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

Example 1 with FlexibleTree

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

the class ARGTraceAnalysis method analyzeARG.

/**
	 * Actually analyzes a particular tree using the trace given the burnin
	 */
public final Tree analyzeARG(String target) {
    int n = getTreeCount();
    FlexibleTree meanTree = null;
    for (int i = 0; i < n; i++) {
        Tree tree = getARG(i);
        if (TreeUtils.uniqueNewick(tree, tree.getRoot()).equals(target)) {
            meanTree = new FlexibleTree(tree);
            break;
        }
    }
    if (meanTree == null)
        throw new RuntimeException("No target tree in trace");
    int m = meanTree.getInternalNodeCount();
    for (int j = 0; j < m; j++) {
        double[] heights = new double[n];
        NodeRef node1 = meanTree.getInternalNode(j);
        Set<String> leafSet = TreeUtils.getDescendantLeaves(meanTree, node1);
        for (int i = 0; i < n; i++) {
            Tree tree = getARG(i);
            NodeRef node2 = TreeUtils.getCommonAncestorNode(tree, leafSet);
            heights[i] = tree.getNodeHeight(node2);
        }
        meanTree.setNodeHeight(node1, dr.stats.DiscreteStatistics.mean(heights));
        meanTree.setNodeAttribute(node1, "upper", new Double(dr.stats.DiscreteStatistics.quantile(0.975, heights)));
        meanTree.setNodeAttribute(node1, "lower", new Double(dr.stats.DiscreteStatistics.quantile(0.025, heights)));
    }
    return meanTree;
}

Example 2 with FlexibleTree

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

the class TempestFrame method readFromFile.

protected boolean readFromFile(File file) throws IOException {
    Reader reader = new FileReader(file);
    BufferedReader bufferedReader = new BufferedReader(reader);
    String line = bufferedReader.readLine();
    while (line != null && line.length() == 0) {
        line = bufferedReader.readLine();
    }
    boolean isNexus = (line != null && line.toUpperCase().contains("#NEXUS"));
    reader = new FileReader(file);
    Tree tree = null;
    try {
        if (isNexus) {
            NexusImporter importer = new NexusImporter(reader);
            tree = importer.importTree(taxa);
        } else {
            NewickImporter importer = new NewickImporter(reader);
            tree = importer.importTree(taxa);
        }
    } catch (Importer.ImportException ime) {
        JOptionPane.showMessageDialog(this, "Error parsing imported file: " + ime, "Error reading file", JOptionPane.ERROR_MESSAGE);
        ime.printStackTrace();
        return false;
    } catch (IOException ioex) {
        JOptionPane.showMessageDialog(this, "File I/O Error: " + ioex, "File I/O Error", JOptionPane.ERROR_MESSAGE);
        ioex.printStackTrace();
        return false;
    } catch (Exception ex) {
        JOptionPane.showMessageDialog(this, "Fatal exception: " + ex, "Error reading file", JOptionPane.ERROR_MESSAGE);
        ex.printStackTrace();
        return false;
    }
    if (tree == null) {
        JOptionPane.showMessageDialog(this, "The file is not in a suitable format or contains no trees.", "Error reading file", JOptionPane.ERROR_MESSAGE);
        return false;
    }
    FlexibleTree binaryTree = new FlexibleTree(tree, true);
    binaryTree.resolveTree();
    trees.add(binaryTree);
    if (taxa == null) {
        taxa = binaryTree;
    }
    getExportTreeAction().setEnabled(true);
    getExportDataAction().setEnabled(true);
    return true;
}

Example 3 with FlexibleTree

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

the class ExchangeOperatorTest method testWideExchangeOperator2.

public void testWideExchangeOperator2() throws IOException, ImportException {
    // probability of picking (A,B) node is 1/(2n-2) = 1/8
    // probability of swapping with D is 1/2
    // total = 1/16
    //probability of picking {D} node is 1/(2n-2) = 1/8
    //probability of picking {A,B} is 1/5
    // total = 1/40
    //total = 1/16 + 1/40 = 0.0625 + 0.025 = 0.0875
    // new test:
    // probability of picking (A,B) node is 1/(2n-2) = 1/8
    // probability of swapping with D is 1/(2n-3) = 1/7
    // total = 1/56
    //probability of picking {D} node is 1/(2n-2) = 1/8
    //probability of picking {A,B} is 1/(2n-3) = 1/7
    // total = 1/56
    //total = 1/56 + 1/56 = 1/28
    System.out.println("Test 1: Forward");
    String treeMatch = "(((D,C),(A,B)),E);";
    int count = 0;
    int reps = 1000000;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5);
        ExchangeOperator operator = new ExchangeOperator(ExchangeOperator.WIDE, treeModel, 1.0);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_1 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_1);
    System.out.println("Number of expected ratio:\t" + 1.0 / 28.0);
    assertExpectation(1.0 / 28.0, p_1, reps);
    // since this operator is supposed to be symmetric it got a hastings ratio of one
    // this means, it should propose the same move just backwards with the same probability
    // BUT:
    // (((D:2.0,C:2.0):1.0,(A:1.0,B:1.0):2.0):1.0,E:4.0) -> ((((A,B),C),D),E)
    // probability of picking (A,B) node is 1/(2n-2) = 1/8
    // probability of swapping with D is 1/3
    // total = 1/24
    //probability of picking {D} node is 1/(2n-2) = 1/8
    //probability of picking {A,B} is 1/4
    // total = 1/32
    //total = 1/24 + 1/32 = 7/96 = 0.07291666666
    // new test:
    // probability of picking (A,B) node is 1/(2n-2) = 1/8
    // probability of swapping with D is 1/(2n-3) = 1/7
    // total = 1/56
    //probability of picking {D} node is 1/(2n-2) = 1/8
    //probability of picking {A,B} is 1/(2n-3) = 1/7
    // total = 1/56
    //total = 1/56 + 1/56 = 1/28
    System.out.println("Test 2: Backward");
    treeMatch = "((((A,B),C),D),E);";
    NewickImporter importer = new NewickImporter("(((D:2.0,C:2.0):1.0,(A:1.0,B:1.0):2.0):1.0,E:4.0);");
    FlexibleTree tree5_2 = (FlexibleTree) importer.importTree(null);
    count = 0;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5_2);
        ExchangeOperator operator = new ExchangeOperator(ExchangeOperator.WIDE, treeModel, 1.0);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_2 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_2);
    System.out.println("Number of expected ratio:\t" + 1.0 / 28.0);
    assertExpectation(1.0 / 28.0, p_2, reps);
}

Example 4 with FlexibleTree

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

the class ImportancePruneAndRegraftTestProblem method testDoOperation.

/**
	 * Test method for {@link SimpleMCMCOperator#doOperation()}.
	 * @throws ImportException 
	 * @throws IOException 
	 */
public void testDoOperation() throws IOException, ImportException {
    // probability of picking (A,B) node is 1/(2n-3) = 1/7
    // probability of swapping with D is 1/2
    // total = 1/14
    //probability of picking {D} node is 1/(2n-3) = 1/7
    //probability of picking {A,B} is 1/5
    // total = 1/35
    //total = 1/14 + 1/35 = 7/70 = 0.1
    System.out.println("Test 1: Forward");
    String treeMatch = "(((D,C),(A,B)),E);";
    int count = 0;
    int reps = 1000000;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5);
        ImportancePruneAndRegraft operator = new ImportancePruneAndRegraft(treeModel, 1.0, 0);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_1 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_1);
    System.out.println("Number of expected ratio:\t" + 0.1);
    assertExpectation(0.1, p_1, reps);
    // lets see what the backward probability is for the hastings ratio
    // (((D:2.0,C:2.0):1.0,(A:1.0,B:1.0):2.0):1.0,E:4.0) -> ((((A,B),C),D),E)
    // probability of picking (A,B) node is 1/(2n-3) = 1/7
    // probability of swapping with D is 1/3
    // total = 1/21
    //probability of picking {D} node is 1/(2n-2) = 1/7
    //probability of picking {A,B} is 1/4
    // total = 1/28
    //total = 1/21 + 1/28 = 7/84 = 0.08333333
    System.out.println("Test 2: Backward");
    treeMatch = "((((A,B),C),D),E);";
    NewickImporter importer = new NewickImporter("(((D:2.0,C:2.0):1.0,(A:1.0,B:1.0):2.0):1.0,E:4.0);");
    FlexibleTree tree5_2 = (FlexibleTree) importer.importTree(null);
    count = 0;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5_2);
        ImportancePruneAndRegraft operator = new ImportancePruneAndRegraft(treeModel, 1.0, 1);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_2 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_2);
    System.out.println("Number of expected ratio:\t" + 0.0833333);
    assertExpectation(0.0833333, p_2, reps);
}

Example 5 with FlexibleTree

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

the class ImportanceSubtreeSwapTestProblem method testDoOperation.

/**
	 * Test method for {@link SimpleMCMCOperator#doOperation()}.
	 * @throws ImportException 
	 * @throws IOException 
	 */
public void testDoOperation() throws IOException, ImportException {
    // probability of picking (A,B) node is 1/(2n-3) = 1/7
    // probability of swapping with D is 1/2
    // total = 1/14
    //probability of picking {D} node is 1/(2n-3) = 1/7
    //probability of picking {A,B} is 1/5
    // total = 1/35
    //total = 1/14 + 1/35 = 7/70 = 0.1
    System.out.println("Test 1: Forward");
    String treeMatch = "(((D,C),(A,B)),E);";
    int count = 0;
    int reps = 100000;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5);
        ImportanceSubtreeSwap operator = new ImportanceSubtreeSwap(treeModel, 1.0, 0);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_1 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_1);
    System.out.println("Number of expected ratio:\t" + 0.1);
    assertExpectation(0.1, p_1, reps);
    // lets see what the backward probability is for the hastings ratio
    // (((D:2.0,C:2.0):1.0,(A:1.0,B:1.0):2.0):1.0,E:4.0) -> ((((A,B),C),D),E)
    // probability of picking (A,B) node is 1/(2n-3) = 1/7
    // probability of swapping with D is 1/3
    // total = 1/21
    //probability of picking {D} node is 1/(2n-2) = 1/7
    //probability of picking {A,B} is 1/4
    // total = 1/28
    //total = 1/21 + 1/28 = 7/84 = 0.08333333
    System.out.println("Test 2: Backward");
    treeMatch = "((((A,B),C),D),E);";
    NewickImporter importer = new NewickImporter("(((D:2.0,C:2.0):1.0,(A:1.0,B:1.0):2.0):1.0,E:4.0);");
    FlexibleTree tree5_2 = (FlexibleTree) importer.importTree(null);
    count = 0;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new TreeModel("treeModel", tree5_2);
        ImportanceSubtreeSwap operator = new ImportanceSubtreeSwap(treeModel, 1.0, 0);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_2 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_2);
    System.out.println("Number of expected ratio:\t" + 0.0833333);
    assertExpectation(0.0833333, p_2, reps);
}