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

Example 21 with MultiTypeNode

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

the class TypeBirthDeath method retypeSubtree.

/**
 * Retype subtree including edge from changeIdx to changeIdx+1 on node
 * with new type changeType.
 *
 * @param changeIdx
 * @param node
 * @param changeType
 */
private void retypeSubtree(int changeIdx, MultiTypeNode node, int changeType) {
    if (changeIdx < 0) {
        MultiTypeNode startNode = findDecendentNodeWithMigration((MultiTypeNode) node.getLeft());
        startNode.setChangeType(startNode.getChangeCount() - 1, changeType);
        retypeSubtreeRecurse(changeType, (MultiTypeNode) startNode.getParent(), startNode);
    } else {
        node.setChangeType(changeIdx, changeType);
        if (changeIdx + 1 >= node.getChangeCount())
            retypeSubtreeRecurse(changeType, (MultiTypeNode) node.getParent(), node);
    }
}

Example 22 with MultiTypeNode

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

the class TypeMergeSplitExtended method proposal.

@Override
public double proposal() {
    // Select internal node to operate around:
    int nodeID = mtTree.getLeafNodeCount() + Randomizer.nextInt(mtTree.getInternalNodeCount());
    MultiTypeNode node = (MultiTypeNode) mtTree.getNode(nodeID);
    // Special root move
    if (node.isRoot())
        return rootProposal(node);
    // Regular merge/split moves
    if (Randomizer.nextBoolean())
        return mergeProposal(node);
    else
        return splitProposal(node);
}

Example 23 with MultiTypeNode

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

the class TypeMergeSplitExtended method mergeProposal.

/**
 * Merge proposal
 * @return log of Hastings Ratio
 */
private double mergeProposal(MultiTypeNode node) {
    double logHR = 0.0;
    // Select which branch forms the destination branch in this move:
    int destBranch = Randomizer.nextInt(3);
    if (destBranch == 2) {
        // Branch is the parent branch (ordinary merge)
        MultiTypeNode left = (MultiTypeNode) node.getLeft();
        MultiTypeNode right = (MultiTypeNode) node.getRight();
        // Reject if nothing to merge
        if (left.getChangeCount() == 0 || right.getChangeCount() == 0)
            return Double.NEGATIVE_INFINITY;
        // Change-removal half of merge
        int changeType = node.getNodeType();
        left.removeChange(left.getChangeCount() - 1);
        right.removeChange(right.getChangeCount() - 1);
        // Reject if types below deleted changes don't match:
        if (left.getFinalType() != right.getFinalType())
            return Double.NEGATIVE_INFINITY;
        // HR contribution of reverse move
        logHR += Math.log(1.0 / ((node.getHeight() - left.getFinalChangeTime()) * (node.getHeight() - right.getFinalChangeTime())));
        // Maximum time of new change
        double newTimeMax;
        if (node.getChangeCount() > 0)
            newTimeMax = node.getChangeTime(0);
        else
            newTimeMax = node.getParent().getHeight();
        // HR contribution of forward move
        logHR -= Math.log(1.0 / (newTimeMax - node.getHeight()));
        // Add new merged change
        double newTime = node.getHeight() + (newTimeMax - node.getHeight()) * Randomizer.nextDouble();
        node.insertChange(0, changeType, newTime);
        // Update node typ:
        node.setNodeType(left.getFinalType());
    } else {
        // Destination is one of the child branches (generalised move)
        MultiTypeNode destBranchNode = (MultiTypeNode) node.getChild(destBranch);
        MultiTypeNode otherBranchNode = (MultiTypeNode) node.getChild(1 - destBranch);
        // Reject if nothing to merge
        if (node.getChangeCount() == 0 || otherBranchNode.getChangeCount() == 0)
            return Double.NEGATIVE_INFINITY;
        // Change removal half of merge
        int changeType = node.getChangeType(0);
        otherBranchNode.removeChange(otherBranchNode.getChangeCount() - 1);
        if (otherBranchNode.getFinalType() != node.getChangeType(0))
            return Double.NEGATIVE_INFINITY;
        node.removeChange(0);
        // HR calculation
        double timeMaxParent;
        if (node.getChangeCount() == 0)
            timeMaxParent = node.getParent().getHeight();
        else
            timeMaxParent = node.getChangeTime(0);
        double timeMinOther = otherBranchNode.getFinalChangeTime();
        logHR += Math.log(1.0 / ((timeMaxParent - node.getHeight()) * (node.getHeight() - timeMinOther)));
        // Minimum time of new change
        double newTimeMin = destBranchNode.getFinalChangeTime();
        // HR contribution of forward move
        logHR -= Math.log(1.0 / (node.getHeight() - newTimeMin));
        // Add new merged change
        double newTime = newTimeMin + (node.getHeight() - newTimeMin) * Randomizer.nextDouble();
        destBranchNode.addChange(changeType, newTime);
        // Update node type:
        node.setNodeType(changeType);
    }
    return logHR;
}

Example 24 with MultiTypeNode

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

the class TypeMergeSplitExtended method splitProposal.

private double splitProposal(MultiTypeNode node) {
    double logHR = 0.0;
    int sourceBranch = Randomizer.nextInt(3);
    if (sourceBranch == 2) {
        // Reject if nothing to split:
        if (node.getChangeCount() == 0)
            return Double.NEGATIVE_INFINITY;
        MultiTypeNode left = (MultiTypeNode) node.getLeft();
        MultiTypeNode right = (MultiTypeNode) node.getRight();
        // Change removal half of split move:
        int changeType = node.getChangeType(0);
        node.removeChange(0);
        // HR contribution of reverse move
        double timeMaxParent;
        if (node.getChangeCount() == 0)
            timeMaxParent = node.getParent().getHeight();
        else
            timeMaxParent = node.getChangeTime(0);
        logHR += Math.log(1.0 / (timeMaxParent - node.getHeight()));
        // HR contribution of forward move
        logHR -= Math.log(1.0 / ((node.getHeight() - left.getFinalChangeTime()) * (node.getHeight() - right.getFinalChangeTime())));
        // Select new change times
        double newTimeLeft = left.getFinalChangeTime() + (node.getHeight() - left.getFinalChangeTime()) * Randomizer.nextDouble();
        double newTimeRight = right.getFinalChangeTime() + (node.getHeight() - right.getFinalChangeTime()) * Randomizer.nextDouble();
        // Add new changes to child branches
        left.addChange(changeType, newTimeLeft);
        right.addChange(changeType, newTimeRight);
        // Update node type
        node.setNodeType(changeType);
    } else {
        // Source branch is a child (generalized situation)
        MultiTypeNode sourceBranchNode = (MultiTypeNode) node.getChild(sourceBranch);
        MultiTypeNode otherBranchNode = (MultiTypeNode) node.getChild(1 - sourceBranch);
        // Reject if nothing to split:
        if (sourceBranchNode.getChangeCount() == 0)
            return Double.NEGATIVE_INFINITY;
        // Change removal half of merge:
        sourceBranchNode.removeChange(sourceBranchNode.getChangeCount() - 1);
        // HR contribution of reverse move:
        logHR += Math.log(1.0 / (node.getHeight() - sourceBranchNode.getFinalChangeTime()));
        // HR contribution of forward move:
        double maxTimeParent;
        if (node.getChangeCount() == 0)
            maxTimeParent = node.getParent().getHeight();
        else
            maxTimeParent = node.getChangeTime(0);
        logHR -= Math.log(1.0 / ((node.getHeight() - otherBranchNode.getFinalChangeTime()) * (maxTimeParent - node.getHeight())));
        // Select new change times
        double newTimeNode = node.getHeight() + (maxTimeParent - node.getHeight()) * Randomizer.nextDouble();
        double newTimeOther = otherBranchNode.getFinalChangeTime() + (node.getHeight() - otherBranchNode.getFinalChangeTime()) * Randomizer.nextDouble();
        // Add new changes
        node.insertChange(0, node.getNodeType(), newTimeNode);
        otherBranchNode.addChange(sourceBranchNode.getFinalType(), newTimeOther);
        // Update node type
        node.setNodeType(sourceBranchNode.getFinalType());
    }
    return logHR;
}

Example 25 with MultiTypeNode

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

the class TypeMergeSplitExtended method rootProposal.

/**
 * Proposal involving root
 * @return log of Hastings Ratio
 */
private double rootProposal(MultiTypeNode root) {
    double logHR = 0.0;
    // Slide change from A to B
    MultiTypeNode A, B;
    if (Randomizer.nextBoolean()) {
        A = (MultiTypeNode) root.getLeft();
        B = (MultiTypeNode) root.getRight();
    } else {
        B = (MultiTypeNode) root.getLeft();
        A = (MultiTypeNode) root.getRight();
    }
    // Reject if there's no change to slide
    if (A.getChangeCount() == 0)
        return Double.NEGATIVE_INFINITY;
    // Remove old change
    A.removeChange(A.getChangeCount() - 1);
    // Record HR:
    logHR += Math.log(1.0 / (root.getHeight() - A.getFinalChangeTime()));
    logHR -= Math.log(1.0 / (root.getHeight() - B.getFinalChangeTime()));
    // Select new change time:
    double newTime = B.getFinalChangeTime() + Randomizer.nextDouble() * (root.getHeight() - B.getFinalChangeTime());
    // Add new change to B:
    B.addChange(A.getFinalType(), newTime);
    // Update node type:
    root.setNodeType(A.getFinalType());
    return logHR;
}