Examples with Taxon dr.evolution.util.Taxon used on opensource projects

Example 86 with Taxon

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

the class DateGuesser method guessDates.

public void guessDates(List<Taxon> taxonList, Map<Taxon, String> taxonDateMap) {
    dateFormat = new SimpleDateFormat(calendarDateFormat);
    dateFormat.setTimeZone(TimeZone.getTimeZone("GMT"));
    for (int i = 0; i < taxonList.size(); i++) {
        Taxon taxon = taxonList.get(i);
        // Allocates a Date object and initializes it to represent the specified number of milliseconds since the
        // standard base time known as "the epoch", namely January 1, 1970, 00:00:00 GMT
        java.util.Date origin = new java.util.Date(0);
        double[] values = new double[2];
        try {
            if (taxonDateMap != null) {
                String dateString = taxonDateMap.get(taxon);
                parseDate(taxon.getId(), dateString, values);
            } else {
                switch(guessType) {
                    case ORDER:
                        guessDateFromOrder(taxonList.get(i).getId(), order, fromLast, values);
                        break;
                    case PREFIX:
                        guessDateFromPrefix(taxonList.get(i).getId(), prefix, order, fromLast, values);
                        break;
                    case REGEX:
                        guessDateFromRegex(taxonList.get(i).getId(), regex, values);
                        break;
                    default:
                        throw new IllegalArgumentException("unknown GuessType");
                }
            }
        } catch (GuessDatesException gfe) {
        // @todo catch errors and give to user
        }
        double d = values[0];
        if (!parseCalendarDates && !parseCalendarDatesAndPrecision) {
            if (offset > 0) {
                if (unlessLessThan > 0) {
                    if (d < unlessLessThan) {
                        d += offset2;
                    } else {
                        d += offset;
                    }
                } else {
                    d += offset;
                }
            }
        }
        // @todo if any taxa aren't set then return warning
        Date date = Date.createTimeSinceOrigin(d, Units.Type.YEARS, origin);
        date.setPrecision(values[1]);
        taxon.setAttribute("date", date);
    }
}

Example 87 with Taxon

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

the class XMLGenerator method writeTaxa.

// END: writeBranchRatesModel
private void writeTaxa(Taxa taxa, XMLWriter writer, String suffix) {
    // tagname
    writer.writeOpenTag(// tagname
    TaxaParser.TAXA, new Attribute[] { // attributes[]
    new Attribute.Default<String>(XMLParser.ID, TaxaParser.TAXA + suffix) });
    for (int i = 0; i < taxa.getTaxonCount(); i++) {
        Taxon taxon = taxa.getTaxon(i);
        writer.writeTag(// tagname
        TaxonParser.TAXON, new Attribute[] { // attributes[]
        new Attribute.Default<String>(XMLParser.ID, taxon.getId()) }, // close
        true);
    }
    // END: i loop
    writer.writeCloseTag(TaxaParser.TAXA);
}

Example 88 with Taxon

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

the class BeagleSeqSimTest method simulateTopology.

// END: annotateTree
static void simulateTopology() {
    try {
        System.out.println("Test case 1: simulateTopology");
        MathUtils.setSeed(666);
        int sequenceLength = 10;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        // create tree
        NewickImporter importer = new NewickImporter("(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981);");
        Tree tree = importer.importTree(null);
        // set demographic function
        ExponentialGrowth exponentialGrowth = new ExponentialGrowth(Units.Type.YEARS);
        exponentialGrowth.setN0(10);
        exponentialGrowth.setGrowthRate(0.5);
        Taxa taxa = new Taxa();
        for (Taxon taxon : tree.asList()) {
            double absoluteHeight = Utils.getAbsoluteTaxonHeight(taxon, tree);
            taxon.setAttribute(Utils.ABSOLUTE_HEIGHT, absoluteHeight);
            // taxon.setAttribute("date", new Date(absoluteHeight,
            // Units.Type.YEARS, true));
            taxa.addTaxon(taxon);
        }
        // END: taxon loop
        CoalescentSimulator topologySimulator = new CoalescentSimulator();
        TreeModel treeModel = new TreeModel(topologySimulator.simulateTree(taxa, exponentialGrowth));
        System.out.println(treeModel.toString());
        Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
        FrequencyModel freqModel = new FrequencyModel(Nucleotides.INSTANCE, freqs);
        // create substitution model
        Parameter kappa = new Parameter.Default(1, 10);
        HKY hky = new HKY(kappa, freqModel);
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(hky);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        0, // to
        sequenceLength - 1, // every
        1);
        partitionsList.add(partition1);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        System.out.println(simulator.simulate(simulateInPar, false).toString());
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch block
}

Example 89 with Taxon

use of dr.evolution.util.Taxon 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 90 with Taxon

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

the class AncestralStateBeagleTreeLikelihoodTest method testJointLikelihood.

public void testJointLikelihood() {
    TreeModel treeModel = new TreeModel("treeModel", tree);
    Sequence[] sequence = new Sequence[3];
    sequence[0] = new Sequence(new Taxon("0"), "A");
    sequence[1] = new Sequence(new Taxon("1"), "C");
    sequence[2] = new Sequence(new Taxon("2"), "C");
    Taxa taxa = new Taxa();
    for (Sequence s : sequence) {
        taxa.addTaxon(s.getTaxon());
    }
    SimpleAlignment alignment = new SimpleAlignment();
    for (Sequence s : sequence) {
        alignment.addSequence(s);
    }
    Parameter mu = new Parameter.Default(1, 1.0);
    Parameter kappa = new Parameter.Default(1, 1.0);
    double[] pi = { 0.25, 0.25, 0.25, 0.25 };
    Parameter freqs = new Parameter.Default(pi);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    GammaSiteRateModel siteRateModel = new GammaSiteRateModel("gammaModel", mu, null, -1, null);
    siteRateModel.setSubstitutionModel(hky);
    BranchModel branchModel = new HomogeneousBranchModel(siteRateModel.getSubstitutionModel());
    BranchRateModel branchRateModel = null;
    AncestralStateBeagleTreeLikelihood treeLikelihood = new AncestralStateBeagleTreeLikelihood(alignment, treeModel, branchModel, siteRateModel, branchRateModel, null, false, PartialsRescalingScheme.DEFAULT, true, null, hky.getDataType(), "stateTag", // useMap = true
    true, false);
    double logLike = treeLikelihood.getLogLikelihood();
    StringBuffer buffer = new StringBuffer();
    //        Tree.Utils.newick(treeModel, treeModel.getRoot(), false, Tree.BranchLengthType.LENGTHS_AS_TIME,
    //                null, null, new NodeAttributeProvider[]{treeLikelihood}, null, null, buffer);
    TreeUtils.newick(treeModel, treeModel.getRoot(), false, TreeUtils.BranchLengthType.LENGTHS_AS_TIME, null, null, new TreeTraitProvider[] { treeLikelihood }, null, buffer);
    System.out.println(buffer);
    System.out.println("t_CA(2) = " + t(false, 2.0));
    System.out.println("t_CC(1) = " + t(true, 1.0));
    double trueValue = 0.25 * t(false, 2.0) * Math.pow(t(true, 1.0), 3.0);
    assertEquals(logLike, Math.log(trueValue), 1e-6);
}