Examples with Node beast.evolution.tree.Node used on opensource projects

Example 91 with Node

use of beast.evolution.tree.Node in project MultiTypeTree by tgvaughan.

the class NodeRetypeRandom method proposal.

@Override
public double proposal() {
    double logHR = 0.0;
    // Select node:
    Node node;
    do {
        node = mtTree.getNode(Randomizer.nextInt(mtTree.getNodeCount()));
    } while (node.isLeaf());
    // Record probability of current types along attached branches:
    if (!node.isRoot())
        logHR += getBranchTypeProb(node);
    logHR += getBranchTypeProb(node.getLeft()) + getBranchTypeProb(node.getRight());
    // Select new node type:
    ((MultiTypeNode) node).setNodeType(Randomizer.nextInt(migModel.getNTypes()));
    // Retype attached branches, forcing reject if inconsistent:
    if (!node.isRoot()) {
        logHR -= retypeBranch(node);
        if (((MultiTypeNode) node).getFinalType() != ((MultiTypeNode) node.getParent()).getNodeType())
            return Double.NEGATIVE_INFINITY;
    }
    logHR -= retypeBranch(node.getLeft()) + retypeBranch(node.getRight());
    if ((((MultiTypeNode) node.getLeft()).getFinalType() != ((MultiTypeNode) node).getNodeType()) || (((MultiTypeNode) node.getRight()).getFinalType() != ((MultiTypeNode) node).getNodeType()))
        return Double.NEGATIVE_INFINITY;
    // WHY IS THIS NECESSARY!?
    node.makeDirty(Tree.IS_DIRTY);
    node.getLeft().makeDirty(Tree.IS_DIRTY);
    node.getRight().makeDirty(Tree.IS_DIRTY);
    return logHR;
}

Example 92 with Node

use of beast.evolution.tree.Node in project MultiTypeTree by tgvaughan.

the class TypeMergeSplit method splitProposalRoot.

private double splitProposalRoot() {
    Node root = mtTree.getRoot();
    // Select new root type:
    int oldType = ((MultiTypeNode) root).getNodeType();
    int type;
    do {
        type = Randomizer.nextInt(migModel.getNTypes());
    } while (type == oldType);
    // Update node type:
    ((MultiTypeNode) root).setNodeType(type);
    // Select new change times:
    double tminLeft = ((MultiTypeNode) root.getLeft()).getFinalChangeTime();
    double tnewLeft = (root.getHeight() - tminLeft) * Randomizer.nextDouble() + tminLeft;
    double tminRight = ((MultiTypeNode) root.getRight()).getFinalChangeTime();
    double tnewRight = (root.getHeight() - tminRight) * Randomizer.nextDouble() + tminRight;
    // Add new changes below node:
    ((MultiTypeNode) root.getLeft()).addChange(type, tnewLeft);
    ((MultiTypeNode) root.getRight()).addChange(type, tnewRight);
    return Math.log((root.getHeight() - tminRight) * (root.getHeight() - tminLeft) * (migModel.getNTypes() - 1));
}

Example 93 with Node

use of beast.evolution.tree.Node in project MultiTypeTree by tgvaughan.

the class TypeBirthDeath method proposal.

@Override
public double proposal() {
    // Immediate reject if <3 types in model
    if (migModel.getNTypes() < 3)
        return Double.NEGATIVE_INFINITY;
    // Select event at random:
    int event = Randomizer.nextInt(mtTree.getTotalNumberOfChanges() + mtTree.getInternalNodeCount() - 1);
    MultiTypeNode node = null;
    int changeIdx = -1;
    if (event < mtTree.getInternalNodeCount() - 1)
        node = (MultiTypeNode) mtTree.getNode(event + mtTree.getLeafNodeCount());
    else {
        event -= mtTree.getInternalNodeCount() - 1;
        for (Node thisNode : mtTree.getNodesAsArray()) {
            if (thisNode.isRoot())
                continue;
            if (event < ((MultiTypeNode) thisNode).getChangeCount()) {
                node = (MultiTypeNode) thisNode;
                changeIdx = event;
                break;
            }
            event -= ((MultiTypeNode) thisNode).getChangeCount();
        }
    }
    // Perform either birth or death move
    if (Randomizer.nextBoolean())
        return birthMove(node, changeIdx);
    else
        return deathMove(node, changeIdx);
}

Example 94 with Node

use of beast.evolution.tree.Node in project MultiTypeTree by tgvaughan.

the class TypePairBirthDeath method proposal.

@Override
public double proposal() {
    int n = mtTree.getLeafNodeCount();
    int m = mtTree.getTotalNumberOfChanges();
    // Select sub-edge at random:
    int edgeNum = Randomizer.nextInt(2 * n - 2 + m);
    // Find edge that sub-edge lies on:
    Node selectedNode = null;
    for (Node node : mtTree.getNodesAsArray()) {
        if (node.isRoot())
            continue;
        if (edgeNum < ((MultiTypeNode) node).getChangeCount() + 1) {
            selectedNode = node;
            break;
        }
        edgeNum -= ((MultiTypeNode) node).getChangeCount() + 1;
    }
    // Complete either pair birth or pair death proposal:
    if (Randomizer.nextDouble() < 0.5)
        return birthProposal(selectedNode, edgeNum, n, m);
    else
        return deathProposal(selectedNode, edgeNum, n, m);
}

Example 95 with Node

use of beast.evolution.tree.Node in project MultiTypeTree by tgvaughan.

the class TypedWilsonBalding method proposal.

@Override
public double proposal() {
    // Check that operator can be applied to tree:
    if (mtTree.getLeafNodeCount() < 3)
        throw new IllegalStateException("Tree too small for" + " TypedWilsonBalding operator.");
    // Select source node:
    Node srcNode;
    do {
        srcNode = mtTree.getNode(Randomizer.nextInt(mtTree.getNodeCount()));
    } while (invalidSrcNode(srcNode));
    Node srcNodeP = srcNode.getParent();
    Node srcNodeS = getOtherChild(srcNodeP, srcNode);
    double t_srcNode = srcNode.getHeight();
    double t_srcNodeP = srcNodeP.getHeight();
    double t_srcNodeS = srcNodeS.getHeight();
    // Select destination branch node:
    Node destNode;
    do {
        destNode = mtTree.getNode(Randomizer.nextInt(mtTree.getNodeCount()));
    } while (invalidDestNode(srcNode, destNode));
    Node destNodeP = destNode.getParent();
    double t_destNode = destNode.getHeight();
    if (destNode.isRoot()) {
        // FORWARD ROOT MOVE
        double logHR = 0.0;
        // Record probability of current colouring:
        logHR += getBranchTypeProb(srcNode);
        // Record srcNode grandmother height:
        double t_srcNodeG = srcNodeP.getParent().getHeight();
        // Choose new root height:
        double newTime = t_destNode + Randomizer.nextExponential(1.0 / (alpha * t_destNode));
        // Implement tree changes:
        disconnectBranch(srcNode);
        connectBranchToRoot(srcNode, destNode, newTime);
        mtTree.setRoot(srcNodeP);
        // Recolour root branches:
        try {
            logHR -= retypeRootBranches(srcNode);
        } catch (NoValidPathException e) {
            return Double.NEGATIVE_INFINITY;
        }
        // Return HR:
        logHR += Math.log(alpha * t_destNode) + (1.0 / alpha) * (newTime / t_destNode - 1.0) - Math.log(t_srcNodeG - Math.max(t_srcNode, t_srcNodeS));
        return logHR;
    }
    if (srcNodeP.isRoot()) {
        // BACKWARD ROOT MOVE
        double logHR = 0.0;
        // Incorporate probability of current colouring:
        logHR += getRootBranchTypeProb(srcNode);
        // Record old srcNode parent height
        double oldTime = t_srcNodeP;
        // Choose height of new attachement point:
        double min_newTime = Math.max(t_srcNode, t_destNode);
        double t_destNodeP = destNodeP.getHeight();
        double span = t_destNodeP - min_newTime;
        double newTime = min_newTime + span * Randomizer.nextDouble();
        // Implement tree changes:
        disconnectBranchFromRoot(srcNode);
        connectBranch(srcNode, destNode, newTime);
        srcNodeS.setParent(null);
        mtTree.setRoot(srcNodeS);
        // Recolour new branch:
        try {
            logHR -= retypeBranch(srcNode);
        } catch (NoValidPathException e) {
            return Double.NEGATIVE_INFINITY;
        }
        // Return HR:
        logHR += Math.log(t_destNodeP - Math.max(t_srcNode, t_destNode)) - Math.log(alpha * t_srcNodeS) - (1.0 / alpha) * (oldTime / t_srcNodeS - 1.0);
        return logHR;
    }
    // NON-ROOT MOVE
    double logHR = 0.0;
    // Incorporate probability of current colouring.
    logHR += getBranchTypeProb(srcNode);
    // Record srcNode grandmother height:
    double t_srcNodeG = srcNodeP.getParent().getHeight();
    // Choose height of new attachment point:
    double min_newTime = Math.max(t_destNode, t_srcNode);
    double t_destNodeP = destNodeP.getHeight();
    double span = t_destNodeP - min_newTime;
    double newTime = min_newTime + span * Randomizer.nextDouble();
    // Implement tree changes:
    disconnectBranch(srcNode);
    connectBranch(srcNode, destNode, newTime);
    // Recolour new branch:
    try {
        logHR -= retypeBranch(srcNode);
    } catch (NoValidPathException e) {
        return Double.NEGATIVE_INFINITY;
    }
    // HR contribution of topology and node height changes:
    logHR += Math.log(t_destNodeP - Math.max(t_srcNode, t_destNode)) - Math.log(t_srcNodeG - Math.max(t_srcNode, t_srcNodeS));
    return logHR;
}