BinaryReader.readDouble(locsFile, 0,0,n, 2);
    double[] data = dclong.io.BinaryReader.readDouble(dataFile, 0, 0, n);
    int[] initArrayPartition = dclong.io.BinaryReader.readInt(iapFile,0,0,n);
    //define partition prior
    FragmentPenalty fragmentPenalty = new PowerFragmentPenalty(1,90);
    //define size penalty
    SizePenalty sizePenalty = new LinearSizePenalty(0);
    //define partition prior
//    PartitionPrior partitionPrior = new DistPartitionPrior(locs,3,fragmentPenalty,sizePenalty);
    PartitionPrior fragPrior = new FragmentPartitionPrior(fragmentPenalty);
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    output += "Initial partition in array representation:\n"+Arrays.toString(initArrayPartition)+"\n";
    output += "Initial partition in list representation:\n"+dclong.util.Arrays.splitArray(initArrayPartition)+"\n";
    output += "burn-in="+warmupStep+", draws="+numberOfDraws+"\n";
    //define partition prior
//    FragmentPenalty fragmentPenalty = new PowerFragmentPenalty(0.5,3);//seems good
    FragmentPenalty fragmentPenalty = new PowerFragmentPenalty(power,powerCoefficient);
    //define partition prior
    FragmentPartitionPrior fragPrior = new FragmentPartitionPrior(fragmentPenalty);
    //define tuning distribution
    RandomGenerator rg = new Well44497b();
    RandomDataImpl rng = new RandomDataImpl(rg);
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Related Classes of common.FragmentPenalty

  • complex1.RunMCMC
  • normal1.RunSimpleMCMC
  • normal2.RunMCMC
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