Prune topologies

Dirk Husmeier, Biomathematics and Statistics Scotland (BioSS)

The posterior distribution over tree topologies can be pruned. Note that this does not require another run of PDM; you only need to keep the intermediate result file resultsAllTopos.out. In oder to prune topologies, proceed as follows. First, create a file called prune.in. This file contains one integer number: the maximum permissible number of tree topologies.

Assuming that you have kept the intermediate results of a PDM simulation in resultsAllTopos.out, you can analyse these results with class JambeAnalyseTopos as usual. All you need to do is edit method run of this class by adding one extra line of code:

Old version:


public void run()
{
Entropy oEntropy= new Entropy(fileName);
oEntropy.doItAll();
Kullback oKullback= new Kullback(oEntropy);
oKullback.doItAll();
}

New version:


public void run()
{
Entropy oEntropy= new Entropy(fileName);
oEntropy.doItAll();
oEntropy.pruning();
Kullback oKullback= new Kullback(oEntropy);
oKullback.doItAll();
}


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