Examples with SiteModel beast.evolution.sitemodel.SiteModel used on opensource projects

Example 21 with SiteModel

use of beast.evolution.sitemodel.SiteModel in project bacter by tgvaughan.

the class SimulatedAlignmentTest method test.

@Test
public void test() throws Exception {
    // Randomizer.setSeed(26);
    Randomizer.setSeed(7);
    Locus locus = new Locus("locus", 100000);
    TaxonSet taxonSet = getTaxonSet(10);
    ConstantPopulation popFunc = new ConstantPopulation();
    popFunc.initByName("popSize", new RealParameter("1.0"));
    ConversionGraph acg = new SimulatedACG();
    acg.initByName("rho", 1.0 / 100000, "delta", 1000.0, "populationModel", popFunc, "locus", locus, "taxonset", taxonSet);
    System.out.println(acg);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", new RealParameter("1.0"), "substModel", jc);
    // Simulate alignment:
    SimulatedAlignment alignment = new SimulatedAlignment();
    alignment.initByName("acg", acg, "siteModel", siteModel, "outputFileName", "simulated_alignment.nexus", "useNexus", true);
    for (Region region : acg.getRegions(locus)) System.out.println(new MarginalTree(acg, region));
    // (Should be enough info here for precise agreement)
    for (Region region : acg.getRegions(locus)) {
        Alignment margAlign = createMarginalAlignment(alignment, region);
        ClusterTree upgmaTree = new ClusterTree();
        upgmaTree.initByName("clusterType", "upgma", "taxa", margAlign);
        MarginalTree marginalTree = new MarginalTree(acg, region);
        // outfMarg.println(marginalTree.getRoot() + ";");
        // outfMarg.flush();
        // 
        // outfUPGMA.println(upgmaTree.getRoot() + ";");
        // outfUPGMA.flush();
        assertTrue(topologiesEquivalent(marginalTree.getRoot(), upgmaTree.getRoot()));
    }
// outfMarg.close();
// outfUPGMA.close();
}

Example 22 with SiteModel

use of beast.evolution.sitemodel.SiteModel in project bacter by tgvaughan.

the class ACGLikelihoodTest method testLikelihoodUsingSimulatedData.

@Test
public void testLikelihoodUsingSimulatedData() throws Exception {
    ConstantPopulation popFunc = new ConstantPopulation();
    popFunc.initByName("popSize", new RealParameter("1.0"));
    Locus locus = new Locus("locus", 10000);
    TaxonSet taxonSet = getTaxonSet(10);
    ConversionGraph acg = new SimulatedACG();
    acg.initByName("rho", 5.0 / locus.getSiteCount(), "delta", 1000.0, "populationModel", popFunc, "locus", locus, "taxonset", taxonSet);
    System.out.println(acg);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", new RealParameter("1"), "substModel", jc);
    // Simulate alignment:
    SimulatedAlignment alignment = new SimulatedAlignment();
    alignment.initByName("acg", acg, "siteModel", siteModel, "outputFileName", "simulated_alignment.nexus", "useNexus", true);
    // Calculate likelihood:
    ACGLikelihood argLikelihood = new ACGLikelihood();
    argLikelihood.initByName("locus", locus, "data", alignment, "tree", acg, "siteModel", siteModel);
    double logP = argLikelihood.calculateLogP();
    // Compare product of likelihoods of "marginal alignments" with
    // likelihood computed using RGL.
    ACGLikelihoodSlow argLikelihoodSlow = new ACGLikelihoodSlow();
    argLikelihoodSlow.initByName("locus", locus, "data", alignment, "tree", acg, "siteModel", siteModel);
    double logPprime = argLikelihoodSlow.calculateLogP();
    double relError = 2.0 * Math.abs(logP - logPprime) / Math.abs(logP + logPprime);
    System.out.format("logP=%g\nlogPprime=%g\nrelError=%g\n", logP, logPprime, relError);
    assertTrue(relError < 1e-13);
}

Example 23 with SiteModel

use of beast.evolution.sitemodel.SiteModel in project bacter by tgvaughan.

the class ACGLikelihoodTest method testBeagleLikelihood.

@Test
public void testBeagleLikelihood() throws Exception {
    Locus locus = new Locus("locus", getAlignment());
    // ConversionGraph
    ConversionGraph acg = new ConversionGraph();
    ClusterTree tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", locus.getAlignment());
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("substModel", jc);
    // Likelihood
    ACGLikelihoodBeagle argLikelihood = new ACGLikelihoodBeagle();
    argLikelihood.initByName("locus", locus, "tree", acg, "siteModel", siteModel);
    ACGLikelihoodSlow argLikelihoodSlow = new ACGLikelihoodSlow();
    argLikelihoodSlow.initByName("locus", locus, "tree", acg, "siteModel", siteModel);
    acg.setEverythingDirty(true);
    try {
        double logP = argLikelihood.calculateLogP();
        double logPtrue = argLikelihoodSlow.calculateLogP();
        double relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
        assertTrue(relativeDiff < 1e-14);
        // Add a single recombination event
        Node node1 = acg.getExternalNodes().get(0);
        Node node2 = node1.getParent();
        double height1 = 0.5 * (node1.getHeight() + node1.getParent().getHeight());
        double height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
        int startLocus = 100;
        int endLocus = 200;
        Conversion recomb1 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
        acg.addConversion(recomb1);
        logP = argLikelihood.calculateLogP();
        logPtrue = argLikelihoodSlow.calculateLogP();
        relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
        assertTrue(relativeDiff < 1e-14);
        // Add another recombination event
        node1 = acg.getExternalNodes().get(0);
        node2 = acg.getNode(20);
        height1 = 0.75 * (node1.getHeight() + node1.getParent().getHeight());
        height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
        startLocus = 250;
        endLocus = 300;
        Conversion recomb2 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
        acg.addConversion(recomb2);
        logP = argLikelihood.calculateLogP();
        logPtrue = argLikelihoodSlow.calculateLogP();
        relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
        assertTrue(relativeDiff < 1e-14);
    } catch (RuntimeException ex) {
        System.err.println("Beagle library not found: skipping beagle likelihood test.");
    }
}

Example 24 with SiteModel

use of beast.evolution.sitemodel.SiteModel in project bacter by tgvaughan.

the class ACGLikelihoodTest method testLikelihoodFixedData.

@Test
public void testLikelihoodFixedData() throws Exception {
    Locus locus = new Locus("locus", getAlignment());
    // ConversionGraph
    ConversionGraph acg = new ConversionGraph();
    ClusterTree tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", locus.getAlignment());
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("substModel", jc);
    // Likelihood
    ACGLikelihood argLikelihood = new ACGLikelihood();
    argLikelihood.initByName("locus", locus, "tree", acg, "siteModel", siteModel);
    ACGLikelihoodSlow argLikelihoodSlow = new ACGLikelihoodSlow();
    argLikelihoodSlow.initByName("locus", locus, "tree", acg, "siteModel", siteModel);
    acg.setEverythingDirty(true);
    double logP = argLikelihood.calculateLogP();
    double logPtrue = argLikelihoodSlow.calculateLogP();
    double relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
    assertTrue(relativeDiff < 1e-14);
    // Add a single recombination event
    Node node1 = acg.getExternalNodes().get(0);
    Node node2 = node1.getParent();
    double height1 = 0.5 * (node1.getHeight() + node1.getParent().getHeight());
    double height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
    int startLocus = 100;
    int endLocus = 200;
    Conversion recomb1 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(recomb1);
    logP = argLikelihood.calculateLogP();
    logPtrue = argLikelihoodSlow.calculateLogP();
    relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
    assertTrue(relativeDiff < 1e-14);
    // Add another recombination event
    node1 = acg.getExternalNodes().get(0);
    node2 = acg.getNode(20);
    height1 = 0.75 * (node1.getHeight() + node1.getParent().getHeight());
    height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
    startLocus = 250;
    endLocus = 300;
    Conversion recomb2 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(recomb2);
    logP = argLikelihood.calculateLogP();
    logPtrue = argLikelihoodSlow.calculateLogP();
    relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
    assertTrue(relativeDiff < 1e-14);
}

Example 25 with SiteModel

use of beast.evolution.sitemodel.SiteModel in project beast2 by CompEvol.

the class BeautiPanel method cloneFrom.

/**
 * Clones partition identified by sourceID to targetID and type (Site/Clock/Tree model)
 * as stored in config.
 * @param sourceID
 * @param targetID
 */
public void cloneFrom(String sourceID, String targetID) {
    if (sourceID.equals(targetID)) {
        return;
    }
    String type = config.hasPartitionsInput.get().toString();
    java.util.List<BEASTInterface> list = doc.getPartitions(type);
    int source = -1, target = -1;
    for (int i = 0; i < list.size(); i++) {
        BEASTInterface partition = list.get(i);
        if (type.equals("SiteModel")) {
            partition = (BEASTInterface) ((GenericTreeLikelihood) partition).siteModelInput.get();
        } else if (type.equals("ClockModel")) {
            partition = ((GenericTreeLikelihood) partition).branchRateModelInput.get();
        } else if (type.equals("Tree")) {
            partition = (BEASTInterface) ((GenericTreeLikelihood) partition).treeInput.get();
        }
        String partitionID = partition.getID();
        partitionID = partitionID.substring(partitionID.lastIndexOf('.') + 1);
        if (partitionID.length() > 1 && partitionID.charAt(1) == ':') {
            partitionID = partitionID.substring(2);
        }
        if (partitionID.equals(sourceID)) {
            source = i;
        }
        if (partitionID.equals(targetID)) {
            target = i;
        }
    }
    if (target == -1) {
        throw new RuntimeException("Programmer error: sourceID and targetID should be in list");
    }
    CompoundDistribution likelihoods = (CompoundDistribution) doc.pluginmap.get("likelihood");
    GenericTreeLikelihood likelihoodSource = (GenericTreeLikelihood) likelihoods.pDistributions.get().get(source);
    GenericTreeLikelihood likelihood = (GenericTreeLikelihood) likelihoods.pDistributions.get().get(target);
    PartitionContext oldContext = doc.getContextFor(likelihoodSource);
    PartitionContext newContext = doc.getContextFor(likelihood);
    // this ensures the config.sync does not set any input value
    config._input.setValue(null, config);
    if (type.equals("SiteModel")) {
        SiteModelInterface siteModelSource = likelihoodSource.siteModelInput.get();
        SiteModelInterface siteModel = null;
        try {
            siteModel = (SiteModel.Base) BeautiDoc.deepCopyPlugin((BEASTInterface) siteModelSource, likelihood, (MCMC) doc.mcmc.get(), oldContext, newContext, doc, null);
        } catch (RuntimeException e) {
            JOptionPane.showMessageDialog(this, "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
            return;
        }
        likelihood.siteModelInput.setValue(siteModel, likelihood);
        return;
    } else if (type.equals("ClockModel")) {
        BranchRateModel clockModelSource = likelihoodSource.branchRateModelInput.get();
        BranchRateModel clockModel = null;
        try {
            clockModel = (BranchRateModel) BeautiDoc.deepCopyPlugin((BEASTInterface) clockModelSource, likelihood, (MCMC) doc.mcmc.get(), oldContext, newContext, doc, null);
        } catch (Exception e) {
            JOptionPane.showMessageDialog(this, "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
            return;
        }
        // make sure that *if* the clock model has a tree as input, it is
        // the same as for the likelihood
        TreeInterface tree = null;
        try {
            for (Input<?> input : ((BEASTInterface) clockModel).listInputs()) {
                if (input.getName().equals("tree")) {
                    tree = (TreeInterface) input.get();
                }
            }
        } catch (IllegalArgumentException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        if (tree != null && tree != likelihood.treeInput.get()) {
            // likelihood.treeInput.setValue(tree, likelihood);
            JOptionPane.showMessageDialog(null, "Cannot clone clock model with different trees");
            return;
        }
        likelihood.branchRateModelInput.setValue(clockModel, likelihood);
        return;
    } else if (type.equals("Tree")) {
        TreeInterface tree = null;
        TreeInterface treeSource = likelihoodSource.treeInput.get();
        try {
            tree = (TreeInterface) BeautiDoc.deepCopyPlugin((BEASTInterface) treeSource, likelihood, (MCMC) doc.mcmc.get(), oldContext, newContext, doc, null);
        } catch (Exception e) {
            JOptionPane.showMessageDialog(this, "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
            return;
        }
        // sanity check: make sure taxon sets are compatible
        Taxon.assertSameTaxa(tree.getID(), tree.getTaxonset().getTaxaNames(), likelihood.dataInput.get().getID(), likelihood.dataInput.get().getTaxaNames());
        likelihood.treeInput.setValue(tree, likelihood);
        return;
    } else {
        throw new RuntimeException("Programmer error calling cloneFrom: Should only clone Site/Clock/Tree model");
    }
}