Examples with NumberFormatter dr.util.NumberFormatter used on opensource projects

Example 11 with NumberFormatter

use of dr.util.NumberFormatter in project beast-mcmc by beast-dev.

the class TestCalibratedYuleModel method yuleTester.

private void yuleTester(TreeModel treeModel, OperatorSchedule schedule, Parameter brParameter, double S, int chainLength) throws IOException, TreeUtils.MissingTaxonException {
    MCMC mcmc = new MCMC("mcmc1");
    MCMCOptions options = new MCMCOptions(chainLength);
    TreeLengthStatistic tls = new TreeLengthStatistic(TL, treeModel);
    TreeHeightStatistic rootHeight = new TreeHeightStatistic(TREE_HEIGHT, treeModel);
    SpeciationModel speciationModel = new BirthDeathGernhard08Model("yule", brParameter, null, null, BirthDeathGernhard08Model.TreeType.UNSCALED, Units.Type.SUBSTITUTIONS, false);
    Likelihood speciationLikelihood = new SpeciationLikelihood(treeModel, speciationModel, "yule.like");
    Taxa halfTaxa = new Taxa();
    for (int i = 0; i < taxa.getTaxonCount() / 2; i++) {
        halfTaxa.addTaxon(new Taxon("T" + Integer.toString(i)));
    }
    TMRCAStatistic tmrca = new TMRCAStatistic("tmrca(halfTaxa)", treeModel, halfTaxa, false, false);
    DistributionLikelihood logNormalLikelihood = new DistributionLikelihood(new LogNormalDistribution(M, S), // meanInRealSpace="false"
    0);
    logNormalLikelihood.addData(tmrca);
    MonophylyStatistic monophylyStatistic = new MonophylyStatistic("monophyly(halfTaxa)", treeModel, halfTaxa, null);
    BooleanLikelihood booleanLikelihood = new BooleanLikelihood();
    booleanLikelihood.addData(monophylyStatistic);
    // CompoundLikelihood
    List<Likelihood> likelihoods = new ArrayList<Likelihood>();
    likelihoods.add(speciationLikelihood);
    likelihoods.add(logNormalLikelihood);
    likelihoods.add(booleanLikelihood);
    Likelihood prior = new CompoundLikelihood(0, likelihoods);
    prior.setId(CompoundLikelihoodParser.PRIOR);
    ArrayLogFormatter logformatter = new ArrayLogFormatter(false);
    MCLogger[] loggers = new MCLogger[1];
    loggers[0] = new MCLogger(logformatter, (int) (options.getChainLength() / 10000), false);
    loggers[0].add(speciationLikelihood);
    loggers[0].add(rootHeight);
    loggers[0].add(tmrca);
    loggers[0].add(tls);
    loggers[0].add(brParameter);
    mcmc.setShowOperatorAnalysis(false);
    mcmc.init(options, prior, schedule, loggers);
    mcmc.run();
    List<Trace> traces = logformatter.getTraces();
    ArrayTraceList traceList = new ArrayTraceList("yuleModelTest", traces, 1000);
    for (int i = 1; i < traces.size(); i++) {
        traceList.analyseTrace(i);
    }
    NumberFormatter formatter = new NumberFormatter(8);
    TraceCorrelation tlStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TL));
    TraceCorrelation treeHeightStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("tmrca(halfTaxa)"));
    // out.write("tmrcaHeight = \t");
    out.write(formatter.format(treeHeightStats.getMean()));
    out.write("\t");
    double expectedNodeHeight = Math.pow(Math.E, (M + (Math.pow(S, 2) / 2)));
    // out.write("expectation = \t");
    out.write(formatter.format(expectedNodeHeight));
    out.write("\t");
    double error = Math.abs((treeHeightStats.getMean() - expectedNodeHeight) / expectedNodeHeight);
    NumberFormat percentFormatter = NumberFormat.getNumberInstance();
    percentFormatter.setMinimumFractionDigits(5);
    percentFormatter.setMinimumFractionDigits(5);
    // out.write("error = \t");
    out.write(percentFormatter.format(error));
    out.write("\t");
    // out.write("tl.ess = \t");
    out.write(Double.toString(tlStats.getESS()));
    System.out.println("tmrcaHeight = " + formatter.format(treeHeightStats.getMean()) + ";  expectation = " + formatter.format(expectedNodeHeight) + ";  error = " + percentFormatter.format(error) + ";  tl.ess = " + tlStats.getESS());
}

Example 12 with NumberFormatter

use of dr.util.NumberFormatter in project beast-mcmc by beast-dev.

the class TempestFrame method setStatusMessage.

private void setStatusMessage() {
    Tree tree = tempestPanel.getTree();
    if (tree != null) {
        String message = "";
        message += "Tree loaded, " + tree.getTaxonCount() + " taxa";
        TemporalRooting tr = tempestPanel.getTemporalRooting();
        if (tr.isContemporaneous()) {
            message += ", contemporaneous tips";
        } else {
            NumberFormatter nf = new NumberFormatter(3);
            message += ", dated tips with range " + nf.format(tr.getDateRange());
        }
        statusLabel.setText(message);
    }
}

Example 13 with NumberFormatter

use of dr.util.NumberFormatter in project beast-mcmc by beast-dev.

the class ARGModel method toARGSummary.

/**
 * Gives a summary of the ARG model.  Should only
 * be used for debugging purposes because it's really slow.
 *
 * @return a summary of the ARG model.
 */
public String toARGSummary() {
    NumberFormatter format = new NumberFormatter(4);
    String space = "   ";
    String a = "----------------------\n" + "ARG Summary \n---------------------- \n";
    a += "Number of nodes: " + nodes.size() + "\n";
    a += "Number of partitions: " + maxNumberOfPartitions + "\n";
    a += "Number of Reassorments: " + this.getReassortmentNodeCount() + "\n";
    a += "Root number: " + getRoot().getNumber() + "\n";
    a += "Node Summary" + "\n----------------------------------------\n" + "ID  LP   RP   LC   RC   Height" + space + "TX  \n" + "----------------------------------------\n";
    for (Node node : nodes) {
        a += node.getNumber() + space;
        if (node.leftParent == null)
            a += "-1" + space;
        else
            a += " " + node.leftParent.number + space;
        if (node.rightParent == null)
            a += "-1" + space;
        else
            a += " " + node.rightParent.number + space;
        if (node.leftChild == null)
            a += "-1" + space;
        else
            a += " " + node.leftChild.number + space;
        if (node.rightChild == null)
            a += "-1" + space;
        else
            a += " " + node.rightChild.number + space;
        a += format.formatDecimal(getNodeHeight(node), 4) + space;
        if (node.partitioning != null) {
            for (int i = 0, n = getNumberOfPartitions(); i < n; i++) {
                a += node.partitioning.getParameterValue(i) + space;
            }
        }
        if (node.taxon == null) {
            a += "internal" + space;
        } else {
            a += node.taxon + space;
        }
        a += "\n";
    }
    a += "\nInduced Trees" + "\n----------------------------------------\n";
    return a;
}

Example 14 with NumberFormatter

use of dr.util.NumberFormatter in project beast-mcmc by beast-dev.

the class ARGTraceAnalysis method report.

public void report() throws IOException {
    int fieldWidth = 14;
    NumberFormatter formatter = new NumberFormatter(6);
    formatter.setPadding(true);
    formatter.setFieldWidth(fieldWidth);
    int n = argSet.size();
    int totalTrees = argSet.getSumFrequency();
    System.out.println();
    System.out.println("burnIn=" + burnin);
    System.out.println("total ARGs used =" + totalTrees);
    System.out.println();
    System.out.println("95% credible set (" + n + " unique ARGs, " + totalTrees + " total):");
    System.out.println("Count\tPercent\tARG");
    int credSet = (95 * totalTrees) / 100;
    int sumFreq = 0;
    NumberFormatter nf = new NumberFormatter(8);
    for (int i = 0; i < n; i++) {
        int freq = argSet.getFrequency(i);
        double prop = ((double) freq) / totalTrees;
        System.out.print(freq);
        System.out.print("\t" + nf.formatDecimal(prop * 100.0, 2) + "%");
        sumFreq += freq;
        double sumProp = ((double) sumFreq) / totalTrees;
        System.out.print("\t" + nf.formatDecimal(sumProp * 100.0, 2) + "%");
        // (String)argSet.get(i);
        String newickTree = argSet.get(i).toString();
        // if (freq > 100) {
        // calculate conditional average node heights
        // Tree meanTree = analyzeTree(newickTree);
        // System.out.println("\t" + Tree.Utils.newick(meanTree));
        /*for (int k = 0; k < meanTree.getInternalNodeCount(); k++) {
								  NodeRef node = meanTree.getInternalNode(k);
								  System.out.println("node " + k + "\t" +
									  meanTree.getNodeHeight(node) + "\t" +
									  meanTree.getNodeAttribute(node, "lower") + "\t" +
									  meanTree.getNodeAttribute(node, "upper"));
							  }*/
        // } else {
        System.out.println("\t" + newickTree);
        if (sumFreq >= credSet) {
            System.out.println();
            System.out.println("95% credible set has " + (i + 1) + " ARGs.");
            break;
        }
    }
    System.out.println();
    System.out.println("DOT Format for most probable ARG:");
    System.out.println(GraphMLUtils.dotFormat(argSet.get(0).toXML()));
    // System.out.println(argSet.);
    /*	System.out.println("Majority rule clades (" + cladeSet.size() + " unique clades):");
				  n = cladeSet.size();
				  for (int i = 0; i < n; i++) {
					  int freq = cladeSet.getFrequency(i);
					  double prop = ((double)freq) / totalTrees;
					  if (prop > 0.5) {
						  System.out.print(freq);
						  System.out.print("\t" + nf.formatDecimal(prop * 100.0, 2) + "%");
						  System.out.println("\t" + cladeSet.getClade(i));
					  }
				  }*/
    System.out.flush();
}