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/*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with this
* work for additional information regarding copyright ownership. The ASF
* licenses this file to You under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law
* or agreed to in writing, software distributed under the License is
* distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the specific language
* governing permissions and limitations under the License.
*/
package org.apache.commons.math3.stat.inference;
import java.math.BigDecimal;
import java.util.Arrays;
import java.util.Iterator;
import org.apache.commons.math3.distribution.KolmogorovSmirnovDistribution;
import org.apache.commons.math3.distribution.RealDistribution;
import org.apache.commons.math3.exception.MathArithmeticException;
import org.apache.commons.math3.exception.MathIllegalArgumentException;
import org.apache.commons.math3.exception.NullArgumentException;
import org.apache.commons.math3.exception.NumberIsTooLargeException;
import org.apache.commons.math3.exception.OutOfRangeException;
import org.apache.commons.math3.exception.TooManyIterationsException;
import org.apache.commons.math3.exception.util.LocalizedFormats;
import org.apache.commons.math3.fraction.BigFraction;
import org.apache.commons.math3.fraction.BigFractionField;
import org.apache.commons.math3.fraction.FractionConversionException;
import org.apache.commons.math3.linear.Array2DRowFieldMatrix;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import org.apache.commons.math3.linear.FieldMatrix;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.util.CombinatoricsUtils;
import org.apache.commons.math3.util.FastMath;
import org.apache.commons.math3.util.MathArrays;
/**
* Implementation of the <a
* href="http://en.wikipedia.org/wiki/Kolmogorov-Smirnov_test">
* Kolmogorov-Smirnov (K-S) test</a> for equality of continuous distributions.
* <p>
* The K-S test uses a statistic based on the maximum deviation of the empirical
* distribution of sample data points from the distribution expected under the
* null hypothesis. Specifically, what is computed is \(D_n=\sup_x
* |F_n(x)-F(x)|\), where \(F\) is the expected distribution and \(F_n\) is the
* empirical distribution of the \(n\) sample data points. The distribution of
* \(D_n\) is estimated using a method based on [1] with certain quick decisions
* for extreme values given in [2].
* </p>
* <p>
* References:
* <ul>
* <li>[1] <a href="http://www.jstatsoft.org/v08/i18/"> Evaluating Kolmogorov's
* Distribution</a> by George Marsaglia, Wai Wan Tsang, and Jingbo Wang</li>
* <li>[2] <a href="http://www.jstatsoft.org/v39/i11/"> Computing the Two-Sided
* Kolmogorov-Smirnov Distribution</a> by Richard Simard and Pierre L'Ecuyer</li>
* </ul>
* Note that [1] contains an error in computing h, refer to <a
* href="https://issues.apache.org/jira/browse/MATH-437">MATH-437</a> for
* details.
* </p>
*
* @since 3.3
* @version $Id$
*/
public class KolmogorovSmirnovTest {
/**
* Bound on the number of partial sums in
* {@link #ksSum(double, double, long)}
*/
private static final long MAXIMUM_PARTIAL_SUM_COUNT = 100000;
/** Convergence criterion for {@link #ksSum(double, double, long)} */
private static final double KS_SUM_CAUCHY_CRITERION = 1e-15;
/** Cutoff for default 2-sample test to use K-S distribution approximation */
private static final long SMALL_SAMPLE_PRODUCT = 10000;
/**
* Computes the <i>p-value</i>, or <i>observed significance level</i>, of a
* one-sample <a
* href="http://en.wikipedia.org/wiki/Kolmogorov-Smirnov_test">
* Kolmogorov-Smirnov test</a> evaluating the null hypothesis that
* {@code data} conforms to {@code distribution}. If {@code exact} is true,
* the distribution used to compute the p-value is computed using extended
* precision. See {@link #cdfExact(double, int)}.
*
* @param distribution reference distribution
* @param data sample being being evaluated
* @param exact whether or not to force exact computation of the p-value
* @return the p-value associated with the null hypothesis that {@code data}
* is a sample from {@code distribution}
*/
public double kolmogorovSmirnovTest(RealDistribution distribution, double[] data, boolean exact) {
return 1d - cdf(kolmogorovSmirnovStatistic(distribution, data), data.length, exact);
}
/**
* Computes the one-sample Kolmogorov-Smirnov test statistic, \(D_n=\sup_x
* |F_n(x)-F(x)|\) where \(F\) is the distribution (cdf) function associated
* with {@code distribution}, \(n\) is the length of {@code data} and
* \(F_n\) is the empirical distribution that puts mass \(1/n\) at each of
* the values in {@code data}.
*
* @param distribution reference distribution
* @param data sample being evaluated
* @return Kolmogorov-Smirnov statistic \(D_n\)
* @throws MathIllegalArgumentException if {@code data} does not have length
* at least 2
*/
public double kolmogorovSmirnovStatistic(RealDistribution distribution, double[] data) {
final int n = data.length;
final double nd = n;
final double[] dataCopy = new double[n];
System.arraycopy(data, 0, dataCopy, 0, n);
Arrays.sort(dataCopy);
double d = 0d;
for (int i = 1; i <= n; i++) {
final double yi = distribution.cumulativeProbability(dataCopy[i - 1]);
final double currD = FastMath.max(yi - (i - 1) / nd, i / nd - yi);
if (currD > d) {
d = currD;
}
}
return d;
}
/**
* Computes the <i>p-value</i>, or <i>observed significance level</i>, of a
* two-sample <a
* href="http://en.wikipedia.org/wiki/Kolmogorov-Smirnov_test">
* Kolmogorov-Smirnov test</a> evaluating the null hypothesis that {@code x}
* and {@code y} are samples drawn from the same probability distribution.
* If {@code exact} is true, the discrete distribution of the test statistic
* is computed and used directly; otherwise the asymptotic
* (Kolmogorov-Smirnov) distribution is used to estimate the p-value.
*
* @param x first sample dataset
* @param y second sample dataset
* @param exact whether or not the exact distribution of the \(D\( statistic
* is used
* @return p-value associated with the null hypothesis that {@code x} and
* {@code y} represent samples from the same distribution
*/
public double kolmogorovSmirnovTest(double[] x, double[] y, boolean exact) {
if (exact) {
return exactP(kolmogorovSmirnovStatistic(x, y), x.length, y.length, false);
} else {
return approximateP(kolmogorovSmirnovStatistic(x, y), x.length, y.length);
}
}
/**
* Computes the <i>p-value</i>, or <i>observed significance level</i>, of a
* two-sample <a
* href="http://en.wikipedia.org/wiki/Kolmogorov-Smirnov_test">
* Kolmogorov-Smirnov test</a> evaluating the null hypothesis that {@code x}
* and {@code y} are samples drawn from the same probability distribution.
* If the product of the lengths of x and y is less than 10,000, the
* discrete distribution of the test statistic is computed and used
* directly; otherwise the asymptotic (Kolmogorov-Smirnov) distribution is
* used to estimate the p-value.
*
* @param x first sample dataset
* @param y second sample dataset
* @return p-value associated with the null hypothesis that {@code x} and
* {@code y} represent samples from the same distribution
*/
public double kolmogorovSmirnovTest(double[] x, double[] y) {
if (x.length * y.length < SMALL_SAMPLE_PRODUCT) {
return kolmogorovSmirnovTest(x, y, true);
} else {
return kolmogorovSmirnovTest(x, y, false);
}
}
/**
* Computes the two-sample Kolmogorov-Smirnov test statistic, \(D_n,m=\sup_x
* |F_n(x)-F_m(x)|\) \(n\) is the length of {@code x}, \(m\) is the length
* of {@code y}, \(F_n\) is the empirical distribution that puts mass
* \(1/n\) at each of the values in {@code x} and \(F_m\) is the empirical
* distribution of the {@code y} values.
*
* @param x first sample
* @param y second sample
* @return test statistic \(D_n,m\) used to evaluate the null hypothesis
* that {@code x} and {@code y} represent samples from the same
* underlying distribution
* @throws MathIllegalArgumentException if either {@code x} or {@code y}
* does not have length at least 2.
*/
public double kolmogorovSmirnovStatistic(double[] x, double[] y) {
checkArray(x);
checkArray(y);
// Copy and sort the sample arrays
final double[] sx = MathArrays.copyOf(x);
final double[] sy = MathArrays.copyOf(y);
Arrays.sort(sx);
Arrays.sort(sy);
final int n = sx.length;
final int m = sy.length;
// Compare empirical distribution cdf values at each (combined) sample
// point.
// D_n.m is the max difference.
// cdf value is (insertion point - 1) / length if not an element;
// index / n if element is in the array.
double supD = 0d;
// First walk x points
for (int i = 0; i < n; i++) {
final double cdf_x = (i + 1d) / n;
final int yIndex = Arrays.binarySearch(sy, sx[i]);
final double cdf_y = yIndex >= 0 ? (yIndex + 1d) / m : (-yIndex - 1d) / m;
final double curD = FastMath.abs(cdf_x - cdf_y);
if (curD > supD) {
supD = curD;
}
}
// Now look at y
for (int i = 0; i < m; i++) {
final double cdf_y = (i + 1d) / m;
final int xIndex = Arrays.binarySearch(sx, sy[i]);
final double cdf_x = xIndex >= 0 ? (xIndex + 1d) / n : (-xIndex - 1d) / n;
final double curD = FastMath.abs(cdf_x - cdf_y);
if (curD > supD) {
supD = curD;
}
}
return supD;
}
/**
* Computes the <i>p-value</i>, or <i>observed significance level</i>, of a
* one-sample <a
* href="http://en.wikipedia.org/wiki/Kolmogorov-Smirnov_test">
* Kolmogorov-Smirnov test</a> evaluating the null hypothesis that
* {@code data} conforms to {@code distribution}.
*
* @param distribution reference distribution
* @param data sample being being evaluated
* @return the p-value associated with the null hypothesis that {@code data}
* is a sample from {@code distribution}
*/
public double kolmogorovSmirnovTest(RealDistribution distribution, double[] data) {
return kolmogorovSmirnovTest(distribution, data, false);
}
/**
* Performs a <a
* href="http://en.wikipedia.org/wiki/Kolmogorov-Smirnov_test">
* Kolmogorov-Smirnov test</a> evaluating the null hypothesis that
* {@code data} conforms to {@code distribution}.
*
* @param distribution reference distribution
* @param data sample being being evaluated
* @param alpha significance level of the test
* @return true iff the null hypothesis that {@code data} is a sample from
* {@code distribution} can be rejected with confidence 1 -
* {@code alpha}
*/
public boolean kolmogorovSmirnovTest(RealDistribution distribution, double[] data, double alpha) {
if ((alpha <= 0) || (alpha > 0.5)) {
throw new OutOfRangeException(LocalizedFormats.OUT_OF_BOUND_SIGNIFICANCE_LEVEL, alpha, 0, 0.5);
}
return kolmogorovSmirnovTest(distribution, data) < alpha;
}
/**
* Calculates {@code P(D_n < d)} using method described in [1] with quick
* decisions for extreme values given in [2] (see above). The result is not
* exact as with {@link KolmogorovSmirnovDistribution#cdfExact(double)}
* because calculations are based on {@code double} rather than
* {@link org.apache.commons.math3.fraction.BigFraction}.
*
* @param d statistic
* @return the two-sided probability of {@code P(D_n < d)}
* @throws MathArithmeticException if algorithm fails to convert {@code h}
* to a {@link org.apache.commons.math3.fraction.BigFraction} in
* expressing {@code d} as {@code (k - h) / m} for integer
* {@code k, m} and {@code 0 <= h < 1}.
*/
public double cdf(double d, int n)
throws MathArithmeticException {
return cdf(d, n, false);
}
/**
* Calculates {@code P(D_n < d)}. The result is exact in the sense that
* BigFraction/BigReal is used everywhere at the expense of very slow
* execution time. Almost never choose this in real applications unless you
* are very sure; this is almost solely for verification purposes. Normally,
* you would choose {@link KolmogorovSmirnovDistribution#cdf(double)}. See
* the class javadoc for definitions and algorithm description.
*
* @param d statistic
* @return the two-sided probability of {@code P(D_n < d)}
* @throws MathArithmeticException if the algorithm fails to convert
* {@code h} to a
* {@link org.apache.commons.math3.fraction.BigFraction} in
* expressing {@code d} as {@code (k - h) / m} for integer
* {@code k, m} and {@code 0 <= h < 1}.
*/
public double cdfExact(double d, int n)
throws MathArithmeticException {
return cdf(d, n, true);
}
/**
* Calculates {@code P(D_n < d)} using method described in [1] with quick
* decisions for extreme values given in [2] (see above).
*
* @param d statistic
* @param exact whether the probability should be calculated exact using
* {@link org.apache.commons.math3.fraction.BigFraction} everywhere
* at the expense of very slow execution time, or if {@code double}
* should be used convenient places to gain speed. Almost never
* choose {@code true} in real applications unless you are very sure;
* {@code true} is almost solely for verification purposes.
* @return the two-sided probability of {@code P(D_n < d)}
* @throws MathArithmeticException if algorithm fails to convert {@code h}
* to a {@link org.apache.commons.math3.fraction.BigFraction} in
* expressing {@code d} as {@code (k - h) / m} for integer
* {@code k, m} and {@code 0 <= h < 1}.
*/
public double cdf(double d, int n, boolean exact)
throws MathArithmeticException {
final double ninv = 1 / ((double) n);
final double ninvhalf = 0.5 * ninv;
if (d <= ninvhalf) {
return 0;
} else if (ninvhalf < d && d <= ninv) {
double res = 1;
final double f = 2 * d - ninv;
// n! f^n = n*f * (n-1)*f * ... * 1*x
for (int i = 1; i <= n; ++i) {
res *= i * f;
}
return res;
} else if (1 - ninv <= d && d < 1) {
return 1 - 2 * Math.pow(1 - d, n);
} else if (1 <= d) {
return 1;
}
return exact ? exactK(d, n) : roundedK(d, n);
}
/**
* Calculates the exact value of {@code P(D_n < d)} using method described
* in [1] and {@link org.apache.commons.math3.fraction.BigFraction} (see
* above).
*
* @param d statistic
* @return the two-sided probability of {@code P(D_n < d)}
* @throws MathArithmeticException if algorithm fails to convert {@code h}
* to a {@link org.apache.commons.math3.fraction.BigFraction} in
* expressing {@code d} as {@code (k - h) / m} for integer
* {@code k, m} and {@code 0 <= h < 1}.
*/
private double exactK(double d, int n)
throws MathArithmeticException {
final int k = (int) Math.ceil(n * d);
final FieldMatrix<BigFraction> H = this.createH(d, n);
final FieldMatrix<BigFraction> Hpower = H.power(n);
BigFraction pFrac = Hpower.getEntry(k - 1, k - 1);
for (int i = 1; i <= n; ++i) {
pFrac = pFrac.multiply(i).divide(n);
}
/*
* BigFraction.doubleValue converts numerator to double and the
* denominator to double and divides afterwards. That gives NaN quite
* easy. This does not (scale is the number of digits):
*/
return pFrac.bigDecimalValue(20, BigDecimal.ROUND_HALF_UP).doubleValue();
}
/**
* Calculates {@code P(D_n < d)} using method described in [1] and doubles
* (see above).
*
* @param d statistic
* @return the two-sided probability of {@code P(D_n < d)}
* @throws MathArithmeticException if algorithm fails to convert {@code h}
* to a {@link org.apache.commons.math3.fraction.BigFraction} in
* expressing {@code d} as {@code (k - h) / m} for integer
* {@code k, m} and {@code 0 <= h < 1}.
*/
private double roundedK(double d, int n)
throws MathArithmeticException {
final int k = (int) Math.ceil(n * d);
final FieldMatrix<BigFraction> HBigFraction = this.createH(d, n);
final int m = HBigFraction.getRowDimension();
/*
* Here the rounding part comes into play: use RealMatrix instead of
* FieldMatrix<BigFraction>
*/
final RealMatrix H = new Array2DRowRealMatrix(m, m);
for (int i = 0; i < m; ++i) {
for (int j = 0; j < m; ++j) {
H.setEntry(i, j, HBigFraction.getEntry(i, j).doubleValue());
}
}
final RealMatrix Hpower = H.power(n);
double pFrac = Hpower.getEntry(k - 1, k - 1);
for (int i = 1; i <= n; ++i) {
pFrac *= (double) i / (double) n;
}
return pFrac;
}
/***
* Creates {@code H} of size {@code m x m} as described in [1] (see above).
*
* @param d statistic
* @return H matrix
* @throws NumberIsTooLargeException if fractional part is greater than 1
* @throws FractionConversionException if algorithm fails to convert
* {@code h} to a
* {@link org.apache.commons.math3.fraction.BigFraction} in
* expressing {@code d} as {@code (k - h) / m} for integer
* {@code k, m} and {@code 0 <= h < 1}.
*/
private FieldMatrix<BigFraction> createH(double d, int n)
throws NumberIsTooLargeException, FractionConversionException {
final int k = (int) Math.ceil(n * d);
final int m = 2 * k - 1;
final double hDouble = k - n * d;
if (hDouble >= 1) {
throw new NumberIsTooLargeException(hDouble, 1.0, false);
}
BigFraction h = null;
try {
h = new BigFraction(hDouble, 1.0e-20, 10000);
} catch (final FractionConversionException e1) {
try {
h = new BigFraction(hDouble, 1.0e-10, 10000);
} catch (final FractionConversionException e2) {
h = new BigFraction(hDouble, 1.0e-5, 10000);
}
}
final BigFraction[][] Hdata = new BigFraction[m][m];
/*
* Start by filling everything with either 0 or 1.
*/
for (int i = 0; i < m; ++i) {
for (int j = 0; j < m; ++j) {
if (i - j + 1 < 0) {
Hdata[i][j] = BigFraction.ZERO;
} else {
Hdata[i][j] = BigFraction.ONE;
}
}
}
/*
* Setting up power-array to avoid calculating the same value twice:
* hPowers[0] = h^1 ... hPowers[m-1] = h^m
*/
final BigFraction[] hPowers = new BigFraction[m];
hPowers[0] = h;
for (int i = 1; i < m; ++i) {
hPowers[i] = h.multiply(hPowers[i - 1]);
}
/*
* First column and last row has special values (each other reversed).
*/
for (int i = 0; i < m; ++i) {
Hdata[i][0] = Hdata[i][0].subtract(hPowers[i]);
Hdata[m - 1][i] = Hdata[m - 1][i].subtract(hPowers[m - i - 1]);
}
/*
* [1] states: "For 1/2 < h < 1 the bottom left element of the matrix
* should be (1 - 2*h^m + (2h - 1)^m )/m!" Since 0 <= h < 1, then if h >
* 1/2 is sufficient to check:
*/
if (h.compareTo(BigFraction.ONE_HALF) == 1) {
Hdata[m - 1][0] = Hdata[m - 1][0].add(h.multiply(2).subtract(1).pow(m));
}
/*
* Aside from the first column and last row, the (i, j)-th element is
* 1/(i - j + 1)! if i - j + 1 >= 0, else 0. 1's and 0's are already
* put, so only division with (i - j + 1)! is needed in the elements
* that have 1's. There is no need to calculate (i - j + 1)! and then
* divide - small steps avoid overflows. Note that i - j + 1 > 0 <=> i +
* 1 > j instead of j'ing all the way to m. Also note that it is started
* at g = 2 because dividing by 1 isn't really necessary.
*/
for (int i = 0; i < m; ++i) {
for (int j = 0; j < i + 1; ++j) {
if (i - j + 1 > 0) {
for (int g = 2; g <= i - j + 1; ++g) {
Hdata[i][j] = Hdata[i][j].divide(g);
}
}
}
}
return new Array2DRowFieldMatrix<BigFraction>(BigFractionField.getInstance(), Hdata);
}
/**
* Verifies that array has length at least 2, throwing MIAE if not.
*
* @param array array to test
* @throws NullArgumentException if array is null
* @throws MathIllegalArgumentException if array is too short
*/
private void checkArray(double[] array) {
if (array == null) {
throw new NullArgumentException(LocalizedFormats.NULL_NOT_ALLOWED);
}
if (array.length < 2) {
throw new MathIllegalArgumentException(LocalizedFormats.INSUFFICIENT_OBSERVED_POINTS_IN_SAMPLE,
array.length, 2);
}
}
/**
* Compute \( \sum_{k=-\infty}^\infty (-1)^k e^{-2 k^2 x^2} = 1 + 2
* \sum_{k=1}^\infty (-1)^k e^{-2 k^2 x^2} = \frac{\sqrt{2\pi}}{x}
* \sum_{k=1}^\infty \exp(-(2k-1)^2\pi^2/(8x^2)) \) See e.g. J. Durbin
* (1973), Distribution Theory for Tests Based on the Sample Distribution
* Function. SIAM. The 'standard' series expansion obviously cannot be used
* close to 0; we use the alternative series for x < 1, and a rather crude
* estimate of the series remainder term in this case, in particular using
* that \(ue^(-lu^2) \le e^(-lu^2 + u) \le e^(-(l-1)u^2 - u^2+u) \le
* e^(-(l-1))\) provided that u and l are >= 1. (But note that for
* reasonable tolerances, one could simply take 0 as the value for x < 0.2,
* and use the standard expansion otherwise.)
*/
public double pkstwo(double x, double tol) {
final double M_PI_2 = Math.PI / 2;
final double M_PI_4 = Math.PI / 4;
final double M_1_SQRT_2PI = 1 / Math.sqrt(Math.PI * 2);
double newx, old, s;
int k;
final int k_max = (int) Math.sqrt(2 - Math.log(tol));
if (x < 1) {
final double z = -(M_PI_2 * M_PI_4) / (x * x);
final double w = Math.log(x);
s = 0;
for (k = 1; k < k_max; k += 2) {
s += Math.exp(k * k * z - w);
}
return s / M_1_SQRT_2PI;
} else {
final double z = -2 * x * x;
s = -1;
k = 1;
old = 0;
newx = 1;
while (Math.abs(old - newx) > tol) {
old = newx;
newx += 2 * s * Math.exp(z * k * k);
s *= -1;
k++;
}
return newx;
}
}
/**
* Computes \( 1 + 2 \sum_{i=1}^\infty (-1)^i e^{-2 i^2 t^2} \) stopping
* when successive partial sums are within {@code tolerance} of one another,
* or when {@code maxIter} partial sums have been computed. If the sum does
* not converge before {@code maxIter} iterations a
* {@link TooManyIterationsException} is thrown.
*
* @param t argument
* @param tolerance Cauchy criterion for partial sums
* @param maxIter maximum number of partial sums to compute
* @throws TooManyIterationsException if the series does not converge
*/
public double ksSum(double t, double tolerance, long maxIter) {
final double x = -2 * t * t;
double sign = -1;
int i = 1;
double lastPartialSum = -1d;
double partialSum = 0.5d;
long iterationCount = 0;
while (FastMath.abs(lastPartialSum - partialSum) > tolerance && iterationCount < maxIter) {
lastPartialSum = partialSum;
partialSum += sign * FastMath.exp(x * i * i);
sign *= -1;
i++;
}
if (iterationCount == maxIter) {
throw new TooManyIterationsException(maxIter);
}
return partialSum * 2;
}
public double exactP(double d, int n, int m, boolean strict) {
Iterator<int[]> combinationsIterator = CombinatoricsUtils.combinationsIterator(n + m, n);
long tail = 0;
final double[] nSet = new double[n];
final double[] mSet = new double[m];
while (combinationsIterator.hasNext()) {
// Generate an n-set
final int[] nSetI = combinationsIterator.next();
// Copy the n-set to nSet and its complement to mSet
int j = 0;
int k = 0;
for (int i = 0; i < n + m; i++) {
if (j < n && nSetI[j] == i) {
nSet[j++] = i;
} else {
mSet[k++] = i;
}
}
final double curD = kolmogorovSmirnovStatistic(nSet, mSet);
if (curD > d) {
tail++;
} else if (curD == d && !strict) {
tail++;
}
}
return (double) tail / (double) CombinatoricsUtils.binomialCoefficient(n + m, n);
}
public double approximateP(double d, int n, int m) {
return 1 - ksSum(d * FastMath.sqrt((double) (m * n) / (double) (m + n)), KS_SUM_CAUCHY_CRITERION,
MAXIMUM_PARTIAL_SUM_COUNT);
}
}