Examples with Clade dr.evolution.tree.Clade used on opensource projects

Example 1 with Clade

use of dr.evolution.tree.Clade in project beast-mcmc by beast-dev.

the class ConditionalCladeFrequency method addTree.

/**
     * increments the number of occurrences for all conditional clades
     *
     * @param tree - the tree to be added
     */
public void addTree(Tree tree, HashMap<String, Integer> taxonMap) {
    samples++;
    List<Clade> clades = new ArrayList<Clade>();
    List<Clade> parentClades = new ArrayList<Clade>();
    // get clades contained in the tree
    getClades(tree, tree.getRoot(), parentClades, clades, taxonMap);
    // add the clade containing all taxa as well so that it get counted
    clades.add(parentClades.get(parentClades.size() - 1));
    parentClades.add(clades.get(clades.size() - 1));
    int size = clades.size();
    // tree probability
    for (int i = 0; i < size; i++) {
        Clade c = clades.get(i);
        // get the bits of the clade
        Clade parent = parentClades.get(i);
        HashMap<BitSet, Clade> coFreqs;
        // increment the clade occurrences
        if (cladeProbabilities.containsKey(c.getBits())) {
            Clade tmp = cladeProbabilities.get(c.getBits());
            // tmp.addSample();
            tmp.addHeight(c.getHeight());
        // add the amount to the current occurences
        // frequency += cladeProbabilities.get(c);
        } else {
            // just to set the first value of the height value list
            // c.addSample();
            c.addHeight(c.getHeight());
            cladeProbabilities.put(c.getBits(), c);
        }
        // increment the conditional clade occurrences
        if (!parent.equals(c)) {
            if (cladeCoProbabilities.containsKey(parent.getBits())) {
                coFreqs = cladeCoProbabilities.get(parent.getBits());
            } else {
                // if it's the first time we observe the parent then we need
                // a new list for its conditional clades
                coFreqs = new HashMap<BitSet, Clade>();
                cladeCoProbabilities.put(parent.getBits(), coFreqs);
            }
            // clade
            if (coFreqs.containsKey(c.getBits())) {
                Clade tmp = coFreqs.get(c.getBits());
                tmp.addHeight(c.getHeight());
            // coFrequency += coFreqs.get(c.getBits());
            } else {
                // TODO check this code, especially if the cloning is needed
                // and not just the clade could be added
                Clade tmp = new Clade((BitSet) c.getBits().clone(), c.getHeight());
                tmp.addHeight(c.getHeight());
                coFreqs.put(c.getBits(), tmp);
            }
        }
    }
}

Example 2 with Clade

use of dr.evolution.tree.Clade in project beast-mcmc by beast-dev.

the class WeightedMultiplicativeBinary method addTree.

/**
     * increments the number of occurrences for all conditional clades
     *
     * @param tree - the tree to be added
     */
public void addTree(Tree tree) {
    samples++;
    List<Clade> clades = new ArrayList<Clade>();
    List<Clade> parentClades = new ArrayList<Clade>();
    // get clades contained in the tree
    getClades(tree, tree.getRoot(), parentClades, clades);
    // increment the occurrences of the clade and the conditional clade
    for (Clade c : clades) {
        // increment the clade occurrences
        if (cladeProbabilities.containsKey(c.getBits())) {
            Clade tmp = cladeProbabilities.get(c.getBits());
            tmp.addHeight(c.getHeight());
        // frequency += cladeProbabilities.get(c);
        } else {
            // just to set the first value of the height value list
            c.addHeight(c.getHeight());
            cladeProbabilities.put(c.getBits(), c);
        }
    }
}

Example 3 with Clade

use of dr.evolution.tree.Clade in project beast-mcmc by beast-dev.

the class ConditionalCladeFrequency method getTreeProbability.

/**
     * Calculates the probability of a given tree.
     *
     * @param tree - the tree to be analyzed
     * @return estimated posterior probability in log
     */
public double getTreeProbability(Tree tree) {
    double prob = 0.0;
    List<Clade> clades = new ArrayList<Clade>();
    List<Clade> parentClades = new ArrayList<Clade>();
    // get clades contained in the tree
    getNonComplementaryClades(tree, tree.getRoot(), parentClades, clades);
    int size = clades.size();
    // for every clade multiply its conditional clade probability to the tree probability
    for (int i = 0; i < size; i++) {
        Clade c = clades.get(i);
        // get the bits of the clade
        Clade parent = parentClades.get(i);
        // set the occurrences to epsilon
        double tmp = EPSILON;
        double parentOccurrences = 0.0;
        BitSet parentBits = parent.getBits();
        if (cladeProbabilities.containsKey(parentBits)) {
            // if we observed this clade in the trace, add the occurrences to epsilon
            parentOccurrences += cladeProbabilities.get(parentBits).getSampleCount();
        }
        if (cladeCoProbabilities.containsKey(parentBits)) {
            // if we observed the parent clade
            HashMap<BitSet, Clade> conditionalProbs = cladeCoProbabilities.get(parentBits);
            BitSet bits = c.getBits();
            if (conditionalProbs.containsKey(bits)) {
                // if we observed this conditional clade in the trace, add the occurrences to epsilon
                tmp += conditionalProbs.get(bits).getSampleCount();
            }
        }
        // add epsilon for each clade
        final double splits = Math.pow(2, parent.getSize() - 1) - 1;
        parentOccurrences += EPSILON * splits;
        // multiply the conditional clade probability to the tree
        // probability
        prob += Math.log(tmp / parentOccurrences);
    }
    return prob;
}

Example 4 with Clade

use of dr.evolution.tree.Clade in project beast-mcmc by beast-dev.

the class ConditionalCladeFrequency method splitClade.

public double splitClade(Clade parent, Clade[] children) {
    // the number of all possible clades is 2^n with n the number of tips
    // reduced by 2 because we wont consider the clades with all or no tips
    // contained
    // divide this number by 2 because every clade has a matching clade to
    // form the split
    // #splits = 2^(n-1) - 1
    final double splits = Math.pow(2, parent.getSize() - 1) - 1;
    double prob = 0;
    if (cladeCoProbabilities.containsKey(parent.getBits())) {
        HashMap<BitSet, Clade> childClades = cladeCoProbabilities.get(parent.getBits());
        double noChildClades = 0.0;
        double sum = 0.0;
        Set<BitSet> keys = childClades.keySet();
        for (BitSet child : keys) {
            Clade tmp = childClades.get(child);
            if (parent.getSize() > tmp.getSize() + 1) {
                sum += (tmp.getSampleCount() + EPSILON) / 2.0;
                noChildClades += 0.5;
            } else {
                sum += (tmp.getSampleCount() + EPSILON);
                noChildClades += 1.0;
            }
        }
        // add epsilon for each not observed clade
        sum += EPSILON * (splits - noChildClades);
        // roulette wheel
        double randomNumber = Math.random() * sum;
        for (BitSet child : keys) {
            Clade tmp = childClades.get(child);
            if (parent.getSize() > tmp.getSize() + 1) {
                randomNumber -= (tmp.getSampleCount() + EPSILON) / 2.0;
            } else {
                randomNumber -= (tmp.getSampleCount() + EPSILON);
            }
            if (randomNumber < 0) {
                children[0] = tmp;
                prob = (tmp.getSampleCount() + EPSILON) / sum;
                break;
            }
        }
        if (randomNumber >= 0) {
            // randomNumber /= EPSILON;
            prob = EPSILON / sum;
            BitSet newChild;
            BitSet inverseBits;
            do {
                do {
                    newChild = (BitSet) parent.getBits().clone();
                    int index = -1;
                    do {
                        index = newChild.nextSetBit(index + 1);
                        if (index > -1 && MathUtils.nextBoolean()) {
                            newChild.clear(index);
                        }
                    } while (index > -1);
                } while (newChild.cardinality() == 0 || newChild.cardinality() == parent.getSize());
                inverseBits = (BitSet) newChild.clone();
                inverseBits.xor(parent.getBits());
            } while (childClades.containsKey(newChild) || childClades.containsKey(inverseBits));
            Clade randomClade = new Clade(newChild, 0.9999 * parent.getHeight());
            children[0] = randomClade;
            BitSet secondChild = (BitSet) children[0].getBits().clone();
            secondChild.xor(parent.getBits());
            children[1] = new Clade(secondChild, 0.9999 * parent.getHeight());
        } else {
            BitSet secondChild = (BitSet) children[0].getBits().clone();
            secondChild.xor(parent.getBits());
            children[1] = childClades.get(secondChild);
            if (children[1] == null) {
                children[1] = new Clade(secondChild, 0.9999 * parent.getHeight());
            }
        }
    } else {
        prob = 1.0 / splits;
        BitSet newChild;
        do {
            newChild = (BitSet) parent.getBits().clone();
            int index = -1;
            do {
                index = newChild.nextSetBit(index + 1);
                if (index > -1 && MathUtils.nextBoolean()) {
                    newChild.clear(index);
                }
            } while (index > -1);
        } while (newChild.cardinality() == 0 || newChild.cardinality() == parent.getSize());
        Clade randomClade = new Clade(newChild, 0.9999 * parent.getHeight());
        // randomClade.addSample();
        randomClade.addHeight(0.9999 * parent.getHeight());
        children[0] = randomClade;
        BitSet secondChild = (BitSet) children[0].getBits().clone();
        secondChild.xor(parent.getBits());
        children[1] = new Clade(secondChild, 0.9999 * parent.getHeight());
        // children[1].addSample();
        randomClade.addHeight(0.9999 * parent.getHeight());
    }
    return Math.log(prob);
}

Example 5 with Clade

use of dr.evolution.tree.Clade in project beast-mcmc by beast-dev.

the class AbstractCladeImportanceDistribution method getClade.

/**
     * Creates a list with all clades of the tree
     *
     * @param tree - the tree from which the clades are extracted
     * @param node - the starting node. All clades below starting at this branch
     *             are added
     */
protected Clade getClade(Tree tree, NodeRef node) {
    // create a new bit set for this clade
    BitSet bits = new BitSet();
    // check if the node is external
    if (tree.isExternal(node)) {
        // if so, the only taxon in the clade am I
        int index = node.getNumber();
        bits.set(index);
    } else {
        // clade
        for (int i = 0; i < tree.getChildCount(node); i++) {
            NodeRef child = tree.getChild(node, i);
            Clade c = getClade(tree, child);
            bits.or(c.getBits());
        }
    }
    Clade c = new Clade(bits, tree.getNodeHeight(node));
    return c;
}