public void forwardIBD() {
int numNodes = treeModel.getNodeCount();
int stateCount = substitutionModel.getStateCount();
getDiagonalRates(diag);
for (int nodeId = 0; nodeId < numNodes; ++nodeId) {
NodeRef node = treeModel.getNode(nodeId);
NodeRef parent = treeModel.getParent(node);
if (parent == null) { // handle the root
} else if (treeModel.isExternal(node)) { // Handle the tip
double branchTime =
branchRateModel.getBranchRate(treeModel, node)
* (treeModel.getNodeHeight(parent) - treeModel.getNodeHeight(node));
for (int state = 0; state < stateCount; ++state) {
ibdForward[nodeId][state] = Math.exp(-diag[state] * branchTime);
}
} else { // Handle internal node
double branchTime =
branchRateModel.getBranchRate(treeModel, node)
* (treeModel.getNodeHeight(parent) - treeModel.getNodeHeight(node));
int childCount = treeModel.getChildCount(node);
for (int state = 0; state < stateCount; ++state) {
ibdForward[nodeId][state] = 0;
for (int child = 0; child < childCount; ++child) {
int childNodeId = treeModel.getChild(node, child).getNumber();
ibdForward[nodeId][state] += ibdForward[childNodeId][state];
}
ibdForward[nodeId][state] *= Math.exp(-diag[state] * branchTime);
}
}
}
}
public void backwardIBD(NodeRef node) {
int stateCount = substitutionModel.getStateCount();
if (node == null) {
node = treeModel.getRoot();
int nodeId = node.getNumber();
for (int state = 0; state < stateCount; ++state) {
ibdBackward[nodeId][state] = 0;
}
}
getDiagonalRates(diag);
int childCount = treeModel.getChildCount(node);
int nodeId = node.getNumber();
for (int child = 0; child < childCount; ++child) {
NodeRef childNode = treeModel.getChild(node, child);
int childNodeId = childNode.getNumber();
double branchTime =
branchRateModel.getBranchRate(treeModel, childNode)
* (treeModel.getNodeHeight(node) - treeModel.getNodeHeight(childNode));
for (int state = 0; state < stateCount; ++state) {
ibdBackward[childNodeId][state] = ibdBackward[nodeId][state];
for (int sibling = 0; sibling < childCount; ++sibling) {
if (sibling != child) {
int siblingId = treeModel.getChild(node, sibling).getNumber();
ibdBackward[childNodeId][state] += ibdForward[siblingId][state];
}
}
ibdBackward[childNodeId][state] *= Math.exp(-diag[state] * branchTime);
}
}
for (int child = 0; child < childCount; ++child) {
NodeRef childNode = treeModel.getChild(node, child);
backwardIBD(childNode);
}
}
/** Calculates the actual rates corresponding to the category indices. */
protected void setupRates() {
// System.out.println("BRRRTTZZZ " + distributionIndexParameter.getValue(0));
for (int i = 0; i < tree.getNodeCount(); i++) {
// rates[i] = distributionModel.quantile(rateCategoryQuantiles.getNodeValue(
// rateCategoryQuantiles.getTreeModel(), rateCategoryQuantiles.getTreeModel().getNode(i) ));
if (!tree.isRoot(tree.getNode(i))) {
if (useQuantilesForRates) {
/* Using quantiles to represent rates */
rates[tree.getNode(i).getNumber()] =
distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].quantile(
rateCategoryQuantiles.getNodeValue(tree, tree.getNode(i)));
} else {
/* Not using quantiles to represent rates. This is practically useless for anything else other than simulation */
rates[tree.getNode(i).getNumber()] =
rateCategoryQuantiles.getNodeValue(tree, tree.getNode(i));
}
}
}
/*System.out.print(distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].getClass().getName() + "\t" + (int) Math.round(distributionIndexParameter.getValue(0)) + "\t" + rates[1] + "\t" + rateCategoryQuantiles.getNodeValue(tree, tree.getNode(1)));// + "\t" + distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].);
if(distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].getClass().getName().equals("dr.inference.distribution.LogNormalDistributionModel")) {
LogNormalDistributionModel lndm = (LogNormalDistributionModel) distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))];
System.out.println("\t" + lndm.getS());
}
else if (distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].getClass().getName().equals("dr.inference.distribution.InverseGaussianDistributionModel")) {
InverseGaussianDistributionModel lndm = (InverseGaussianDistributionModel) distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))];
System.out.println("\t" + lndm.getS());
}*/
if (normalize) computeFactor();
}
/** provide information to the categoriesParameter about the number of sites */
public void setCategoriesParameter(int siteCount) {
categoriesParameter.setDimension(siteCount);
categoriesParameter.addBounds(new Parameter.DefaultBounds(categoryCount, 0.0, siteCount));
for (int i = 0; i < siteCount; i++) {
int r = (int) (Math.random() * categoryCount);
categoriesParameter.setParameterValue(i, r);
}
for (int j = 0; j < categoryCount; j++) {
sitesInCategory[j] = 0;
}
for (int i = 0; i < siteCount; i++) {
int value = (int) categoriesParameter.getParameterValue(i);
sitesInCategory[value] = sitesInCategory[value] + 1;
}
}
public static Transform[] parseListOfTransforms(XMLObject xo, int maxDim)
throws XMLParseException {
Transform[] transforms = null;
boolean anyTransforms = false;
for (int i = 0; i < xo.getChildCount(); ++i) {
if (xo.getChild(i) instanceof Transform.ParsedTransform) {
Transform.ParsedTransform t = (Transform.ParsedTransform) xo.getChild(i);
if (transforms == null) {
transforms = Transform.Util.getListOfNoTransforms(maxDim);
}
t.end = Math.max(t.end, maxDim);
if (t.start < 0 || t.end < 0 || t.start > t.end) {
throw new XMLParseException("Invalid bounds for transform in " + xo.getId());
}
for (int j = t.start; j < t.end; j += t.every) {
transforms[j] = t.transform;
anyTransforms = true;
}
}
}
if (anyTransforms) {
StringBuilder sb =
new StringBuilder("Using distributional transforms in " + xo.getId() + "\n");
for (int i = 0; i < transforms.length; ++i) {
if (transforms[i] != Transform.NONE) {
sb.append("\t")
.append(transforms[i].getTransformName())
.append(" on index ")
.append(i + 1)
.append("\n");
}
}
sb.append("Please cite:\n").append(Citable.Utils.getCitationString(Transform.LOG));
Logger.getLogger("dr.utils.Transform").info(sb.toString());
}
return transforms;
}
