Examples with GY94CodonModel dr.evomodel.substmodel.codon.GY94CodonModel used on opensource projects

Example 6 with GY94CodonModel

use of dr.evomodel.substmodel.codon.GY94CodonModel in project beast-mcmc by beast-dev.

the class RandomBranchModel method setup.

// END: Constructor
private void setup() {
    DataType dataType = baseSubstitutionModel.getDataType();
    FrequencyModel freqModel = baseSubstitutionModel.getFrequencyModel();
    Parameter kappaParameter = new Parameter.Default("kappa", 1, baseSubstitutionModel.getKappa());
    substitutionModels = new LinkedList<SubstitutionModel>();
    branchAssignmentMap = new LinkedHashMap<NodeRef, Integer>();
    int branchClass = 0;
    for (NodeRef node : treeModel.getNodes()) {
        if (!treeModel.isRoot(node)) {
            double nodeHeight = treeModel.getNodeHeight(node);
            double parentHeight = treeModel.getNodeHeight(treeModel.getParent(node));
            double time = 0.5 * (parentHeight + nodeHeight);
            double baseOmega = baseSubstitutionModel.getOmega();
            double fixed = baseOmega * time;
            //Math.exp((random.nextGaussian() * stdev + mean));
            double epsilon = (Math.log(1 - random.nextDouble()) / (-rate));
            double value = fixed + epsilon;
            Parameter omegaParameter = new Parameter.Default("omega", 1, value);
            GY94CodonModel gy94 = new GY94CodonModel((Codons) dataType, omegaParameter, kappaParameter, freqModel);
            substitutionModels.add(gy94);
            branchAssignmentMap.put(node, branchClass);
            branchClass++;
        }
    //END: root check
    }
// END: nodes loop
}