Examples with DefaultTreeModel dr.evomodel.tree.DefaultTreeModel used on opensource projects

Example 36 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class MCMCTest method testMCMC.

public void testMCMC() {
    // Sub model
    // new double[]{0.25, 0.25, 0.25, 0.25});
    Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
    Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 1.0, 1.0E-8, Double.POSITIVE_INFINITY);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    // siteModel
    GammaSiteModel siteModel = new GammaSiteModel(hky);
    Parameter mu = new Parameter.Default(GammaSiteModelParser.MUTATION_RATE, 1.0, 0, Double.POSITIVE_INFINITY);
    siteModel.setMutationRateParameter(mu);
    // treeLikelihood
    SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
    TreeLikelihood treeLikelihood = new TreeLikelihood(patterns, treeModel, siteModel, null, null, false, false, true, false, false);
    treeLikelihood.setId(TreeLikelihoodParser.TREE_LIKELIHOOD);
    // Operators
    OperatorSchedule schedule = new SimpleOperatorSchedule();
    MCMCOperator operator = new ScaleOperator(kappa, 0.5);
    operator.setWeight(1.0);
    schedule.addOperator(operator);
    // Parameter rootParameter = treeModel.createNodeHeightsParameter(true, false, false);
    // ScaleOperator scaleOperator = new ScaleOperator(rootParameter, 0.75, AdaptationMode.ADAPTATION_ON, 1.0);
    Parameter rootHeight = ((DefaultTreeModel) treeModel).getRootHeightParameter();
    rootHeight.setId(TREE_HEIGHT);
    operator = new ScaleOperator(rootHeight, 0.5);
    operator.setWeight(1.0);
    schedule.addOperator(operator);
    Parameter internalHeights = ((DefaultTreeModel) treeModel).createNodeHeightsParameter(false, true, false);
    operator = new UniformOperator(internalHeights, 10.0);
    schedule.addOperator(operator);
    operator = new SubtreeSlideOperator(((DefaultTreeModel) treeModel), 1, 1, true, false, false, false, AdaptationMode.ADAPTATION_ON, AdaptableMCMCOperator.DEFAULT_ADAPTATION_TARGET);
    schedule.addOperator(operator);
    operator = new ExchangeOperator(ExchangeOperator.NARROW, treeModel, 1.0);
    // operator.doOperation();
    schedule.addOperator(operator);
    operator = new ExchangeOperator(ExchangeOperator.WIDE, treeModel, 1.0);
    // operator.doOperation();
    schedule.addOperator(operator);
    operator = new WilsonBalding(treeModel, 1.0);
    // operator.doOperation();
    schedule.addOperator(operator);
    // Log
    ArrayLogFormatter formatter = new ArrayLogFormatter(false);
    MCLogger[] loggers = new MCLogger[2];
    loggers[0] = new MCLogger(formatter, 1000, false);
    loggers[0].add(treeLikelihood);
    loggers[0].add(rootHeight);
    loggers[0].add(kappa);
    loggers[1] = new MCLogger(new TabDelimitedFormatter(System.out), 100000, false);
    loggers[1].add(treeLikelihood);
    loggers[1].add(rootHeight);
    loggers[1].add(kappa);
    // MCMC
    MCMC mcmc = new MCMC("mcmc1");
    MCMCOptions options = new MCMCOptions(10000000);
    mcmc.setShowOperatorAnalysis(true);
    mcmc.init(options, treeLikelihood, schedule, loggers);
    mcmc.run();
    // time
    System.out.println(mcmc.getTimer().toString());
    // Tracer
    List<Trace> traces = formatter.getTraces();
    ArrayTraceList traceList = new ArrayTraceList("MCMCTest", traces, 0);
    for (int i = 1; i < traces.size(); i++) {
        traceList.analyseTrace(i);
    }
    // <expectation name="likelihood" value="-1815.75"/>
    // <expectation name="treeModel.rootHeight" value="6.42048E-2"/>
    // <expectation name="hky.kappa" value="32.8941"/>
    TraceCorrelation likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TreeLikelihoodParser.TREE_LIKELIHOOD));
    assertExpectation(TreeLikelihoodParser.TREE_LIKELIHOOD, likelihoodStats, -1815.75);
    TraceCorrelation treeHeightStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TREE_HEIGHT));
    assertExpectation(TREE_HEIGHT, treeHeightStats, 6.42048E-2);
    TraceCorrelation kappaStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(HKYParser.KAPPA));
    assertExpectation(HKYParser.KAPPA, kappaStats, 32.8941);
}

Example 37 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class TraceCorrelationAssert method createTreeModel.

private void createTreeModel(ConstantPopulation constant) {
    CoalescentSimulator simulator = new CoalescentSimulator();
    Tree tree = simulator.simulateTree(alignment, constant);
    // treeModel
    treeModel = new DefaultTreeModel(tree);
}

Example 38 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class BASTADensityTester method createSpecifiedTree.

private static TreeModel createSpecifiedTree(String t) throws Exception {
    NewickImporter importer = new NewickImporter(t);
    Tree tree = importer.importTree(null);
    // treeModel
    return new DefaultTreeModel(tree);
}

Example 39 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class TreeModelParser method parseXMLObject.

/**
 * @return a tree object based on the XML element it was passed.
 */
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Tree tree = (Tree) xo.getChild(Tree.class);
    boolean fixHeights = xo.getAttribute(FIX_HEIGHTS, false);
    boolean fixTree = xo.getAttribute(FIX_TREE, false);
    DefaultTreeModel treeModel = new DefaultTreeModel(xo.getId(), tree, fixHeights, fixTree);
    Logger.getLogger("dr.evomodel").info("\nCreating the tree model, '" + xo.getId() + "'");
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof XMLObject) {
            XMLObject cxo = (XMLObject) xo.getChild(i);
            if (cxo.getName().equals(ROOT_HEIGHT)) {
                ParameterParser.replaceParameter(cxo, treeModel.getRootHeightParameter());
            } else if (cxo.getName().equals(LEAF_HEIGHT)) {
                String taxonName;
                if (cxo.hasAttribute(TAXON)) {
                    taxonName = cxo.getStringAttribute(TAXON);
                } else {
                    throw new XMLParseException("taxa element missing from leafHeight element in treeModel element");
                }
                int index = treeModel.getTaxonIndex(taxonName);
                if (index == -1) {
                    throw new XMLParseException("taxon " + taxonName + " not found for leafHeight element in treeModel element");
                }
                NodeRef node = treeModel.getExternalNode(index);
                Parameter newParameter = treeModel.getLeafHeightParameter(node);
                ParameterParser.replaceParameter(cxo, newParameter);
                Taxon taxon = treeModel.getTaxon(index);
                setUncertaintyBounds(newParameter, taxon);
            } else if (cxo.getName().equals(LEAF_HEIGHTS)) {
                // get a set of leaf height parameters out as a compound parameter...
                TaxonList taxa = (TaxonList) cxo.getChild(TaxonList.class);
                Parameter offsetParameter = (Parameter) cxo.getChild(Parameter.class);
                CompoundParameter leafHeights = new CompoundParameter("leafHeights");
                for (Taxon taxon : taxa) {
                    int index = treeModel.getTaxonIndex(taxon);
                    if (index == -1) {
                        throw new XMLParseException("taxon " + taxon.getId() + " not found for leafHeight element in treeModel element");
                    }
                    NodeRef node = treeModel.getExternalNode(index);
                    Parameter newParameter = treeModel.getLeafHeightParameter(node);
                    leafHeights.addParameter(newParameter);
                    setUncertaintyBounds(newParameter, taxon);
                }
                ParameterParser.replaceParameter(cxo, leafHeights);
            } else if (cxo.getName().equals(NODE_HEIGHTS)) {
                boolean rootNode = cxo.getAttribute(ROOT_NODE, false);
                boolean internalNodes = cxo.getAttribute(INTERNAL_NODES, false);
                boolean leafNodes = cxo.getAttribute(LEAF_NODES, false);
                if (!rootNode && !internalNodes && !leafNodes) {
                    throw new XMLParseException("one or more of root, internal or leaf nodes must be selected for the nodeHeights element");
                }
                ParameterParser.replaceParameter(cxo, treeModel.createNodeHeightsParameter(rootNode, internalNodes, leafNodes));
            } else if (cxo.getName().equals(NODE_RATES)) {
                boolean rootNode = cxo.getAttribute(ROOT_NODE, false);
                boolean internalNodes = cxo.getAttribute(INTERNAL_NODES, false);
                boolean leafNodes = cxo.getAttribute(LEAF_NODES, false);
                double[] initialValues = null;
                if (cxo.hasAttribute(INITIAL_VALUE)) {
                    initialValues = cxo.getDoubleArrayAttribute(INITIAL_VALUE);
                }
                if (!rootNode && !internalNodes && !leafNodes) {
                    throw new XMLParseException("one or more of root, internal or leaf nodes must be selected for the nodeRates element");
                }
                ParameterParser.replaceParameter(cxo, treeModel.createNodeRatesParameter(initialValues, rootNode, internalNodes, leafNodes));
            } else if (cxo.getName().equals(NODE_TRAITS)) {
                parseNodeTraits(cxo, treeModel);
            } else if (cxo.getName().equals(LEAF_TRAIT)) {
                String name = cxo.getAttribute(NAME, "trait");
                String taxonName;
                if (cxo.hasAttribute(TAXON)) {
                    taxonName = cxo.getStringAttribute(TAXON);
                } else {
                    throw new XMLParseException("taxa element missing from leafTrait element in treeModel element");
                }
                int index = treeModel.getTaxonIndex(taxonName);
                if (index == -1) {
                    throw new XMLParseException("taxon '" + taxonName + "' not found for leafTrait element in treeModel element");
                }
                NodeRef node = treeModel.getExternalNode(index);
                Parameter parameter = treeModel.getNodeTraitParameter(node, name);
                if (parameter == null)
                    throw new XMLParseException("trait '" + name + "' not found for leafTrait (taxon, " + taxonName + ") element in treeModel element");
                ParameterParser.replaceParameter(cxo, parameter);
            } else {
                throw new XMLParseException("illegal child element in " + getParserName() + ": " + cxo.getName());
            }
        } else if (xo.getChild(i) instanceof Tree) {
        // do nothing - already handled
        } else {
            throw new XMLParseException("illegal child element in  " + getParserName() + ": " + xo.getChildName(i) + " " + xo.getChild(i));
        }
    }
    // Logger.getLogger("dr.evomodel").info("  initial tree topology = " + TreeUtils.uniqueNewick(treeModel, treeModel.getRoot()));
    Logger.getLogger("dr.evomodel").info("  taxon count = " + treeModel.getExternalNodeCount());
    Logger.getLogger("dr.evomodel").info("  tree height = " + treeModel.getNodeHeight(treeModel.getRoot()));
    return treeModel;
}

Example 40 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class MRCATraitStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(NAME, xo.getId());
    String trait = xo.getStringAttribute(TRAIT);
    DefaultTreeModel tree = (DefaultTreeModel) xo.getChild(DefaultTreeModel.class);
    TaxonList taxa = (TaxonList) xo.getElementFirstChild(MRCA);
    try {
        return new MRCATraitStatistic(name, trait, tree, taxa);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
    }
}