/* * adding the parameters only if its not a submodel. */ protected void addParam(Variable<Double> param) { if (isNested) { nestedParams.add(param); } else { super.addVariable(param); } }
/* * The One Phase Models are special cases of the birth-death chain, * and therefore we can use this to calculate the stationay distribution * given a infinitesimal rate matrix. */ public void computeStationaryDistribution() { if (useStationaryFreqs) { computeOnePhaseStationaryDistribution(); } super.computeStationaryDistribution(); }