Commons Math example source code file (OLSMultipleLinearRegressionTest.java)
The Commons Math OLSMultipleLinearRegressionTest.java source code/*
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* 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.math.stat.regression;
import static org.junit.Assert.assertEquals;
import org.apache.commons.math.TestUtils;
import org.apache.commons.math.linear.DefaultRealMatrixChangingVisitor;
import org.apache.commons.math.linear.MatrixUtils;
import org.apache.commons.math.linear.MatrixVisitorException;
import org.apache.commons.math.linear.RealMatrix;
import org.apache.commons.math.linear.Array2DRowRealMatrix;
import org.junit.Before;
import org.junit.Test;
public class OLSMultipleLinearRegressionTest extends MultipleLinearRegressionAbstractTest {
private double[] y;
private double[][] x;
@Before
@Override
public void setUp(){
y = new double[]{11.0, 12.0, 13.0, 14.0, 15.0, 16.0};
x = new double[6][];
x[0] = new double[]{1.0, 0, 0, 0, 0, 0};
x[1] = new double[]{1.0, 2.0, 0, 0, 0, 0};
x[2] = new double[]{1.0, 0, 3.0, 0, 0, 0};
x[3] = new double[]{1.0, 0, 0, 4.0, 0, 0};
x[4] = new double[]{1.0, 0, 0, 0, 5.0, 0};
x[5] = new double[]{1.0, 0, 0, 0, 0, 6.0};
super.setUp();
}
@Override
protected OLSMultipleLinearRegression createRegression() {
OLSMultipleLinearRegression regression = new OLSMultipleLinearRegression();
regression.newSampleData(y, x);
return regression;
}
@Override
protected int getNumberOfRegressors() {
return x[0].length;
}
@Override
protected int getSampleSize() {
return y.length;
}
@Test(expected=IllegalArgumentException.class)
public void cannotAddXSampleData() {
createRegression().newSampleData(new double[]{}, null);
}
@Test(expected=IllegalArgumentException.class)
public void cannotAddNullYSampleData() {
createRegression().newSampleData(null, new double[][]{});
}
@Test(expected=IllegalArgumentException.class)
public void cannotAddSampleDataWithSizeMismatch() {
double[] y = new double[]{1.0, 2.0};
double[][] x = new double[1][];
x[0] = new double[]{1.0, 0};
createRegression().newSampleData(y, x);
}
@Test
public void testPerfectFit() {
double[] betaHat = regression.estimateRegressionParameters();
TestUtils.assertEquals(betaHat,
new double[]{ 11.0, 1.0 / 2.0, 2.0 / 3.0, 3.0 / 4.0, 4.0 / 5.0, 5.0 / 6.0 },
1e-14);
double[] residuals = regression.estimateResiduals();
TestUtils.assertEquals(residuals, new double[]{0d,0d,0d,0d,0d,0d},
1e-14);
RealMatrix errors =
new Array2DRowRealMatrix(regression.estimateRegressionParametersVariance(), false);
final double[] s = { 1.0, -1.0 / 2.0, -1.0 / 3.0, -1.0 / 4.0, -1.0 / 5.0, -1.0 / 6.0 };
RealMatrix referenceVariance = new Array2DRowRealMatrix(s.length, s.length);
referenceVariance.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
@Override
public double visit(int row, int column, double value)
throws MatrixVisitorException {
if (row == 0) {
return s[column];
}
double x = s[row] * s[column];
return (row == column) ? 2 * x : x;
}
});
assertEquals(0.0,
errors.subtract(referenceVariance).getNorm(),
5.0e-16 * referenceVariance.getNorm());
}
/**
* Test Longley dataset against certified values provided by NIST.
* Data Source: J. Longley (1967) "An Appraisal of Least Squares
* Programs for the Electronic Computer from the Point of View of the User"
* Journal of the American Statistical Association, vol. 62. September,
* pp. 819-841.
*
* Certified values (and data) are from NIST:
* http://www.itl.nist.gov/div898/strd/lls/data/LINKS/DATA/Longley.dat
*/
@Test
public void testLongly() {
// Y values are first, then independent vars
// Each row is one observation
double[] design = new double[] {
60323,83.0,234289,2356,1590,107608,1947,
61122,88.5,259426,2325,1456,108632,1948,
60171,88.2,258054,3682,1616,109773,1949,
61187,89.5,284599,3351,1650,110929,1950,
63221,96.2,328975,2099,3099,112075,1951,
63639,98.1,346999,1932,3594,113270,1952,
64989,99.0,365385,1870,3547,115094,1953,
63761,100.0,363112,3578,3350,116219,1954,
66019,101.2,397469,2904,3048,117388,1955,
67857,104.6,419180,2822,2857,118734,1956,
68169,108.4,442769,2936,2798,120445,1957,
66513,110.8,444546,4681,2637,121950,1958,
68655,112.6,482704,3813,2552,123366,1959,
69564,114.2,502601,3931,2514,125368,1960,
69331,115.7,518173,4806,2572,127852,1961,
70551,116.9,554894,4007,2827,130081,1962
};
// Transform to Y and X required by interface
int nobs = 16;
int nvars = 6;
// Estimate the model
OLSMultipleLinearRegression model = new OLSMultipleLinearRegression();
model.newSampleData(design, nobs, nvars);
// Check expected beta values from NIST
double[] betaHat = model.estimateRegressionParameters();
TestUtils.assertEquals(betaHat,
new double[]{-3482258.63459582, 15.0618722713733,
-0.358191792925910E-01,-2.02022980381683,
-1.03322686717359,-0.511041056535807E-01,
1829.15146461355}, 2E-8); //
// Check expected residuals from R
double[] residuals = model.estimateResiduals();
TestUtils.assertEquals(residuals, new double[]{
267.340029759711,-94.0139423988359,46.28716775752924,
-410.114621930906,309.7145907602313,-249.3112153297231,
-164.0489563956039,-13.18035686637081,14.30477260005235,
455.394094551857,-17.26892711483297,-39.0550425226967,
-155.5499735953195,-85.6713080421283,341.9315139607727,
-206.7578251937366},
1E-8);
// Check standard errors from NIST
double[] errors = model.estimateRegressionParametersStandardErrors();
TestUtils.assertEquals(new double[] {890420.383607373,
84.9149257747669,
0.334910077722432E-01,
0.488399681651699,
0.214274163161675,
0.226073200069370,
455.478499142212}, errors, 1E-6);
}
/**
* Test R Swiss fertility dataset against R.
* Data Source: R datasets package
*/
@Test
public void testSwissFertility() {
double[] design = new double[] {
80.2,17.0,15,12,9.96,
83.1,45.1,6,9,84.84,
92.5,39.7,5,5,93.40,
85.8,36.5,12,7,33.77,
76.9,43.5,17,15,5.16,
76.1,35.3,9,7,90.57,
83.8,70.2,16,7,92.85,
92.4,67.8,14,8,97.16,
82.4,53.3,12,7,97.67,
82.9,45.2,16,13,91.38,
87.1,64.5,14,6,98.61,
64.1,62.0,21,12,8.52,
66.9,67.5,14,7,2.27,
68.9,60.7,19,12,4.43,
61.7,69.3,22,5,2.82,
68.3,72.6,18,2,24.20,
71.7,34.0,17,8,3.30,
55.7,19.4,26,28,12.11,
54.3,15.2,31,20,2.15,
65.1,73.0,19,9,2.84,
65.5,59.8,22,10,5.23,
65.0,55.1,14,3,4.52,
56.6,50.9,22,12,15.14,
57.4,54.1,20,6,4.20,
72.5,71.2,12,1,2.40,
74.2,58.1,14,8,5.23,
72.0,63.5,6,3,2.56,
60.5,60.8,16,10,7.72,
58.3,26.8,25,19,18.46,
65.4,49.5,15,8,6.10,
75.5,85.9,3,2,99.71,
69.3,84.9,7,6,99.68,
77.3,89.7,5,2,100.00,
70.5,78.2,12,6,98.96,
79.4,64.9,7,3,98.22,
65.0,75.9,9,9,99.06,
92.2,84.6,3,3,99.46,
79.3,63.1,13,13,96.83,
70.4,38.4,26,12,5.62,
65.7,7.7,29,11,13.79,
72.7,16.7,22,13,11.22,
64.4,17.6,35,32,16.92,
77.6,37.6,15,7,4.97,
67.6,18.7,25,7,8.65,
35.0,1.2,37,53,42.34,
44.7,46.6,16,29,50.43,
42.8,27.7,22,29,58.33
};
// Transform to Y and X required by interface
int nobs = 47;
int nvars = 4;
// Estimate the model
OLSMultipleLinearRegression model = new OLSMultipleLinearRegression();
model.newSampleData(design, nobs, nvars);
// Check expected beta values from R
double[] betaHat = model.estimateRegressionParameters();
TestUtils.assertEquals(betaHat,
new double[]{91.05542390271397,
-0.22064551045715,
-0.26058239824328,
-0.96161238456030,
0.12441843147162}, 1E-12);
// Check expected residuals from R
double[] residuals = model.estimateResiduals();
TestUtils.assertEquals(residuals, new double[]{
7.1044267859730512,1.6580347433531366,
4.6944952770029644,8.4548022690166160,13.6547432343186212,
-9.3586864458500774,7.5822446330520386,15.5568995563859289,
0.8113090736598980,7.1186762732484308,7.4251378771228724,
2.6761316873234109,0.8351584810309354,7.1769991119615177,
-3.8746753206299553,-3.1337779476387251,-0.1412575244091504,
1.1186809170469780,-6.3588097346816594,3.4039270429434074,
2.3374058329820175,-7.9272368576900503,-7.8361010968497959,
-11.2597369269357070,0.9445333697827101,6.6544245101380328,
-0.9146136301118665,-4.3152449403848570,-4.3536932047009183,
-3.8907885169304661,-6.3027643926302188,-7.8308982189289091,
-3.1792280015332750,-6.7167298771158226,-4.8469946718041754,
-10.6335664353633685,11.1031134362036958,6.0084032641811733,
5.4326230830188482,-7.2375578629692230,2.1671550814448222,
15.0147574652763112,4.8625103516321015,-7.1597256413907706,
-0.4515205619767598,-10.2916870903837587,-15.7812984571900063},
1E-12);
// Check standard errors from R
double[] errors = model.estimateRegressionParametersStandardErrors();
TestUtils.assertEquals(new double[] {6.94881329475087,
0.07360008972340,
0.27410957467466,
0.19454551679325,
0.03726654773803}, errors, 1E-10);
}
/**
* Test hat matrix computation
*
* @throws Exception
*/
@Test
public void testHat() throws Exception {
/*
* This example is from "The Hat Matrix in Regression and ANOVA",
* David C. Hoaglin and Roy E. Welsch,
* The American Statistician, Vol. 32, No. 1 (Feb., 1978), pp. 17-22.
*
*/
double[] design = new double[] {
11.14, .499, 11.1,
12.74, .558, 8.9,
13.13, .604, 8.8,
11.51, .441, 8.9,
12.38, .550, 8.8,
12.60, .528, 9.9,
11.13, .418, 10.7,
11.7, .480, 10.5,
11.02, .406, 10.5,
11.41, .467, 10.7
};
int nobs = 10;
int nvars = 2;
// Estimate the model
OLSMultipleLinearRegression model = new OLSMultipleLinearRegression();
model.newSampleData(design, nobs, nvars);
RealMatrix hat = model.calculateHat();
// Reference data is upper half of symmetric hat matrix
double[] referenceData = new double[] {
.418, -.002, .079, -.274, -.046, .181, .128, .222, .050, .242,
.242, .292, .136, .243, .128, -.041, .033, -.035, .004,
.417, -.019, .273, .187, -.126, .044, -.153, .004,
.604, .197, -.038, .168, -.022, .275, -.028,
.252, .111, -.030, .019, -.010, -.010,
.148, .042, .117, .012, .111,
.262, .145, .277, .174,
.154, .120, .168,
.315, .148,
.187
};
// Check against reference data and verify symmetry
int k = 0;
for (int i = 0; i < 10; i++) {
for (int j = i; j < 10; j++) {
assertEquals(referenceData[k], hat.getEntry(i, j), 10e-3);
assertEquals(hat.getEntry(i, j), hat.getEntry(j, i), 10e-12);
k++;
}
}
/*
* Verify that residuals computed using the hat matrix are close to
* what we get from direct computation, i.e. r = (I - H) y
*/
double[] residuals = model.estimateResiduals();
RealMatrix I = MatrixUtils.createRealIdentityMatrix(10);
double[] hatResiduals = I.subtract(hat).operate(model.Y).getData();
TestUtils.assertEquals(residuals, hatResiduals, 10e-12);
}
}
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