Example usage for org.apache.commons.math3.stat.inference TTest TTest

List of usage examples for org.apache.commons.math3.stat.inference TTest TTest

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Introduction

In this page you can find the example usage for org.apache.commons.math3.stat.inference TTest TTest.

Prototype

TTest

Source Link

Usage

From source file:GeMSE.GS.Analysis.Stats.OneSampleTTestPanel.java

public OneSampleTTestPanel() {
    initComponents();/*from   w w  w .ja va  2 s.  c om*/
    _sample = new double[0];
    _studentTest = new TTest();

    _decFor = new DecimalFormat("#.#########");
    _decFor.setRoundingMode(RoundingMode.CEILING);
    DecimalFormatSymbols decFors = _decFor.getDecimalFormatSymbols();
    decFors.setNaN("NaN");
    decFors.setInfinity("");
    _decFor.setDecimalFormatSymbols(decFors);
}

From source file:coolmap.utils.statistics.test.CTest.java

public static void ttest(CoolMapObject obj, Dimension direction, VNode leafNode1, VNode leafNode2) {
    try {/*w  w w .j av a  2  s . co  m*/
        ArrayList<VNode> leafNodes = new ArrayList<VNode>();
        if (direction == Dimension.ROW) {
            leafNodes.addAll(obj.getViewNodesRow());
        } else if (direction == Dimension.COLUMN) {
            leafNodes.addAll(obj.getViewNodesColumn());
        } else {
            return;
        }

        if (leafNodes.contains(leafNode1) && leafNodes.contains(leafNode2)) {

            double[] data1 = null;
            double[] data2 = null;

            if (direction == Dimension.ROW) {
                data1 = extractRow(obj, leafNode1);
                data2 = extractRow(obj, leafNode2);
            } else if (direction == Dimension.COLUMN) {
                data1 = extractColumn(obj, leafNode1);
                data2 = extractColumn(obj, leafNode2);
            }

            TTest test = new TTest();
            double pValue = test.pairedTTest(data1, data2);

            TestResult result = new TestResult("Student Paired T-Test",
                    "Two tailed paired t-test with alpha = 0.05.\nData: " + obj.getName() + "\nDirection: "
                            + direction + "\nGroups: " + leafNode1 + ", " + leafNode2,
                    pValue);
            CMConsole.log(result.toString());

        } else {
            CMConsole.logError(
                    "T-test error: group dimension mismatch, must both be row ontology group or column ontology groups.");
        }

    } catch (Exception e) {
        CMConsole.logError("T-test error: " + " Dataset:" + obj + " Direction:" + direction + " Group1:"
                + leafNode1 + " Group2:" + leafNode2);
    }
}

From source file:GeMSE.GS.Analysis.Stats.TwoSampleTTestPanel.java

public TwoSampleTTestPanel() {
    initComponents();/*from   www.  j a  va  2  s. c o m*/
    _sample1 = new double[0];
    _sample2 = new double[0];

    _decFor = new DecimalFormat("#.#########");
    _decFor.setRoundingMode(RoundingMode.CEILING);
    DecimalFormatSymbols decFors = _decFor.getDecimalFormatSymbols();
    decFors.setNaN("NaN");
    decFors.setInfinity("");
    _decFor.setDecimalFormatSymbols(decFors);

    _variance = new Variance();
    _studentTest = new TTest();
}

From source file:carskit.alg.cars.transformation.prefiltering.splitting.ItemSplitting.java

public Table<Integer, Integer, Integer> split(SparseMatrix sm, int min) {
    Table<Integer, Integer, Integer> datatable = HashBasedTable.create();

    for (Integer j : itemRatingList.keySet()) {
        Collection<Integer> uis = itemRatingList.get(j);
        double maxt = Double.MIN_VALUE;
        int splitcond = -1;

        for (Integer cond : condContextsList.keySet()) {
            Collection<Integer> ctx = condContextsList.get(cond);
            // start to extract two rating list
            HashMultiset<Double> rate1 = HashMultiset.create();
            HashMultiset<Double> rate2 = HashMultiset.create();

            for (Integer ui : uis) {
                List<Integer> uctx = sm.getColumns(ui);
                for (Integer c : uctx) {
                    double rate = sm.get(ui, c);
                    if (ctx.contains(c))
                        rate1.add(rate);
                    else
                        rate2.add(rate);
                }// w  ww.j a  v a 2  s.c  om
            }

            double[] drate1 = Doubles.toArray(rate1);
            double[] drate2 = Doubles.toArray(rate2);

            if (drate1.length >= min && drate2.length >= min) {
                TTest tt = new TTest();
                double p = tt.tTest(drate1, drate2);
                if (p < 0.05) {
                    double t = tt.t(drate1, drate2);
                    if (t > maxt) {
                        // update the split
                        splitcond = cond;
                        maxt = t;
                    }
                }
            }
        }
        if (splitcond != -1) {
            // put u, ctx, new uid into datatable
            int newid = startId++;
            Collection<Integer> ctx = condContextsList.get(splitcond);
            for (Integer c : ctx)
                datatable.put(j, c, newid);
        }

    }
    Logs.info(datatable.rowKeySet().size() + " items have been splitted.");
    return datatable;
}

From source file:carskit.alg.cars.transformation.prefiltering.splitting.UserSplitting.java

public Table<Integer, Integer, Integer> split(SparseMatrix sm, int min) {
    Logs.debug("UserSplitting: startId = " + startId);
    Table<Integer, Integer, Integer> datatable = HashBasedTable.create();

    for (Integer u : userRatingList.keySet()) {
        Collection<Integer> uis = userRatingList.get(u);
        double maxt = Double.MIN_VALUE;
        int splitcond = -1;

        for (Integer cond : condContextsList.keySet()) {
            Collection<Integer> ctx = condContextsList.get(cond);
            // start to extract two rating list
            HashMultiset<Double> rate1 = HashMultiset.create();
            HashMultiset<Double> rate2 = HashMultiset.create();

            for (Integer ui : uis) {
                List<Integer> uctx = sm.getColumns(ui);
                for (Integer c : uctx) {
                    double rate = sm.get(ui, c);
                    if (ctx.contains(c))
                        rate1.add(rate);
                    else
                        rate2.add(rate);
                }/*from w w  w . jav  a 2 s .c  o m*/
            }

            double[] drate1 = Doubles.toArray(rate1);
            double[] drate2 = Doubles.toArray(rate2);

            if (drate1.length >= min && drate2.length >= min) {
                TTest tt = new TTest();
                double p = tt.tTest(drate1, drate2);
                if (p < 0.05) {
                    double t = tt.t(drate1, drate2);
                    if (t > maxt) {
                        // update the split
                        splitcond = cond;
                        maxt = t;
                    }
                }
            }
        }

        if (splitcond != -1) {
            // put u, ctx, new uid into datatable
            int newid = startId++;
            Collection<Integer> ctx = condContextsList.get(splitcond);
            for (Integer c : ctx)
                datatable.put(u, c, newid);
        }

    }
    Logs.info(datatable.rowKeySet().size() + " users have been splitted.");
    return datatable;
}

From source file:io.druid.query.aggregation.datasketches.tuple.ArrayOfDoublesSketchTTestPostAggregator.java

@Override
public double[] compute(final Map<String, Object> combinedAggregators) {
    final ArrayOfDoublesSketch sketch1 = (ArrayOfDoublesSketch) getFields().get(0).compute(combinedAggregators);
    final ArrayOfDoublesSketch sketch2 = (ArrayOfDoublesSketch) getFields().get(1).compute(combinedAggregators);
    if (sketch1.getNumValues() != sketch2.getNumValues()) {
        throw new IAE("Sketches have different number of values: %d and %d", sketch1.getNumValues(),
                sketch2.getNumValues());
    }/*from www.  j a  va  2 s .  co m*/

    final SummaryStatistics[] stats1 = getStats(sketch1);
    final SummaryStatistics[] stats2 = getStats(sketch2);

    final int numberOfValues = sketch1.getNumValues();
    final double[] pValues = new double[numberOfValues];
    final TTest test = new TTest();
    for (int i = 0; i < pValues.length; i++) {
        pValues[i] = test.tTest(stats1[i], stats2[i]);
    }
    return pValues;
}

From source file:Query7Servlet.java

/**
 * Processes requests for both HTTP <code>GET</code> and <code>POST</code>
 * methods./*from  w  w  w .  ja va 2  s.  c om*/
 *
 * @param request servlet request
 * @param response servlet response
 * @throws ServletException if a servlet-specific error occurs
 * @throws IOException if an I/O error occurs
 */
protected void processRequest(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {
    Connection connection = null;
    Statement stmt = null;

    String patientsWithAllSqlQuery = null;
    String patientsWithoutAllSqlQuery = null;

    ResultSet expWithAllResultSet = null;
    ResultSet expWithoutAllResultSet = null;

    String geneID = null;
    double expValue = 0;
    List<Double> exprValuesForGeneID = null;

    Map<String, List<Double>> geneToExpValueALL = new HashMap<String, List<Double>>();
    Map<String, List<Double>> geneToExpValueNOTALL = new HashMap<String, List<Double>>();

    Set<String> geneIDSet = null;
    String[] geneIDs = null;
    List<Double> listOneForGeneId = null;
    List<Double> listTwoForGeneId = null;
    Double[] listOneForGeneIdArr = null;
    Double[] listTwoForGeneIdArr = null;

    double p_value = 0;
    JSONArray informativeGenes = new JSONArray();
    JSONObject informativeGene = null;

    response.setContentType("text/html;charset=UTF-8");
    try (PrintWriter out = response.getWriter()) {
        Class.forName("oracle.jdbc.driver.OracleDriver");

        connection = DriverManager.getConnection("jdbc:oracle:thin:@VIVEK:1521/ORCL", "system", "vivek");

        stmt = connection.createStatement();

        patientsWithAllSqlQuery = "SELECT P.USER_ID, M.EXPRESSION FROM MICROARRAY_FACT M, PROBE P, CLINICAL_FACT C "
                + "WHERE M.PB_ID = P.PB_ID " + "AND M.S_ID = C.S_ID "
                + "AND C.P_ID IN (SELECT P_ID FROM CLINICAL_FACT, DISEASE "
                + "WHERE CLINICAL_FACT.DS_ID = DISEASE.DS_ID AND NAME = 'ALL')";

        patientsWithoutAllSqlQuery = "SELECT P.USER_ID, M.EXPRESSION FROM MICROARRAY_FACT M, PROBE P, CLINICAL_FACT C "
                + "WHERE M.PB_ID = P.PB_ID " + "AND M.S_ID = C.S_ID "
                + "AND C.P_ID IN (SELECT P_ID FROM CLINICAL_FACT, DISEASE "
                + "WHERE CLINICAL_FACT.DS_ID = DISEASE.DS_ID AND NAME <> 'ALL')";

        //Expression Values for patients with "ALL"
        expWithAllResultSet = stmt.executeQuery(patientsWithAllSqlQuery);

        //Converting the result set for "ALL" to the map
        while (expWithAllResultSet.next()) {
            geneID = expWithAllResultSet.getString(1);
            expValue = expWithAllResultSet.getDouble(2);

            if (geneToExpValueALL.get(geneID) != null) {
                exprValuesForGeneID = geneToExpValueALL.get(geneID);
            } else {
                exprValuesForGeneID = new ArrayList<Double>();
            }

            exprValuesForGeneID.add(expValue);
            geneToExpValueALL.put(geneID, exprValuesForGeneID);
        }

        //Expression Values for patients without "ALL"
        expWithoutAllResultSet = stmt.executeQuery(patientsWithoutAllSqlQuery);

        while (expWithoutAllResultSet.next()) {
            geneID = expWithoutAllResultSet.getString(1);
            expValue = expWithoutAllResultSet.getDouble(2);

            if (geneToExpValueNOTALL.get(geneID) != null) {
                exprValuesForGeneID = geneToExpValueNOTALL.get(geneID);
            } else {
                exprValuesForGeneID = new ArrayList<Double>();
            }

            exprValuesForGeneID.add(expValue);
            geneToExpValueNOTALL.put(geneID, exprValuesForGeneID);
        }

        //Calculating the p value for genes between two groups
        geneIDSet = geneToExpValueALL.keySet();
        geneIDs = new String[geneIDSet.size()];
        geneIDSet.toArray(geneIDs);

        for (int i = 0; i < geneIDs.length; i++) {
            listOneForGeneId = geneToExpValueALL.get(geneIDs[i]);
            listTwoForGeneId = geneToExpValueNOTALL.get(geneIDs[i]);

            listOneForGeneIdArr = new Double[listOneForGeneId.size()];
            listTwoForGeneIdArr = new Double[listTwoForGeneId.size()];

            listOneForGeneId.toArray(listOneForGeneIdArr);
            listTwoForGeneId.toArray(listTwoForGeneIdArr);

            p_value = new TTest().tTest(ArrayUtils.toPrimitive(listOneForGeneIdArr),
                    ArrayUtils.toPrimitive(listTwoForGeneIdArr));

            if (p_value < 0.01) {
                informativeGene = new JSONObject();
                informativeGene.put("infogene", geneIDs[i]);
                informativeGenes.put(informativeGene);
            }
        }

        out.print(informativeGenes);
        //Closing the statement and connection
        stmt.close();
        connection.close();
    } catch (SQLException e) {
        System.out.println("Connection Failed! Check output console");
        e.printStackTrace();
        return;
    } catch (ClassNotFoundException e) {
        System.out.println("Where is your Oracle JDBC Driver?");
        e.printStackTrace();
        return;
    } catch (JSONException e) {
        System.out.println("Where is your Oracle JDBC Driver?");
        e.printStackTrace();
        return;
    }
}

From source file:calculators.Calculator.java

/**
 * Calculates the pvalue.//from   w  w  w .j a v a 2 s  .c o m
 *
 * @param control the control group intensities
 * @param target the target group intensities
 * @return
 */
private Double calculatePvalue(final double[] control, final double[] target) {
    TTest t_test = new TTest();
    Log10 logTen = new Log10();
    return -logTen.value(t_test.tTest(target, control));
}

From source file:info.debatty.jinu.CaseResult.java

/**
 *
 * @param test//from  www .j a  v a 2s  .co  m
 * @param other_test
 * @param result
 * @param param_value
 * @return
 */
public final double getSimilarity(final TestInterface test, final TestInterface other_test, final long result,
        final double param_value) {

    double[] test_results = new double[testcase.getIterations()];
    double[] other_results = new double[testcase.getIterations()];

    int i = 0;
    for (TestResult tr : results.get(new TestAndValue(test, param_value))) {
        test_results[i] = tr.getValue(result);
        i++;
    }

    i = 0;
    TestAndValue test_and_value = new TestAndValue(other_test, param_value);
    for (TestResult tr : results.get(test_and_value)) {
        other_results[i] = tr.getValue(result);
        i++;
    }

    TTest t_test = new TTest();
    return t_test.tTest(test_results, other_results);
}

From source file:eu.betaas.taas.securitymanager.taastrustmanager.taastrustcalculator.StatisticsCalculator.java

public boolean isSimilarMean(double[] valuesA, double[] valuesB) {
    TTest studentTest = new TTest();
    boolean testResult = false;
    double error = 0;
    double tValue = 0;

    double meanA = StatUtils.mean(valuesA);
    double meanB = StatUtils.mean(valuesB);

    try {/*from  ww  w .  ja  v a  2  s  .  c o m*/
        testResult = studentTest.tTest(valuesA, valuesB, 0.05);
        error = studentTest.tTest(valuesA, valuesB);
        tValue = studentTest.t(valuesA, valuesB);
        logger.debug("Test result --> MA = " + meanA + " -- MB = " + meanB);
        logger.debug("Test result --> " + testResult + " with p " + error + " and tValue = " + tValue);
    } catch (Exception ex) {
        logger.error("There was an error when trying to calculate Student's t test!");
        ex.printStackTrace();
        return false;
    }

    return testResult;

}