@Override
public void initAndValidate() throws Exception {
popFunction = popFunctionInput.get();
popSizesBottom = popSizesBottomInput.get();
popSizesTop = popSizesTopInput.get();
// set up sizes of population functions
final int nSpecies = treeInput.get().getLeafNodeCount();
final int nNodes = treeInput.get().getNodeCount();
switch (popFunction) {
case constant:
popSizesBottom.setDimension(nNodes);
break;
case linear:
if (popSizesTop == null) {
throw new Exception("topPopSize must be specified");
}
popSizesBottom.setDimension(nSpecies);
popSizesTop.setDimension(nNodes);
break;
case linear_with_constant_root:
if (popSizesTop == null) {
throw new Exception("topPopSize must be specified");
}
popSizesBottom.setDimension(nSpecies);
popSizesTop.setDimension(nNodes - 1);
break;
}
// bottom prior = Gamma(2,Psi)
gamma2Prior = new Gamma();
gamma2Prior.betaInput.setValue(gammaParameterInput.get(), gamma2Prior);
// top prior = Gamma(4,Psi)
gamma4Prior = new Gamma();
final RealParameter parameter = new RealParameter(new Double[] {4.0});
gamma4Prior.alphaInput.setValue(parameter, gamma4Prior);
gamma4Prior.betaInput.setValue(gammaParameterInput.get(), gamma4Prior);
if (popFunction != PopSizeFunction.constant && gamma4Prior == null) {
throw new Exception("Top prior must be specified when population function is not constant");
}
// make sure the m_taxonSet is a set of taxonsets
// HACK to make Beauti initialise: skip the check here
// for (Taxon taxon : m_taxonSet.get().m_taxonset.get()) {
// if (!(taxon instanceof TaxonSet)) {
// throw new Exception("taxonset should be sets of taxa only, not individual taxons");
// }
// }
}
@Override
public double calculateLogP() {
logP = 0;
// make sure the root branch length is positive
// if (m_rootHeightParameter.get().getValue() < m_speciesTree.get().getRoot().getHeight()) {
// logP = Double.NEGATIVE_INFINITY;
// return logP;
// }
final Node[] speciesNodes = treeInput.get().getNodesAsArray();
try {
switch (popFunction) {
case constant:
// constant pop size function
logP += gamma2Prior.calcLogP(popSizesBottom);
// for (int i = 0; i < speciesNodes.length; i++) {
// double fPopSize = m_fPopSizesBottom.getValue(i);
// logP += m_bottomPrior.logDensity(fPopSize);
// }
break;
case linear:
// linear pop size function
// int nSpecies = m_tree.get().getLeafNodeCount();
// m_fPopSizesBottom.setDimension(nSpecies);
// logP += m_gamma4Prior.calcLogP(m_fPopSizesBottom);
// int nNodes = m_tree.get().getNodeCount();
// m_fPopSizesTop.setDimension(nNodes-1);
// logP += m_gamma2Prior.calcLogP(m_fPopSizesTop);
for (int i = 0; i < speciesNodes.length; i++) {
final Node node = speciesNodes[i];
final double fPopSizeBottom;
if (node.isLeaf()) {
// Gamma(4, fPsi) prior
fPopSizeBottom = popSizesBottom.getValue(i);
logP += gamma4Prior.logDensity(fPopSizeBottom);
}
final double fPopSizeTop = popSizesTop.getValue(i);
logP += gamma2Prior.logDensity(fPopSizeTop);
}
break;
case linear_with_constant_root:
// logP += m_gamma4Prior.calcLogP(m_fPopSizesBottom);
// logP += m_gamma2Prior.calcLogP(m_fPopSizesTop);
// int iRoot = m_tree.get().getRoot().getNr();
// double fPopSize = m_fPopSizesTop.getValue(iRoot);
// logP -= m_gamma2Prior.logDensity(fPopSize);
for (int i = 0; i < speciesNodes.length; i++) {
final Node node = speciesNodes[i];
if (node.isLeaf()) {
final double fPopSizeBottom = popSizesBottom.getValue(i);
logP += gamma4Prior.logDensity(fPopSizeBottom);
}
if (!node.isRoot()) {
if (i < speciesNodes.length - 1) {
final double fPopSizeTop = popSizesTop.getArrayValue(i);
logP += gamma2Prior.logDensity(fPopSizeTop);
} else {
final int iNode = treeInput.get().getRoot().getNr();
final double fPopSizeTop = popSizesTop.getArrayValue(iNode);
logP += gamma2Prior.logDensity(fPopSizeTop);
}
}
}
break;
}
} catch (Exception e) {
// exceptions can be thrown by the gamma priors
e.printStackTrace();
return Double.NEGATIVE_INFINITY;
}
return logP;
}