Examples with CompoundDistribution beast.core.util.CompoundDistribution used on opensource projects

Example 16 with CompoundDistribution

use of beast.core.util.CompoundDistribution in project beast2 by CompEvol.

the class BeautiDoc method collectClockModels.

private void collectClockModels() {
    // collect branch rate models from model
    CompoundDistribution likelihood = (CompoundDistribution) pluginmap.get("likelihood");
    while (clockModels.size() < partitionNames.size()) {
        try {
            GenericTreeLikelihood treelikelihood = new GenericTreeLikelihood();
            treelikelihood.branchRateModelInput.setValue(new StrictClockModel(), treelikelihood);
            List<BeautiSubTemplate> availableBEASTObjects = inputEditorFactory.getAvailableTemplates(treelikelihood.branchRateModelInput, treelikelihood, null, this);
            BEASTInterface beastObject = availableBEASTObjects.get(0).createSubNet(partitionNames.get(clockModels.size()), true);
            clockModels.add((BranchRateModel.Base) beastObject);
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    int k = 0;
    for (Distribution d : likelihood.pDistributions.get()) {
        BranchRateModel clockModel = ((GenericTreeLikelihood) d).branchRateModelInput.get();
        // sanity check
        Tree tree = null;
        try {
            for (Input<?> input : ((BEASTInterface) clockModel).listInputs()) {
                if (input.getName().equals("tree")) {
                    tree = (Tree) input.get();
                }
            }
            if (tree != null && tree != ((GenericTreeLikelihood) d).treeInput.get()) {
                clockModel = clockModels.get(k);
                Log.warning.println("WARNING: unlinking clock model for " + d.getID());
                // TODO #557: this should move to the event of clock model drop box
                // JOptionPane.showMessageDialog(beauti.getSelectedComponent(),
                // "Cannot link all clock model(s) except strict clock with different trees !");
                ((GenericTreeLikelihood) d).branchRateModelInput.setValue(clockModel, d);
            }
        } catch (Exception e) {
        // ignore
        }
        if (clockModel != null) {
            String id = ((BEASTInterface) clockModel).getID();
            id = parsePartition(id);
            String partition = alignments.get(k).getID();
            if (id.equals(partition)) {
                clockModels.set(k, clockModel);
            }
            k++;
        }
    }
}

Example 17 with CompoundDistribution

use of beast.core.util.CompoundDistribution in project beast2 by CompEvol.

the class SiteModelInputEditor method setUpOperator.

/**
 * set up relative weights and parameter input *
 */
public void setUpOperator() {
    boolean isAllClocksAreEqual = true;
    try {
        boolean hasOneEstimatedRate = customConnector(doc);
        if (doc.autoUpdateFixMeanSubstRate) {
            fixMeanRatesCheckBox.setSelected(hasOneEstimatedRate);
            doFixMeanRates(hasOneEstimatedRate);
        }
        try {
            double commonClockRate = -1;
            CompoundDistribution likelihood = (CompoundDistribution) doc.pluginmap.get("likelihood");
            for (Distribution d : likelihood.pDistributions.get()) {
                GenericTreeLikelihood treelikelihood = (GenericTreeLikelihood) d;
                if (treelikelihood.siteModelInput.get() instanceof SiteModel) {
                    SiteModel siteModel = (SiteModel) treelikelihood.siteModelInput.get();
                    RealParameter mutationRate = siteModel.muParameterInput.get();
                    // clockRate.m_bIsEstimated.setValue(true, clockRate);
                    if (mutationRate.isEstimatedInput.get()) {
                        if (commonClockRate < 0) {
                            commonClockRate = mutationRate.valuesInput.get().get(0);
                        } else {
                            if (Math.abs(commonClockRate - mutationRate.valuesInput.get().get(0)) > 1e-10) {
                                isAllClocksAreEqual = false;
                            }
                        }
                    }
                }
            }
        } catch (Exception e) {
        }
        List<RealParameter> parameters = operator.parameterInput.get();
        if (!fixMeanRatesCheckBox.isSelected()) {
            fixMeanRatesValidateLabel.setVisible(false);
            repaint();
            return;
        }
        if (parameters.size() == 0) {
            fixMeanRatesValidateLabel.setVisible(true);
            fixMeanRatesValidateLabel.m_circleColor = Color.red;
            fixMeanRatesValidateLabel.setToolTipText("The model is invalid: At least one substitution rate should be estimated.");
            repaint();
            return;
        }
        if (!isAllClocksAreEqual) {
            fixMeanRatesValidateLabel.setVisible(true);
            fixMeanRatesValidateLabel.m_circleColor = Color.orange;
            fixMeanRatesValidateLabel.setToolTipText("Not all substitution rates are equal. Are you sure this is what you want?");
        } else if (parameters.size() == 1) {
            fixMeanRatesValidateLabel.setVisible(true);
            fixMeanRatesValidateLabel.m_circleColor = Color.orange;
            fixMeanRatesValidateLabel.setToolTipText("At least 2 clock models should have their rate estimated");
        } else if (parameters.size() < doc.getPartitions("SiteModel").size()) {
            fixMeanRatesValidateLabel.setVisible(true);
            fixMeanRatesValidateLabel.m_circleColor = Color.orange;
            fixMeanRatesValidateLabel.setToolTipText("Not all partitions have their rate estimated");
        } else {
            fixMeanRatesValidateLabel.setVisible(false);
        }
        repaint();
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 18 with CompoundDistribution

use of beast.core.util.CompoundDistribution in project beast2 by CompEvol.

the class MCMC method reportLogLikelihoods.

/*
     * report posterior and subcomponents recursively, for debugging
     * incorrectly recalculated posteriors *
     */
protected void reportLogLikelihoods(final Distribution distr, final String tabString) {
    final double full = distr.logP, last = distr.storedLogP;
    final String changed = full == last ? "" : "  **";
    Log.info.println(tabString + "P(" + distr.getID() + ") = " + full + " (was " + last + ")" + changed);
    if (distr instanceof CompoundDistribution) {
        for (final Distribution distr2 : ((CompoundDistribution) distr).pDistributions.get()) {
            reportLogLikelihoods(distr2, tabString + "\t");
        }
    }
}

Example 19 with CompoundDistribution

use of beast.core.util.CompoundDistribution in project beast2 by CompEvol.

the class MCMC method initAndValidate.

@Override
public void initAndValidate() {
    Log.info.println("===============================================================================");
    Log.info.println("Citations for this model:");
    Log.info.println(getCitations());
    Log.info.println("===============================================================================");
    operatorSchedule = operatorScheduleInput.get();
    for (final Operator op : operatorsInput.get()) {
        operatorSchedule.addOperator(op);
    }
    if (sampleFromPriorInput.get()) {
        // remove beastObject with id likelihood from posterior, if it is a CompoundDistribution
        if (posteriorInput.get() instanceof CompoundDistribution) {
            final CompoundDistribution posterior = (CompoundDistribution) posteriorInput.get();
            final List<Distribution> distrs = posterior.pDistributions.get();
            final int distrCount = distrs.size();
            for (int i = 0; i < distrCount; i++) {
                final Distribution distr = distrs.get(i);
                final String id = distr.getID();
                if (id != null && id.equals("likelihood")) {
                    distrs.remove(distr);
                    break;
                }
            }
            if (distrs.size() == distrCount) {
                throw new RuntimeException("Sample from prior flag is set, but distribution with id 'likelihood' is " + "not an input to posterior.");
            }
        } else {
            throw new RuntimeException("Don't know how to sample from prior since posterior is not a compound distribution. " + "Suggestion: set sampleFromPrior flag to false.");
        }
    }
    // StateNode initialisation, only required when the state is not read from file
    if (restoreFromFile) {
        final HashSet<StateNode> initialisedStateNodes = new HashSet<>();
        for (final StateNodeInitialiser initialiser : initialisersInput.get()) {
            // make sure that the initialiser does not re-initialises a StateNode
            final List<StateNode> list = new ArrayList<>(1);
            initialiser.getInitialisedStateNodes(list);
            for (final StateNode stateNode : list) {
                if (initialisedStateNodes.contains(stateNode)) {
                    throw new RuntimeException("Trying to initialise stateNode (id=" + stateNode.getID() + ") more than once. " + "Remove an initialiser from MCMC to fix this.");
                }
            }
            initialisedStateNodes.addAll(list);
        // do the initialisation
        // initialiser.initStateNodes();
        }
    }
    // State initialisation
    final HashSet<StateNode> operatorStateNodes = new HashSet<>();
    for (final Operator op : operatorsInput.get()) {
        for (final StateNode stateNode : op.listStateNodes()) {
            operatorStateNodes.add(stateNode);
        }
    }
    if (startStateInput.get() != null) {
        this.state = startStateInput.get();
        if (storeEveryInput.get() > 0) {
            this.state.m_storeEvery.setValue(storeEveryInput.get(), this.state);
        }
    } else {
        // create state from scratch by collecting StateNode inputs from Operators
        this.state = new State();
        for (final StateNode stateNode : operatorStateNodes) {
            this.state.stateNodeInput.setValue(stateNode, this.state);
        }
        this.state.m_storeEvery.setValue(storeEveryInput.get(), this.state);
    }
    // grab the interval for storing the state to file
    if (storeEveryInput.get() > 0) {
        storeEvery = storeEveryInput.get();
    } else {
        storeEvery = state.m_storeEvery.get();
    }
    this.state.initialise();
    this.state.setPosterior(posteriorInput.get());
    // sanity check: all operator state nodes should be in the state
    final List<StateNode> stateNodes = this.state.stateNodeInput.get();
    for (final Operator op : operatorsInput.get()) {
        List<StateNode> nodes = op.listStateNodes();
        if (nodes.size() == 0) {
            throw new RuntimeException("Operator " + op.getID() + " has no state nodes in the state. " + "Each operator should operate on at least one estimated state node in the state. " + "Remove the operator or add its statenode(s) to the state and/or set estimate='true'.");
        // otherwise the chain may hang without obvious reason
        }
        for (final StateNode stateNode : op.listStateNodes()) {
            if (!stateNodes.contains(stateNode)) {
                throw new RuntimeException("Operator " + op.getID() + " has a statenode " + stateNode.getID() + " in its inputs that is missing from the state.");
            }
        }
    }
    // sanity check: at least one operator required to run MCMC
    if (operatorsInput.get().size() == 0) {
        Log.warning.println("Warning: at least one operator required to run the MCMC properly, but none found.");
    }
    // sanity check: all state nodes should be operated on
    for (final StateNode stateNode : stateNodes) {
        if (!operatorStateNodes.contains(stateNode)) {
            Log.warning.println("Warning: state contains a node " + stateNode.getID() + " for which there is no operator.");
        }
    }
}