public GMRFSkyrideLikelihood(
List<Tree> treeList,
Parameter popParameter,
Parameter groupParameter,
Parameter precParameter,
Parameter lambda,
Parameter beta,
MatrixParameter dMatrix,
boolean timeAwareSmoothing,
boolean rescaleByRootHeight) {
super(GMRFSkyrideLikelihoodParser.SKYLINE_LIKELIHOOD);
this.popSizeParameter = popParameter;
this.groupSizeParameter = groupParameter;
this.precisionParameter = precParameter;
this.lambdaParameter = lambda;
this.betaParameter = beta;
this.dMatrix = dMatrix;
this.timeAwareSmoothing = timeAwareSmoothing;
this.rescaleByRootHeight = rescaleByRootHeight;
addVariable(popSizeParameter);
addVariable(precisionParameter);
addVariable(lambdaParameter);
if (betaParameter != null) {
addVariable(betaParameter);
}
setTree(treeList);
int correctFieldLength = getCorrectFieldLength();
if (popSizeParameter.getDimension() <= 1) {
// popSize dimension hasn't been set yet, set it here:
popSizeParameter.setDimension(correctFieldLength);
}
fieldLength = popSizeParameter.getDimension();
if (correctFieldLength != fieldLength) {
throw new IllegalArgumentException(
"Population size parameter should have length " + correctFieldLength);
}
// Field length must be set by this point
wrapSetupIntervals();
coalescentIntervals = new double[fieldLength];
storedCoalescentIntervals = new double[fieldLength];
sufficientStatistics = new double[fieldLength];
storedSufficientStatistics = new double[fieldLength];
setupGMRFWeights();
addStatistic(new DeltaStatistic());
initializationReport();
/* Force all entries in groupSizeParameter = 1 for compatibility with Tracer */
if (groupSizeParameter != null) {
for (int i = 0; i < groupSizeParameter.getDimension(); i++)
groupSizeParameter.setParameterValue(i, 1.0);
}
}
