def testFstatistic(self):
# Test on a model with more than one regressor
expectedFstatistic = 48625.747064132738
self.assertAlmostEqual(self.linearFit.Fstatistic(weighted=False), expectedFstatistic, places=7)
# Test on a model with only one regressor
expectedFstatistic = 17403.423925909559
linearModel = LinearModel([np.square(self.time)], ["t^2"])
linearFit = linearModel.fitData(self.observations)
self.assertAlmostEqual(linearFit.Fstatistic(weighted=False), expectedFstatistic, places=7)
def testFstatistic(self):
# Test on a model with more than one regressor
expectedFstatistic = 48625.747064132738
self.assertAlmostEqual(self.linearFit.Fstatistic(weighted=False), expectedFstatistic, places=7)
# Test on a model with only one regressor
expectedFstatistic = 17403.423925909559
linearModel = LinearModel([np.square(self.time)], ["t^2"])
linearFit = linearModel.fitData(self.observations)
self.assertAlmostEqual(linearFit.Fstatistic(weighted=False), expectedFstatistic, places=7)
def testCoefficientOfDetermination(self):
# Test using a model with an intercept
expectedCoefficientOfDetermination = 0.99983550516908659
self.assertAlmostEqual(self.linearFit.coefficientOfDetermination(weighted=False), expectedCoefficientOfDetermination, places=7)
# Test using a model without an intercept
linearModel = LinearModel([self.time**2], ["t^2"])
linearFit = linearModel.fitData(self.observations)
expectedCoefficientOfDetermination = 0.99948312767720937
self.assertAlmostEqual(linearFit.coefficientOfDetermination(weighted=False), expectedCoefficientOfDetermination, places=7)
def testThypothesisTest(self):
regressorList = [np.ones_like(self.time), self.time ** 2, self.time ** 3]
regressorNames = ["1", "t^2", "t^3"]
linearModel = LinearModel(regressorList, regressorNames)
linearFit = linearModel.fitData(self.observations)
alpha = 0.05 # significance level
expectedOutput = np.array([True, True, False])
nullRejected = linearFit.regressorTtest(alpha)
self.assertTrue(isinstance(nullRejected, np.ndarray))
self.assertTrue(nullRejected.dtype == np.bool)
self.assertEqual(len(nullRejected), len(regressorList))
self.assertTrue(np.all(nullRejected == expectedOutput))
def testThypothesisTest(self):
regressorList = [np.ones_like(self.time), self.time**2, self.time**3]
regressorNames = ["1", "t^2", "t^3"]
linearModel = LinearModel(regressorList, regressorNames)
linearFit = linearModel.fitData(self.observations)
alpha = 0.05 # significance level
expectedOutput = np.array([True, True, False])
nullRejected = linearFit.regressorTtest(alpha)
self.assertTrue(isinstance(nullRejected, np.ndarray))
self.assertTrue(nullRejected.dtype == np.bool)
self.assertEqual(len(nullRejected), len(regressorList))
self.assertTrue(np.all(nullRejected == expectedOutput))
def testCoefficientOfDetermination(self):
# Test using a model with an intercept
expectedCoefficientOfDetermination = 0.99983550516908659
self.assertAlmostEqual(
self.linearFit.coefficientOfDetermination(weighted=False), expectedCoefficientOfDetermination, places=7
)
# Test using a model without an intercept
linearModel = LinearModel([self.time ** 2], ["t^2"])
linearFit = linearModel.fitData(self.observations)
expectedCoefficientOfDetermination = 0.99948312767720937
self.assertAlmostEqual(
linearFit.coefficientOfDetermination(weighted=False), expectedCoefficientOfDetermination, places=7
)
class LinearFitTestCase(unittest.TestCase):
"""
Test the LinearFit class and its methods
"""
def setUp(self):
# Generate a simple dataset.
# Noise-values are drawn from a N(0,1), but are truncated.
self.nObservations = 10
self.nParameters = 2
self.time = np.arange(self.nObservations, dtype=np.double)
self.noise = np.array([-0.72, -1.02, 0.52, 0.24, -0.17, -1.78, 0.56, 0.33, 0.19, 1.03])
self.observations = 3.0 + 2.0 * self.time ** 2 + self.noise
regressorList = [np.ones_like(self.time), self.time ** 2]
regressorNames = ["1", "t^2"]
self.linearModel = LinearModel(regressorList, regressorNames)
self.linearFit = self.linearModel.fitData(self.observations)
def tearDown(self):
pass
def testLinearFit(self):
self.assertTrue(isinstance(self.linearFit, LinearFit))
def testObservations(self):
# Since the linear model did not have a covariance matrix specified, the
# decorrelated observations, should be simply the original observations
self.assertTrue(isinstance(self.linearFit.observations(weighted=True), np.ndarray))
self.assertEqual(self.linearFit.observations(weighted=True).shape, (self.nObservations,))
self.assertTrue(np.alltrue(self.observations == self.linearFit.observations(weighted=True)))
self.assertTrue(np.alltrue(self.observations == self.linearFit.observations(weighted=False)))
def testRegressionCoefficients(self):
expectedCoeff = np.array([2.47811858, 2.01543444])
self.assertTrue(isinstance(self.linearFit.regressionCoefficients(), np.ndarray))
self.assertEqual(self.linearFit.regressionCoefficients().shape, (self.nParameters,))
self.assertTrue(np.allclose(self.linearFit.regressionCoefficients(), expectedCoeff, rtol=1.0e-6, atol=1.0e-08))
def testResiduals(self):
expectedResiduals = np.array(
[
-0.19811858,
-0.51355301,
0.98014368,
0.6229715,
0.10493045,
-1.64397947,
0.52624173,
0.09559406,
-0.27592247,
0.30169212,
]
)
self.assertTrue(isinstance(self.linearFit.residuals(weighted=False), np.ndarray))
self.assertEqual(self.linearFit.residuals(weighted=False).shape, (self.nObservations,))
self.assertTrue(
np.allclose(self.linearFit.residuals(weighted=False), expectedResiduals, rtol=1.0e-6, atol=1.0e-08)
)
def testPredictions(self):
expectedPredictions = np.array(
[
2.47811858,
4.49355301,
10.53985632,
20.6170285,
34.72506955,
52.86397947,
75.03375827,
101.23440594,
131.46592247,
165.72830788,
]
)
self.assertTrue(isinstance(self.linearFit.predictions(weighted=False), np.ndarray))
self.assertEqual(self.linearFit.predictions(weighted=False).shape, (self.nObservations,))
self.assertTrue(
np.allclose(self.linearFit.predictions(weighted=False), expectedPredictions, rtol=1.0e-6, atol=1.0e-08)
)
def testCovarianceMatrix(self):
expectedCovMatrix = np.array([[1.28084978e-01, -2.38076167e-03], [-2.38076167e-03, 8.35354974e-05]])
self.assertTrue(isinstance(self.linearFit.covarianceMatrix(), np.ndarray))
self.assertEqual(self.linearFit.covarianceMatrix().shape, (self.nParameters, self.nParameters))
self.assertTrue(np.allclose(self.linearFit.covarianceMatrix(), expectedCovMatrix, rtol=1.0e-6, atol=1.0e-08))
def testErrorBars(self):
expectedErrors = np.array([0.35788962, 0.00913978])
self.assertTrue(isinstance(self.linearFit.errorBars(), np.ndarray))
self.assertEqual(self.linearFit.errorBars().shape, (self.nParameters,))
self.assertTrue(np.allclose(self.linearFit.errorBars(), expectedErrors, rtol=1.0e-6, atol=1.0e-08))
def testConfidenceIntervals(self):
alpha = 0.05
expectedLower = np.array([1.65282364, 1.99435808])
expectedUpper = np.array([3.30341351, 2.0365108])
self.assertEqual(len(self.linearFit.confidenceIntervals(0.05)), 2)
lower, upper = self.linearFit.confidenceIntervals(0.05)
self.assertTrue(isinstance(lower, np.ndarray))
self.assertTrue(isinstance(upper, np.ndarray))
self.assertEqual(len(lower), self.nParameters)
self.assertEqual(len(upper), self.nParameters)
self.assertTrue(np.allclose(lower, expectedLower, rtol=1.0e-6, atol=1.0e-08))
self.assertTrue(np.allclose(upper, expectedUpper, rtol=1.0e-6, atol=1.0e-08))
def testT_values(self):
expectedTvalues = np.array([6.92425385, 220.51235807])
self.assertTrue(isinstance(self.linearFit.t_values(), np.ndarray))
self.assertEqual(self.linearFit.t_values().shape, (self.nParameters,))
self.assertTrue(np.allclose(self.linearFit.t_values(), expectedTvalues, rtol=1.0e-6, atol=1.0e-08))
def testSumOfSquaredResiduals(self):
expectedSumSqResiduals = 4.81866162957
self.assertAlmostEqual(self.linearFit.sumSqResiduals(weighted=False), expectedSumSqResiduals, places=7)
def testResidualVariance(self):
expectedResidualVariance = 0.60233270369599989
self.assertAlmostEqual(self.linearFit.residualVariance(weighted=False), expectedResidualVariance, places=7)
def testCorrelationMatrix(self):
expectedCorrelationMatrix = np.array([[1.0, -0.72783225], [-0.72783225, 1.0]])
self.assertTrue(
np.allclose(self.linearFit.correlationMatrix(), expectedCorrelationMatrix, rtol=1.0e-6, atol=1.0e-08)
)
def testCoefficientOfDetermination(self):
# Test using a model with an intercept
expectedCoefficientOfDetermination = 0.99983550516908659
self.assertAlmostEqual(
self.linearFit.coefficientOfDetermination(weighted=False), expectedCoefficientOfDetermination, places=7
)
# Test using a model without an intercept
linearModel = LinearModel([self.time ** 2], ["t^2"])
linearFit = linearModel.fitData(self.observations)
expectedCoefficientOfDetermination = 0.99948312767720937
self.assertAlmostEqual(
linearFit.coefficientOfDetermination(weighted=False), expectedCoefficientOfDetermination, places=7
)
def testBICvalue(self):
expectedBICvalue = -0.39313345804942657
self.assertAlmostEqual(self.linearFit.BICvalue(), expectedBICvalue, places=7)
def testAICvalue(self):
expectedAICvalue = 2.6991112629684357
self.assertAlmostEqual(self.linearFit.AICvalue(), expectedAICvalue, places=7)
def testThypothesisTest(self):
regressorList = [np.ones_like(self.time), self.time ** 2, self.time ** 3]
regressorNames = ["1", "t^2", "t^3"]
linearModel = LinearModel(regressorList, regressorNames)
linearFit = linearModel.fitData(self.observations)
alpha = 0.05 # significance level
expectedOutput = np.array([True, True, False])
nullRejected = linearFit.regressorTtest(alpha)
self.assertTrue(isinstance(nullRejected, np.ndarray))
self.assertTrue(nullRejected.dtype == np.bool)
self.assertEqual(len(nullRejected), len(regressorList))
self.assertTrue(np.all(nullRejected == expectedOutput))
def testFstatistic(self):
# Test on a model with more than one regressor
expectedFstatistic = 48625.747064132738
self.assertAlmostEqual(self.linearFit.Fstatistic(weighted=False), expectedFstatistic, places=7)
# Test on a model with only one regressor
expectedFstatistic = 17403.423925909559
linearModel = LinearModel([np.square(self.time)], ["t^2"])
linearFit = linearModel.fitData(self.observations)
self.assertAlmostEqual(linearFit.Fstatistic(weighted=False), expectedFstatistic, places=7)
def testFstatisticTest(self):
# with tested model the same as the true model
alpha = 0.05
expectedOutput = True # null hypothesis rejected
self.assertTrue(self.linearFit.FstatisticTest(alpha) == expectedOutput)
# with a fit on pure noise noise
alpha = 0.05
expectedOutput = False # null hypothesis could not be rejected
linearFit = self.linearModel.fitData(self.noise)
self.assertTrue(linearFit.FstatisticTest(alpha) == expectedOutput)
def testEvaluate(self):
expectedOutput = np.array(
[
52.86397947,
42.8147219,
33.8820485,
26.06595927,
19.36645422,
13.78353335,
9.31719665,
5.96744412,
3.73427577,
2.6176916,
2.6176916,
3.73427577,
5.96744412,
9.31719665,
13.78353335,
19.36645422,
26.06595927,
33.8820485,
42.8147219,
52.86397947,
]
)
xnew = np.linspace(-5.0, +5.0, 20)
newRegressorList = [np.ones_like(xnew), xnew ** 2]
output = self.linearFit.evaluate(newRegressorList)
self.assertTrue(np.allclose(output, expectedOutput, rtol=1.0e-6, atol=1.0e-08))
def testFitData(self):
linearModel = LinearModel(self.regressorList, self.regressorNames)
self.assertTrue(isinstance(linearModel.fitData(self.observations), LinearFit))
class WeightedLinearFitTestCase(unittest.TestCase):
"""
Test the LinearFit class with a specified covariance matrix for the
observations. Test only those method affected by weights.
"""
def setUp(self):
# Generate simple noiseless dataset
self.nObservations = 10
self.nParameters = 2
time = np.arange(self.nObservations, dtype=np.double)
self.observations1 = 1.0 + 0.3 * time
self.observations2 = 1.0 + 0.3 * time
self.regressorList = [np.ones_like(time), time]
self.regressorNames = ["1", "t"]
self.designMatrix = np.column_stack(self.regressorList)
# First covariance matrix: different weights, no correlations
covMatrixObserv1 = np.diag(0.1 + 0.1 * np.arange(self.nObservations))
# Second covariance matrix: different weights and correlations
# Correlation coefficient: 0.6
covMatrixObserv2 = np.diag(0.1 + 0.1 * np.arange(self.nObservations))
for i in range(self.nObservations):
for j in range(self.nObservations):
if i >= j:
continue
covMatrixObserv2[i, j] = 0.6 * sqrt(covMatrixObserv2[i, i] * covMatrixObserv2[j, j])
covMatrixObserv2[j, i] = covMatrixObserv2[i, j]
# Add noise according to the different covariance matrices
noise1 = np.array(
[
-0.26944792,
-0.56542802,
0.62106263,
-0.03113657,
0.98090236,
0.02678669,
1.2237701,
-0.50112787,
-0.47742454,
1.16351356,
]
)
noise2 = np.array(
[
0.24484502,
-0.22979797,
0.40639882,
0.12137103,
0.20694025,
0.68952746,
-0.30300402,
-0.11136982,
0.3549814,
0.20528704,
]
)
self.observations1 += noise1
self.observations2 += noise2
# Instantiate the (weighted) linear models and their linear fits
self.linearModel1 = LinearModel(self.regressorList, self.regressorNames, covMatrixObserv1)
self.linearModel2 = LinearModel(self.regressorList, self.regressorNames, covMatrixObserv2)
self.linearFit1 = self.linearModel1.fitData(self.observations1)
self.linearFit2 = self.linearModel2.fitData(self.observations2)
def tearDown(self):
pass
def testDecorrelatedObservations(self):
expectedObservations = np.array(
[
3.9365456,
0.03889641,
1.73885587,
0.65979961,
0.82899163,
1.73402234,
-0.1799988,
0.37289876,
1.25537791,
1.05209144,
]
)
self.assertTrue(isinstance(self.linearFit2.observations(weighted=True), np.ndarray))
self.assertEqual(self.linearFit2.observations(weighted=True).shape, (self.nObservations,))
self.assertTrue(
np.allclose(expectedObservations, self.linearFit2.observations(weighted=True), rtol=1.0e-6, atol=1.0e-08)
)
def testWeightedRegressionCoefficients(self):
# A test with a diagonal covariance matrix
expectedWeightedCoeff = np.array([0.76576446, 0.40030724])
self.assertTrue(
np.allclose(self.linearFit1.regressionCoefficients(), expectedWeightedCoeff, rtol=1.0e-6, atol=1.0e-08)
)
# A test with a non-diagonal covariance matrix
expectedWeightedCoeff = np.array([1.1623421, 0.3040605])
self.assertTrue(
np.allclose(self.linearFit2.regressionCoefficients(), expectedWeightedCoeff, rtol=1.0e-6, atol=1.0e-08)
)
def testResiduals(self):
# A test with a diagonal covariance matrix
expectedResiduals = np.array(
[
-0.03521238,
-0.43149972,
0.65468369,
-0.09782275,
0.81390894,
-0.24051397,
0.85616220,
-0.96904301,
-1.04564692,
0.49498394,
]
)
self.assertTrue(
np.allclose(self.linearFit1.residuals(weighted=False), expectedResiduals, rtol=1.0e-6, atol=1.0e-08)
)
# A test with a non-diagonal covariance matrix
expectedResiduals = np.array(
[
0.082502896,
-0.396200554,
0.235935777,
-0.053152473,
0.028356288,
0.506883039,
-0.489708901,
-0.302135160,
0.160155600,
0.006400781,
]
)
self.assertTrue(
np.allclose(self.linearFit2.residuals(weighted=False), expectedResiduals, rtol=1.0e-6, atol=1.0e-08)
)
class WeightedLinearFitTestCase(unittest.TestCase):
"""
Test the LinearFit class with a specified covariance matrix for the
observations. Test only those method affected by weights.
"""
def setUp(self):
# Generate simple noiseless dataset
self.nObservations = 10
self.nParameters = 2
time = np.arange(self.nObservations, dtype=np.double)
self.observations1 = 1.0 + 0.3 * time
self.observations2 = 1.0 + 0.3 * time
self.regressorList = [np.ones_like(time), time]
self.regressorNames = ["1", "t"]
self.designMatrix = np.column_stack(self.regressorList)
# First covariance matrix: different weights, no correlations
covMatrixObserv1 = np.diag(0.1 + 0.1 * np.arange(self.nObservations))
# Second covariance matrix: different weights and correlations
# Correlation coefficient: 0.6
covMatrixObserv2 = np.diag(0.1 + 0.1 * np.arange(self.nObservations))
for i in range(self.nObservations):
for j in range(self.nObservations):
if i>=j: continue
covMatrixObserv2[i,j] = 0.6 * sqrt(covMatrixObserv2[i,i] * covMatrixObserv2[j,j])
covMatrixObserv2[j,i] = covMatrixObserv2[i,j]
# Add noise according to the different covariance matrices
noise1 = np.array([-0.26944792, -0.56542802, 0.62106263, -0.03113657, 0.98090236, \
0.02678669, 1.2237701 , -0.50112787, -0.47742454, 1.16351356])
noise2 = np.array([ 0.24484502, -0.22979797, 0.40639882, 0.12137103, 0.20694025, \
0.68952746, -0.30300402, -0.11136982, 0.3549814 , 0.20528704])
self.observations1 += noise1
self.observations2 += noise2
# Instantiate the (weighted) linear models and their linear fits
self.linearModel1 = LinearModel(self.regressorList, self.regressorNames, covMatrixObserv1)
self.linearModel2 = LinearModel(self.regressorList, self.regressorNames, covMatrixObserv2)
self.linearFit1 = self.linearModel1.fitData(self.observations1)
self.linearFit2 = self.linearModel2.fitData(self.observations2)
def tearDown(self):
pass
def testDecorrelatedObservations(self):
expectedObservations = np.array([3.9365456, 0.03889641, 1.73885587, 0.65979961, 0.82899163,
1.73402234, -0.1799988, 0.37289876, 1.25537791, 1.05209144])
self.assertTrue(isinstance(self.linearFit2.observations(weighted=True), np.ndarray))
self.assertEqual(self.linearFit2.observations(weighted=True).shape, (self.nObservations,))
self.assertTrue(np.allclose(expectedObservations, self.linearFit2.observations(weighted=True), rtol=1.0e-6, atol=1.e-08))
def testWeightedRegressionCoefficients(self):
# A test with a diagonal covariance matrix
expectedWeightedCoeff = np.array([0.76576446, 0.40030724])
self.assertTrue(np.allclose(self.linearFit1.regressionCoefficients(), expectedWeightedCoeff, rtol=1.0e-6, atol=1.e-08))
# A test with a non-diagonal covariance matrix
expectedWeightedCoeff = np.array([1.1623421, 0.3040605])
self.assertTrue(np.allclose(self.linearFit2.regressionCoefficients(), expectedWeightedCoeff, rtol=1.0e-6, atol=1.e-08))
def testResiduals(self):
# A test with a diagonal covariance matrix
expectedResiduals = np.array([-0.03521238, -0.43149972, 0.65468369, -0.09782275, 0.81390894, -0.24051397, 0.85616220, -0.96904301, -1.04564692, 0.49498394])
self.assertTrue(np.allclose(self.linearFit1.residuals(weighted=False), expectedResiduals, rtol=1.0e-6, atol=1.e-08))
# A test with a non-diagonal covariance matrix
expectedResiduals = np.array([0.082502896, -0.396200554, 0.235935777, -0.053152473, 0.028356288, 0.506883039, -0.489708901, -0.302135160, 0.160155600, 0.006400781])
self.assertTrue(np.allclose(self.linearFit2.residuals(weighted=False), expectedResiduals, rtol=1.0e-6, atol=1.e-08))
class LinearFitTestCase(unittest.TestCase):
"""
Test the LinearFit class and its methods
"""
def setUp(self):
# Generate a simple dataset.
# Noise-values are drawn from a N(0,1), but are truncated.
self.nObservations = 10
self.nParameters = 2
self.time = np.arange(self.nObservations, dtype=np.double)
self.noise = np.array([-.72, -1.02, .52, .24, -.17, -1.78, .56, .33, .19, 1.03])
self.observations = 3.0 + 2.0 * self.time**2 + self.noise
regressorList = [np.ones_like(self.time), self.time**2]
regressorNames = ["1", "t^2"]
self.linearModel = LinearModel(regressorList, regressorNames)
self.linearFit = self.linearModel.fitData(self.observations)
def tearDown(self):
pass
def testLinearFit(self):
self.assertTrue(isinstance(self.linearFit, LinearFit))
def testObservations(self):
# Since the linear model did not have a covariance matrix specified, the
# decorrelated observations, should be simply the original observations
self.assertTrue(isinstance(self.linearFit.observations(weighted=True), np.ndarray))
self.assertEqual(self.linearFit.observations(weighted=True).shape, (self.nObservations,))
self.assertTrue(np.alltrue(self.observations == self.linearFit.observations(weighted=True)))
self.assertTrue(np.alltrue(self.observations == self.linearFit.observations(weighted=False)))
def testRegressionCoefficients(self):
expectedCoeff = np.array([2.47811858, 2.01543444])
self.assertTrue(isinstance(self.linearFit.regressionCoefficients(), np.ndarray))
self.assertEqual(self.linearFit.regressionCoefficients().shape, (self.nParameters,))
self.assertTrue(np.allclose(self.linearFit.regressionCoefficients(), expectedCoeff, rtol=1.0e-6, atol=1.e-08))
def testResiduals(self):
expectedResiduals = np.array([-0.19811858, -0.51355301, 0.98014368, 0.6229715,
0.10493045, -1.64397947, 0.52624173, 0.09559406,
-0.27592247, 0.30169212])
self.assertTrue(isinstance(self.linearFit.residuals(weighted=False), np.ndarray))
self.assertEqual(self.linearFit.residuals(weighted=False).shape, (self.nObservations,))
self.assertTrue(np.allclose(self.linearFit.residuals(weighted=False), expectedResiduals, rtol=1.0e-6, atol=1.e-08))
def testPredictions(self):
expectedPredictions = np.array([2.47811858, 4.49355301, 10.53985632, 20.6170285,
34.72506955, 52.86397947, 75.03375827,
101.23440594, 131.46592247, 165.72830788])
self.assertTrue(isinstance(self.linearFit.predictions(weighted=False), np.ndarray))
self.assertEqual(self.linearFit.predictions(weighted=False).shape, (self.nObservations,))
self.assertTrue(np.allclose(self.linearFit.predictions(weighted=False), expectedPredictions, rtol=1.0e-6, atol=1.e-08))
def testCovarianceMatrix(self):
expectedCovMatrix = np.array([[1.28084978e-01, -2.38076167e-03],
[-2.38076167e-03, 8.35354974e-05]])
self.assertTrue(isinstance(self.linearFit.covarianceMatrix(), np.ndarray))
self.assertEqual(self.linearFit.covarianceMatrix().shape, (self.nParameters,self.nParameters))
self.assertTrue(np.allclose(self.linearFit.covarianceMatrix(), expectedCovMatrix, rtol=1.0e-6, atol=1.e-08))
def testErrorBars(self):
expectedErrors = np.array([0.35788962, 0.00913978])
self.assertTrue(isinstance(self.linearFit.errorBars(), np.ndarray))
self.assertEqual(self.linearFit.errorBars().shape, (self.nParameters,))
self.assertTrue(np.allclose(self.linearFit.errorBars(), expectedErrors, rtol=1.0e-6, atol=1.e-08))
def testConfidenceIntervals(self):
alpha = 0.05
expectedLower = np.array([1.65282364, 1.99435808])
expectedUpper = np.array([3.30341351, 2.0365108 ])
self.assertEqual(len(self.linearFit.confidenceIntervals(0.05)), 2)
lower, upper = self.linearFit.confidenceIntervals(0.05)
self.assertTrue(isinstance(lower, np.ndarray))
self.assertTrue(isinstance(upper, np.ndarray))
self.assertEqual(len(lower), self.nParameters)
self.assertEqual(len(upper), self.nParameters)
self.assertTrue(np.allclose(lower, expectedLower, rtol=1.0e-6, atol=1.e-08))
self.assertTrue(np.allclose(upper, expectedUpper, rtol=1.0e-6, atol=1.e-08))
def testT_values(self):
expectedTvalues = np.array([6.92425385, 220.51235807])
self.assertTrue(isinstance(self.linearFit.t_values(), np.ndarray))
self.assertEqual(self.linearFit.t_values().shape, (self.nParameters,))
self.assertTrue(np.allclose(self.linearFit.t_values(), expectedTvalues, rtol=1.0e-6, atol=1.e-08))
def testSumOfSquaredResiduals(self):
expectedSumSqResiduals = 4.81866162957
self.assertAlmostEqual(self.linearFit.sumSqResiduals(weighted=False), expectedSumSqResiduals, places=7)
def testResidualVariance(self):
expectedResidualVariance = 0.60233270369599989
self.assertAlmostEqual(self.linearFit.residualVariance(weighted=False), expectedResidualVariance, places=7)
def testCorrelationMatrix(self):
expectedCorrelationMatrix = np.array([[1., -0.72783225], [-0.72783225, 1.]])
self.assertTrue(np.allclose(self.linearFit.correlationMatrix(), expectedCorrelationMatrix, rtol=1.0e-6, atol=1.e-08))
def testCoefficientOfDetermination(self):
# Test using a model with an intercept
expectedCoefficientOfDetermination = 0.99983550516908659
self.assertAlmostEqual(self.linearFit.coefficientOfDetermination(weighted=False), expectedCoefficientOfDetermination, places=7)
# Test using a model without an intercept
linearModel = LinearModel([self.time**2], ["t^2"])
linearFit = linearModel.fitData(self.observations)
expectedCoefficientOfDetermination = 0.99948312767720937
self.assertAlmostEqual(linearFit.coefficientOfDetermination(weighted=False), expectedCoefficientOfDetermination, places=7)
def testBICvalue(self):
expectedBICvalue = -0.39313345804942657
self.assertAlmostEqual(self.linearFit.BICvalue(), expectedBICvalue, places=7)
def testAICvalue(self):
expectedAICvalue = 2.6991112629684357
self.assertAlmostEqual(self.linearFit.AICvalue(), expectedAICvalue, places=7)
def testThypothesisTest(self):
regressorList = [np.ones_like(self.time), self.time**2, self.time**3]
regressorNames = ["1", "t^2", "t^3"]
linearModel = LinearModel(regressorList, regressorNames)
linearFit = linearModel.fitData(self.observations)
alpha = 0.05 # significance level
expectedOutput = np.array([True, True, False])
nullRejected = linearFit.regressorTtest(alpha)
self.assertTrue(isinstance(nullRejected, np.ndarray))
self.assertTrue(nullRejected.dtype == np.bool)
self.assertEqual(len(nullRejected), len(regressorList))
self.assertTrue(np.all(nullRejected == expectedOutput))
def testFstatistic(self):
# Test on a model with more than one regressor
expectedFstatistic = 48625.747064132738
self.assertAlmostEqual(self.linearFit.Fstatistic(weighted=False), expectedFstatistic, places=7)
# Test on a model with only one regressor
expectedFstatistic = 17403.423925909559
linearModel = LinearModel([np.square(self.time)], ["t^2"])
linearFit = linearModel.fitData(self.observations)
self.assertAlmostEqual(linearFit.Fstatistic(weighted=False), expectedFstatistic, places=7)
def testFstatisticTest(self):
# with tested model the same as the true model
alpha = 0.05
expectedOutput = True # null hypothesis rejected
self.assertTrue(self.linearFit.FstatisticTest(alpha) == expectedOutput)
# with a fit on pure noise noise
alpha = 0.05
expectedOutput = False # null hypothesis could not be rejected
linearFit = self.linearModel.fitData(self.noise)
self.assertTrue(linearFit.FstatisticTest(alpha) == expectedOutput)
def testEvaluate(self):
expectedOutput = np.array([ 52.86397947, 42.8147219 , 33.8820485 , 26.06595927,
19.36645422, 13.78353335, 9.31719665, 5.96744412,
3.73427577, 2.6176916 , 2.6176916 , 3.73427577,
5.96744412, 9.31719665, 13.78353335, 19.36645422,
26.06595927, 33.8820485 , 42.8147219 , 52.86397947])
xnew = np.linspace(-5.0, +5.0, 20)
newRegressorList = [np.ones_like(xnew), xnew**2]
output = self.linearFit.evaluate(newRegressorList)
self.assertTrue(np.allclose(output, expectedOutput, rtol=1.0e-6, atol=1.e-08))
def testFitData(self):
linearModel = LinearModel(self.regressorList, self.regressorNames)
self.assertTrue(isinstance(linearModel.fitData(self.observations), LinearFit))