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

Example 16 with MultiTypeNode

use of beast.evolution.tree.MultiTypeNode 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 17 with MultiTypeNode

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

the class SpecialTypeBirthDeath method proposal.

@Override
public double proposal() {
    if (mtTree.getLeafNodeCount() != 2)
        throw new IllegalArgumentException("SpecialTypeBirthDeath only valid for 2 taxon trees.");
    // Cannot produce or operate on trees without any changes
    if (mtTree.getTotalNumberOfChanges() == 0)
        return Double.NEGATIVE_INFINITY;
    // String startTree = mtTree.toString();
    MultiTypeNode root = (MultiTypeNode) mtTree.getRoot();
    MultiTypeNode left = (MultiTypeNode) root.getLeft();
    MultiTypeNode right = (MultiTypeNode) root.getRight();
    // Select event:
    int event = Randomizer.nextInt(mtTree.getTotalNumberOfChanges());
    MultiTypeNode node, sister;
    int changeIdx;
    if (event < left.getChangeCount()) {
        node = left;
        sister = right;
        changeIdx = event;
    } else {
        node = right;
        sister = left;
        changeIdx = event - left.getChangeCount();
    }
    // Implement birth or death
    double logHR;
    boolean birth = Randomizer.nextBoolean();
    if (birth)
        logHR = birthProposal(node, changeIdx, sister);
    else
        logHR = deathProposal(node, changeIdx, sister);
    return logHR;
}

Example 18 with MultiTypeNode

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

the class TypeMergeSplit method mergeProposal.

/**
 * Remove a pair of migrations below a coalescence event and create
 * one above it.
 *
 * @param node Node representing coalescence event.
 * @return log of Hastings ratio
 */
private double mergeProposal(Node node) {
    MultiTypeNode left = (MultiTypeNode) node.getLeft();
    MultiTypeNode right = (MultiTypeNode) node.getRight();
    MultiTypeNode mtNode = (MultiTypeNode) node;
    int leftIdx = left.getChangeCount() - 1;
    int rightIdx = right.getChangeCount() - 1;
    if (leftIdx < 0 || rightIdx < 0)
        return Double.NEGATIVE_INFINITY;
    int leftType = left.getChangeType(leftIdx);
    int rightType = right.getChangeType(rightIdx);
    if (leftType != rightType)
        return Double.NEGATIVE_INFINITY;
    int leftTypeUnder;
    double tminLeft;
    if (leftIdx > 0) {
        leftTypeUnder = left.getChangeType(leftIdx - 1);
        tminLeft = left.getChangeTime(leftIdx - 1);
    } else {
        leftTypeUnder = left.getNodeType();
        tminLeft = left.getHeight();
    }
    int rightTypeUnder;
    double tminRight;
    if (rightIdx > 0) {
        rightTypeUnder = right.getChangeType(rightIdx - 1);
        tminRight = right.getChangeTime(rightIdx - 1);
    } else {
        rightTypeUnder = right.getNodeType();
        tminRight = right.getHeight();
    }
    if (leftTypeUnder != rightTypeUnder)
        return Double.NEGATIVE_INFINITY;
    double tmax;
    if (mtNode.getChangeCount() > 0)
        tmax = mtNode.getChangeTime(0);
    else
        tmax = node.getParent().getHeight();
    left.removeChange(leftIdx);
    right.removeChange(rightIdx);
    mtNode.setNodeType(leftTypeUnder);
    double tnew = Randomizer.nextDouble() * (tmax - node.getHeight()) + node.getHeight();
    mtNode.insertChange(0, leftType, tnew);
    return Math.log(tmax - node.getHeight()) - Math.log((node.getHeight() - tminLeft) * (node.getHeight() - tminRight));
}

Example 19 with MultiTypeNode

use of beast.evolution.tree.MultiTypeNode 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 20 with MultiTypeNode

use of beast.evolution.tree.MultiTypeNode 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);
}