Examples with TreeTrace dr.evolution.io.TreeTrace used on opensource projects

Example 1 with TreeTrace

use of dr.evolution.io.TreeTrace in project beast-mcmc by beast-dev.

the class TreeTraceAnalysis method analyze.

/**
     * Actually analyzes the trace given the burnin
     *
     * @param verbose if true then progress is logged to stdout
     */
void analyze(boolean verbose) {
    if (verbose) {
        if (traces.length > 1)
            System.out.println("Combining " + traces.length + " traces.");
    }
    final Tree tree0 = getTree(0);
    double[][] changed = new double[tree0.getNodeCount()][tree0.getNodeCount()];
    double[] rateConditionalOnChange = new double[tree0.getNodeCount()];
    boolean changesFound = false;
    cladeSet = new CladeSet(tree0);
    treeSet = new FrequencySet<String>();
    treeSet.add(TreeUtils.uniqueNewick(tree0, tree0.getRoot()));
    final int reportRate = 60;
    for (TreeTrace trace : traces) {
        final int treeCount = trace.getTreeCount(burnin * trace.getStepSize());
        final double stepSize = treeCount / (double) reportRate;
        int counter = 1;
        if (verbose) {
            System.out.println("Analyzing " + treeCount + " trees...");
            System.out.println("0              25             50             75            100");
            System.out.println("|--------------|--------------|--------------|--------------|");
            System.out.print("*");
        }
        for (int i = 1; i < treeCount; i++) {
            Tree tree = trace.getTree(i, burnin * trace.getStepSize());
            for (int j = 0; j < tree.getNodeCount(); j++) {
                if (tree.getNode(j) != tree.getRoot() && tree.getNodeAttribute(tree.getNode(j), "changed") != null) {
                    changesFound = true;
                    final Object o = tree.getNodeAttribute(tree.getNode(j), "changed");
                    if (o != null) {
                        boolean ch = getChanged(tree, j);
                        if (ch) {
                            rateConditionalOnChange[j] += (Double) tree.getNodeAttribute(tree.getNode(j), "rate");
                        }
                        for (int k = 0; k < tree.getNodeCount(); k++) {
                            if (tree.getNode(k) != tree.getRoot()) {
                                changed[j][k] += (ch && getChanged(tree, k)) ? 1 : 0;
                            }
                        }
                    }
                }
            }
            cladeSet.add(tree);
            treeSet.add(TreeUtils.uniqueNewick(tree, tree.getRoot()));
            if (verbose && i >= (int) Math.round(counter * stepSize) && counter <= reportRate) {
                System.out.print("*");
                System.out.flush();
                counter += 1;
            }
        }
        if (verbose) {
            System.out.println("*");
        }
    }
    if (changesFound) {
        for (int j = 0; j < tree0.getNodeCount(); j++) {
            System.out.println(j + "\t" + rateConditionalOnChange[j]);
        }
        System.out.println();
        for (int j = 0; j < tree0.getNodeCount(); j++) {
            for (int k = 0; k < tree0.getNodeCount(); k++) {
                System.out.print(changed[j][k] + "\t");
            }
            System.out.println();
        }
    }
}

Example 2 with TreeTrace

use of dr.evolution.io.TreeTrace in project beast-mcmc by beast-dev.

the class TreeTraceAnalysis method getTree.

final Tree getTree(int index) {
    int oldTreeCount = 0;
    int newTreeCount = 0;
    for (TreeTrace trace : traces) {
        final int br = burnin * trace.getStepSize();
        newTreeCount += trace.getTreeCount(br);
        if (index < newTreeCount) {
            return trace.getTree(index - oldTreeCount, br);
        }
        oldTreeCount = newTreeCount;
    }
    throw new RuntimeException("Couldn't find tree " + index);
}

Example 3 with TreeTrace

use of dr.evolution.io.TreeTrace in project beast-mcmc by beast-dev.

the class WeightedMultiplicativeBinary method analyzeTrace.

/**
     * Actually analyzes the trace given the burn-in. Each tree from the trace
     * is read and the conditional clade frequencies incremented.
     *
     * @param verbose if true then progress is logged to stdout
     */
public void analyzeTrace(boolean verbose) {
    if (verbose) {
        if (traces.length > 1)
            System.out.println("Combining " + traces.length + " traces.");
    }
    // get first tree to extract the taxon
    Tree tree = getTree(0);
    // read every tree from the trace
    for (TreeTrace trace : traces) {
        // do some output stuff
        int treeCount = trace.getTreeCount(burnin * trace.getStepSize());
        double stepSize = treeCount / 60.0;
        int counter = 1;
        if (verbose) {
            System.out.println("Analyzing " + treeCount + " trees...");
            System.out.println("0              25             50             75            100");
            System.out.println("|--------------|--------------|--------------|--------------|");
            System.out.print("*");
        }
        for (int i = 1; i < treeCount; i++) {
            // get the next tree
            tree = trace.getTree(i, burnin * trace.getStepSize());
            // add the tree and its clades to the frequencies
            addTree(tree);
            // some more output stuff
            if (i >= (int) Math.round(counter * stepSize) && counter <= 60) {
                if (verbose) {
                    System.out.print("*");
                    System.out.flush();
                }
                counter += 1;
            }
        }
        if (verbose) {
            System.out.println("*");
        }
    }
}

Example 4 with TreeTrace

use of dr.evolution.io.TreeTrace in project beast-mcmc by beast-dev.

the class WeightedMultiplicativeBinary method getTree.

/**
     * get the i'th tree of the trace
     *
     * @param index
     * @return the i'th tree of the trace
     */
public final Tree getTree(int index) {
    int oldTreeCount = 0;
    int newTreeCount = 0;
    for (TreeTrace trace : traces) {
        newTreeCount += trace.getTreeCount(burnin * trace.getStepSize());
        if (index < newTreeCount) {
            return trace.getTree(index - oldTreeCount, burnin * trace.getStepSize());
        }
        oldTreeCount = newTreeCount;
    }
    throw new RuntimeException("Couldn't find tree " + index);
}

Example 5 with TreeTrace

use of dr.evolution.io.TreeTrace in project beast-mcmc by beast-dev.

the class ConditionalCladeFrequency method getTree.

/**
     * get the i'th tree of the trace
     *
     * @param index
     * @return the i'th tree of the trace
     */
public final Tree getTree(int index) {
    int oldTreeCount = 0;
    int newTreeCount = 0;
    for (TreeTrace trace : traces) {
        newTreeCount += trace.getTreeCount(burnin * trace.getStepSize());
        if (index < newTreeCount) {
            return trace.getTree(index - oldTreeCount, burnin * trace.getStepSize());
        }
        oldTreeCount = newTreeCount;
    }
    throw new RuntimeException("Couldn't find tree " + index);
}