public double mergeValueInLogSpace(
RealParameter removed, RealParameter merge, ParametricDistribution distr) throws Exception {
double val1 = Math.log(removed.getValue());
double val2 = Math.log(merge.getValue());
double x = val1 - val2;
return distr.calcLogP(new RealParameter(new Double[] {x})) - val1;
}
public double mergeDiscreteValue(
RealParameter removed, RealParameter merge, ConditionalCategoricalDistribution distr) {
int removedModel = (int) (double) removed.getValue();
int mergeModel = (int) (double) merge.getValue();
return distr.logConditionalDensity(mergeModel, removedModel);
}
public double mergeValue(RealParameter removed, RealParameter merge, ParametricDistribution distr)
throws Exception {
Double[] x = new Double[removed.getDimension()];
for (int i = 0; i < x.length; i++) {
x[i] = removed.getValue(i) - merge.getValue(i);
}
return distr.calcLogP(new RealParameter(x));
}
private void update() {
final double geneTreeRate = meanRate.getValue();
final double[] speciesTreeRates = speciesTreeRatesX.getRatesArray();
final double[] speciesOccupancy = geneTree.getSpeciesOccupancy();
final int speciesNodeCount = speciesTreeRates.length;
for (int i = 0; i < geneNodeCount - 1; i++) {
double weightedSum = 0.0;
double branchLength = 0.0;
for (int j = 0; j < speciesNodeCount; j++) {
// System.out.println(String.format("%d, %d: %f, %f", i, j, speciesTreeRates[j],
// speciesOccupancy[i * speciesNodeCount + j]));
weightedSum += speciesTreeRates[j] * speciesOccupancy[i * speciesNodeCount + j];
branchLength += speciesOccupancy[i * speciesNodeCount + j];
}
branchRates[i] = geneTreeRate * weightedSum / branchLength;
}
// set the rate for the root branch of this gene to equal the input mean rate
branchRates[geneNodeCount - 1] = geneTreeRate;
needsUpdate = false;
}
