import org.apache.commons.math3.stat.ranking.NaturalRanking; //导入依赖的package包/类
@Test()
public void testRankOfRows() {
    final Random random = new Random();
    final DataFrame<String,String> frame = TestDataFrames.random(double.class, 1000, 100);
    frame.applyDoubles(v -> random.nextDouble() * 100);
    final DataFrame<String,String> rankFrame = frame.rank().ofRows();
    Assert.assertEquals(rankFrame.rowCount(), frame.rowCount(), "The row counts match");
    Assert.assertEquals(rankFrame.colCount(), frame.colCount(), "The column counts match");
    rankFrame.out().print();
    rankFrame.rows().forEach(rankRow -> {
        final String key = rankRow.key();
        final double[] values = frame.row(key).toDoubleStream().toArray();
        final NaturalRanking ranking = new NaturalRanking();
        final double[] ranks = ranking.rank(values);
        for (int i = 0; i < ranks.length; ++i) {
            final double value = frame.data().getDouble(key, i);
            final double expected = ranks[i];
            final double actual = rankFrame.data().getDouble(key, i);
            Assert.assertEquals(value, values[i], "The values match for column " + i);
            Assert.assertEquals(actual, expected, "The ranks match for " + key + " at column " + i);
        }
    });
}
 

import org.apache.commons.math3.stat.ranking.NaturalRanking; //导入依赖的package包/类
@Test()
public void testRankOfColumns() {
    final Random random = new Random();
    final DataFrame<String,String> frame = TestDataFrames.random(double.class, 1000, 100);
    frame.applyDoubles(v -> random.nextDouble() * 100);
    final DataFrame<String,String> rankFrame = frame.rank().ofColumns();
    Assert.assertEquals(rankFrame.rowCount(), frame.rowCount(), "The row counts match");
    Assert.assertEquals(rankFrame.colCount(), frame.colCount(), "The column counts match");
    rankFrame.out().print();
    rankFrame.cols().forEach(rankColumn -> {
        final String key = rankColumn.key();
        final double[] values = frame.col(key).toDoubleStream().toArray();
        final NaturalRanking ranking = new NaturalRanking();
        final double[] ranks = ranking.rank(values);
        for (int i=0; i<ranks.length; ++i) {
            final double value = frame.data().getDouble(i, key);
            final double expected = ranks[i];
            final double actual = rankFrame.data().getDouble(i, key);
            Assert.assertEquals(value, values[i], "The values match for row " + i);
            Assert.assertEquals(actual, expected, "The ranks match for " + key + " at row " + i);
        }
    });
}
 

import org.apache.commons.math3.stat.ranking.NaturalRanking; //导入依赖的package包/类
/**
 * Computes the Spearman's rank correlation coefficient between the two arrays.
 *
 * @param xArray first data array
 * @param yArray second data array
 * @return Returns Spearman's rank correlation coefficient for the two arrays
 * @throws DimensionMismatchException if the arrays lengths do not match
 * @throws MathIllegalArgumentException if the array length is less than 2
 */
public double correlation(final double[] xArray, final double[] yArray) {
    if (xArray.length != yArray.length) {
        throw new DimensionMismatchException(xArray.length, yArray.length);
    } else if (xArray.length < 2) {
        throw new MathIllegalArgumentException(LocalizedFormats.INSUFFICIENT_DIMENSION,
                                               xArray.length, 2);
    } else {
        double[] x = xArray;
        double[] y = yArray;
        if (rankingAlgorithm instanceof NaturalRanking &&
            NaNStrategy.REMOVED == ((NaturalRanking) rankingAlgorithm).getNanStrategy()) {
            final Set<Integer> nanPositions = new HashSet<Integer>();

            nanPositions.addAll(getNaNPositions(xArray));
            nanPositions.addAll(getNaNPositions(yArray));

            x = removeValues(xArray, nanPositions);
            y = removeValues(yArray, nanPositions);
        }
        return new PearsonsCorrelation().correlation(rankingAlgorithm.rank(x), rankingAlgorithm.rank(y));
    }
}
 

import org.apache.commons.math3.stat.ranking.NaturalRanking; //导入依赖的package包/类
@Test
public void testMath891Matrix() {
    final double[] xArray = new double[] { Double.NaN, 1.9, 2, 100, 3 };
    final double[] yArray = new double[] { 10, 2, 10, Double.NaN, 4 };

    RealMatrix matrix = MatrixUtils.createRealMatrix(xArray.length, 2);
    for (int i = 0; i < xArray.length; i++) {
        matrix.addToEntry(i, 0, xArray[i]);
        matrix.addToEntry(i, 1, yArray[i]);
    }

    // compute correlation
    NaturalRanking ranking = new NaturalRanking(NaNStrategy.REMOVED);
    SpearmansCorrelation spearman = new SpearmansCorrelation(matrix, ranking);
    
    Assert.assertEquals(0.5, spearman.getCorrelationMatrix().getEntry(0, 1), Double.MIN_VALUE);
}
 

import org.apache.commons.math3.stat.ranking.NaturalRanking; //导入依赖的package包/类
/**
 * Returns the rank array for the values specified
 * @param values    the values to rank
 * @return          the ranks of input array
 */
static double[] rank(double[] values) {
    final NaNStrategy nanStrategy = (NaNStrategy)optionsMap.get(NaNStrategy.class).get(DataFrameOptions.getNanStrategy());
    final TiesStrategy tieStrategy = (TiesStrategy)optionsMap.get(TiesStrategy.class).get(DataFrameOptions.getTieStrategy());
    if (nanStrategy == null) throw new DataFrameException("Unsupported NaN strategy specified: " + DataFrameOptions.getNanStrategy());
    if (tieStrategy == null) throw new DataFrameException("Unsupported tie strategy specified: " + DataFrameOptions.getTieStrategy());
    final NaturalRanking ranking = new NaturalRanking(nanStrategy, tieStrategy);
    return ranking.rank(values);
}
 

import org.apache.commons.math3.stat.ranking.NaturalRanking; //导入依赖的package包/类
@Test
public void testMath891Array() {
    final double[] xArray = new double[] { Double.NaN, 1.9, 2, 100, 3 };
    final double[] yArray = new double[] { 10, 2, 10, Double.NaN, 4 };

    NaturalRanking ranking = new NaturalRanking(NaNStrategy.REMOVED);
    SpearmansCorrelation spearman = new SpearmansCorrelation(ranking);
    
    Assert.assertEquals(0.5, spearman.correlation(xArray, yArray), Double.MIN_VALUE);
}
 

import org.apache.commons.math3.stat.ranking.NaturalRanking; //导入依赖的package包/类
/**
 * Applies rank transform to each of the columns of <code>matrix</code>
 * using the current <code>rankingAlgorithm</code>.
 *
 * @param matrix matrix to transform
 * @return a rank-transformed matrix
 */
private RealMatrix rankTransform(final RealMatrix matrix) {
    RealMatrix transformed = null;

    if (rankingAlgorithm instanceof NaturalRanking &&
            ((NaturalRanking) rankingAlgorithm).getNanStrategy() == NaNStrategy.REMOVED) {
        final Set<Integer> nanPositions = new HashSet<Integer>();
        for (int i = 0; i < matrix.getColumnDimension(); i++) {
            nanPositions.addAll(getNaNPositions(matrix.getColumn(i)));
        }

        // if we have found NaN values, we have to update the matrix size
        if (!nanPositions.isEmpty()) {
            transformed = new BlockRealMatrix(matrix.getRowDimension() - nanPositions.size(),
                                              matrix.getColumnDimension());
            for (int i = 0; i < transformed.getColumnDimension(); i++) {
                transformed.setColumn(i, removeValues(matrix.getColumn(i), nanPositions));
            }
        }
    }

    if (transformed == null) {
        transformed = matrix.copy();
    }

    for (int i = 0; i < transformed.getColumnDimension(); i++) {
        transformed.setColumn(i, rankingAlgorithm.rank(transformed.getColumn(i)));
    }

    return transformed;
}
 

import org.apache.commons.math3.stat.ranking.NaturalRanking; //导入依赖的package包/类
/**
 * Create a SpearmansCorrelation without data.
 */
public SpearmansCorrelation() {
    this(new NaturalRanking());
}
 

import org.apache.commons.math3.stat.ranking.NaturalRanking; //导入依赖的package包/类
public String compute()throws SQLException{
    Statement stmt = null;
    ResultSet rs = null;

    try{
        //get data
        ResizableDoubleArray data = getData();

        //create columns - dao uses its own transaction
        int numberOfColumns = dao.getColumnCount(conn, tableName);
        int columnNumber = numberOfColumns+1;
        String newVariableLabel = "Rank";
        if(blom) newVariableLabel = "Blom Normal Score";
        if(tukey) newVariableLabel = "Tukey Normal Score";
        if(vdw) newVariableLabel = "van der Waerden Normal Score";
        if(ntiles) newVariableLabel = "Quantiles: " + numGroups + " groups";
        newVariable = new VariableAttributes(newVariableName, newVariableLabel, ItemType.NOT_ITEM, DataType.DOUBLE, columnNumber++, "");

        dao.addColumnToDb(conn, tableName, newVariable);

        //compute ranks
        NaturalRanking ranking = new NaturalRanking(NaNStrategy.REMOVED, tiesStrategy);
        double[] ranks = ranking.rank(data.getElements());

        //begin transaction
        conn.setAutoCommit(false);

        //connect to table and update values
        SelectQuery select = new SelectQuery();
        Table sqlTable = new Table(tableName.getNameForDatabase());
        select.addColumn(sqlTable, newVariable.getName().nameForDatabase());
        stmt = conn.createStatement(ResultSet.TYPE_SCROLL_INSENSITIVE, ResultSet.CONCUR_UPDATABLE);
        rs=stmt.executeQuery(select.toString());

        int nRanks = ranks.length;
        int rankIndex = 0;//array index for ranks (missing values not included)
        int dbIndex = 0;//db row position for case (missing values included)
        double r = Double.NaN;
        boolean missing = false;
        String tempName = "";
        while(rs.next()){
            missing = missingIndex.contains(dbIndex);
            if(missing){
                rs.updateNull(newVariable.getName().nameForDatabase());
            }else{
                r = ranks[rankIndex];
                if(blom){
                    rs.updateDouble(newVariable.getName().nameForDatabase(), normScore.blom(r, (double)nRanks));
                }else if (tukey){
                    rs.updateDouble(newVariable.getName().nameForDatabase(), normScore.tukey(r, (double)nRanks));
                }else if(vdw){
                    rs.updateDouble(newVariable.getName().nameForDatabase(), normScore.vanderWaerden(r, (double)nRanks));
                }else if(ntiles){
                    rs.updateDouble(newVariable.getName().nameForDatabase(), getGroup(r, (double)nRanks, (double)numGroups));
                }else{
                    rs.updateDouble(newVariable.getName().nameForDatabase(), r);
                }
                rankIndex++;
            }
            rs.updateRow();
            updateProgress();
            dbIndex++;
        }
        conn.commit();
        return "Ranks computed";
    }catch(SQLException ex){
        conn.rollback();
        throw ex;
    }finally{
        if(rs!=null) rs.close();
        if(stmt!=null) stmt.close();
        conn.setAutoCommit(true);
    }

}
 

import org.apache.commons.math3.stat.ranking.NaturalRanking; //导入依赖的package包/类
/**
 * Create a SpearmansCorrelation without data.
 */
public SpearmansCorrelation() {
    data = null;
    this.rankingAlgorithm = new NaturalRanking();
    rankCorrelation = null;
}
 

import org.apache.commons.math3.stat.ranking.NaturalRanking; //导入依赖的package包/类
/**
 * Create a test instance where NaN's are left in place and ties get
 * the average of applicable ranks. Use this unless you are very sure
 * of what you are doing.
 */
public WilcoxonSignedRankTest() {
    naturalRanking = new NaturalRanking(NaNStrategy.FIXED,
            TiesStrategy.AVERAGE);
}
 

import org.apache.commons.math3.stat.ranking.NaturalRanking; //导入依赖的package包/类
/**
 * Create a test instance using where NaN's are left in place and ties get
 * the average of applicable ranks. Use this unless you are very sure of
 * what you are doing.
 */
public MannWhitneyUTest() {
    naturalRanking = new NaturalRanking(NaNStrategy.FIXED,
            TiesStrategy.AVERAGE);
}