private double branchLLInPopsIOtree(PopsIONode node, double alpha, double beta) {
int q = node.coalcount;
double gamma = node.coalintensity;
double llhood = 0.0;
for (int i = 1; i <= q - 1; i++) {
llhood += Math.log(alpha + i);
}
llhood += alpha * Math.log(beta);
llhood -= (alpha + q) * Math.log(beta + gamma);
return llhood;
}
private double logsumexp(double x[]) {
double maxx = Double.MIN_VALUE;
for (double d : x) {
if (d > maxx) {
maxx = d;
}
}
double sum = 0.0;
for (double d : x) {
sum += Math.exp(d - maxx);
}
return maxx + Math.log(sum);
}
public double logLhoodAllGeneTreesInSpeciesTree() {
double[] llhoodcpts = new double[priorComponents.length];
double totalweight = 0.0;
for (int i = 0; i < priorComponents.length; i++) {
totalweight += priorComponents[i].weight;
}
for (int i = 0; i < priorComponents.length; i++) {
llhoodcpts[i] = Math.log(priorComponents[i].weight / totalweight);
double sigma = popPriorScale.getParameterValue(0);
double alpha = priorComponents[i].alpha;
double beta = sigma * priorComponents[i].beta;
llhoodcpts[i] += logLhoodAllGeneTreesInSpeciesSubtree(pionodes[rootn], alpha, beta);
}
return logsumexp(llhoodcpts);
}