def test_load_diabetes():
res = load_diabetes()
assert res.data.shape == (442, 10)
assert res.target.size, 442
assert len(res.feature_names) == 10
assert res.DESCR
# test return_X_y option
check_return_X_y(res, partial(load_diabetes))
def test_regression_scorers():
# Test regression scorers.
diabetes = load_diabetes()
X, y = diabetes.data, diabetes.target
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
clf = Ridge()
clf.fit(X_train, y_train)
score1 = get_scorer('r2')(clf, X_test, y_test)
score2 = r2_score(y_test, clf.predict(X_test))
assert_almost_equal(score1, score2)
def test_lasso_cv_with_some_model_selection():
from mrex.pipeline import make_pipeline
from mrex.preprocessing import StandardScaler
from mrex.model_selection import StratifiedKFold
from mrex import datasets
from mrex.linear_model import LassoCV
diabetes = datasets.load_diabetes()
X = diabetes.data
y = diabetes.target
pipe = make_pipeline(StandardScaler(), LassoCV(cv=StratifiedKFold()))
pipe.fit(X, y)
def test_linearsvr():
# check that SVR(kernel='linear') and LinearSVC() give
# comparable results
diabetes = datasets.load_diabetes()
lsvr = svm.LinearSVR(C=1e3).fit(diabetes.data, diabetes.target)
score1 = lsvr.score(diabetes.data, diabetes.target)
svr = svm.SVR(kernel='linear', C=1e3).fit(diabetes.data, diabetes.target)
score2 = svr.score(diabetes.data, diabetes.target)
assert_allclose(np.linalg.norm(lsvr.coef_), np.linalg.norm(svr.coef_), 1,
0.0001)
assert_almost_equal(score1, score2, 2)
def test_svr():
# Test Support Vector Regression
diabetes = datasets.load_diabetes()
for clf in (svm.NuSVR(kernel='linear', nu=.4,
C=1.0), svm.NuSVR(kernel='linear', nu=.4, C=10.),
svm.SVR(kernel='linear',
C=10.), svm.LinearSVR(C=10.), svm.LinearSVR(C=10.)):
clf.fit(diabetes.data, diabetes.target)
assert clf.score(diabetes.data, diabetes.target) > 0.02
# non-regression test; previously, BaseLibSVM would check that
# len(np.unique(y)) < 2, which must only be done for SVC
svm.SVR().fit(diabetes.data, np.ones(len(diabetes.data)))
svm.LinearSVR().fit(diabetes.data, np.ones(len(diabetes.data)))
def test_linearsvr_fit_sampleweight():
# check correct result when sample_weight is 1
# check that SVR(kernel='linear') and LinearSVC() give
# comparable results
diabetes = datasets.load_diabetes()
n_samples = len(diabetes.target)
unit_weight = np.ones(n_samples)
lsvr = svm.LinearSVR(C=1e3).fit(diabetes.data,
diabetes.target,
sample_weight=unit_weight)
score1 = lsvr.score(diabetes.data, diabetes.target)
lsvr_no_weight = svm.LinearSVR(C=1e3).fit(diabetes.data, diabetes.target)
score2 = lsvr_no_weight.score(diabetes.data, diabetes.target)
assert_allclose(np.linalg.norm(lsvr.coef_),
np.linalg.norm(lsvr_no_weight.coef_), 1, 0.0001)
assert_almost_equal(score1, score2, 2)
# check that fit(X) = fit([X1, X2, X3],sample_weight = [n1, n2, n3]) where
# X = X1 repeated n1 times, X2 repeated n2 times and so forth
random_state = check_random_state(0)
random_weight = random_state.randint(0, 10, n_samples)
lsvr_unflat = svm.LinearSVR(C=1e3).fit(diabetes.data,
diabetes.target,
sample_weight=random_weight)
score3 = lsvr_unflat.score(diabetes.data,
diabetes.target,
sample_weight=random_weight)
X_flat = np.repeat(diabetes.data, random_weight, axis=0)
y_flat = np.repeat(diabetes.target, random_weight, axis=0)
lsvr_flat = svm.LinearSVR(C=1e3).fit(X_flat, y_flat)
score4 = lsvr_flat.score(X_flat, y_flat)
assert_almost_equal(score3, score4, 2)
The coefficients, the residual sum of squares and the coefficient of determination are also calculated. """ print(__doc__) # Code source: Jaques Grobler # License: BSD 3 clause import matplotlib.pyplot as plt import numpy as np from mrex import datasets, linear_model from mrex.metrics import mean_squared_error, r2_score # Load the diabetes dataset diabetes_X, diabetes_y = datasets.load_diabetes(return_X_y=True) # Use only one feature diabetes_X = diabetes_X[:, np.newaxis, 2] # Split the data into training/testing sets diabetes_X_train = diabetes_X[:-20] diabetes_X_test = diabetes_X[-20:] # Split the targets into training/testing sets diabetes_y_train = diabetes_y[:-20] diabetes_y_test = diabetes_y[-20:] # Create linear regression object regr = linear_model.LinearRegression()
import pytest
from scipy import linalg
from mrex.model_selection import train_test_split
from mrex.utils.testing import assert_allclose
from mrex.utils.testing import assert_array_almost_equal
from mrex.utils.testing import assert_raises
from mrex.utils.testing import ignore_warnings
from mrex.utils.testing import assert_warns
from mrex.utils.testing import TempMemmap
from mrex.exceptions import ConvergenceWarning
from mrex import linear_model, datasets
from mrex.linear_model.least_angle import _lars_path_residues, LassoLarsIC
# TODO: use another dataset that has multiple drops
diabetes = datasets.load_diabetes()
X, y = diabetes.data, diabetes.target
G = np.dot(X.T, X)
Xy = np.dot(X.T, y)
n_samples = y.size
def test_simple():
# Principle of Lars is to keep covariances tied and decreasing
# also test verbose output
from io import StringIO
import sys
old_stdout = sys.stdout
try:
sys.stdout = StringIO()
# Estimate the score after iterative imputation of the missing values
imputer = IterativeImputer(missing_values=0,
random_state=0,
n_nearest_features=5,
sample_posterior=True)
iterative_impute_scores = get_scores_for_imputer(imputer,
X_missing,
y_missing)
return ((full_scores.mean(), full_scores.std()),
(zero_impute_scores.mean(), zero_impute_scores.std()),
(mean_impute_scores.mean(), mean_impute_scores.std()),
(iterative_impute_scores.mean(), iterative_impute_scores.std()))
results_diabetes = np.array(get_results(load_diabetes()))
mses_diabetes = results_diabetes[:, 0] * -1
stds_diabetes = results_diabetes[:, 1]
results_boston = np.array(get_results(load_boston()))
mses_boston = results_boston[:, 0] * -1
stds_boston = results_boston[:, 1]
n_bars = len(mses_diabetes)
xval = np.arange(n_bars)
x_labels = ['Full data',
'Zero imputation',
'Mean Imputation',
'Multivariate Imputation']
colors = ['r', 'g', 'b', 'orange']
# License: BSD 3 clause
import numpy as np
import pytest
from mrex.utils.testing import assert_almost_equal
from mrex.utils.testing import assert_array_almost_equal
from mrex.utils.testing import assert_array_equal
from mrex.utils.testing import assert_warns
from mrex import datasets
from mrex.covariance import empirical_covariance, EmpiricalCovariance, \
ShrunkCovariance, shrunk_covariance, \
LedoitWolf, ledoit_wolf, ledoit_wolf_shrinkage, OAS, oas
X, _ = datasets.load_diabetes(return_X_y=True)
X_1d = X[:, 0]
n_samples, n_features = X.shape
def test_covariance():
# Tests Covariance module on a simple dataset.
# test covariance fit from data
cov = EmpiricalCovariance()
cov.fit(X)
emp_cov = empirical_covariance(X)
assert_array_almost_equal(emp_cov, cov.covariance_, 4)
assert_almost_equal(cov.error_norm(emp_cov), 0)
assert_almost_equal(cov.error_norm(emp_cov, norm='spectral'), 0)
assert_almost_equal(cov.error_norm(emp_cov, norm='frobenius'), 0)
assert_almost_equal(cov.error_norm(emp_cov, scaling=False), 0)
Xt = np.array(X).T
clf.fit(np.dot(X, Xt), Y)
with pytest.raises(ValueError):
clf.predict(X)
clf = svm.SVC()
clf.fit(X, Y)
with pytest.raises(ValueError):
clf.predict(Xt)
@pytest.mark.parametrize(
'Estimator, data',
[(svm.SVC, datasets.load_iris(return_X_y=True)),
(svm.NuSVC, datasets.load_iris(return_X_y=True)),
(svm.SVR, datasets.load_diabetes(return_X_y=True)),
(svm.NuSVR, datasets.load_diabetes(return_X_y=True)),
(svm.OneClassSVM, datasets.load_iris(return_X_y=True))])
def test_svm_gamma_error(Estimator, data):
X, y = data
est = Estimator(gamma='auto_deprecated')
err_msg = "When 'gamma' is a string, it should be either 'scale' or 'auto'"
with pytest.raises(ValueError, match=err_msg):
est.fit(X, y)
def test_unicode_kernel():
# Test that a unicode kernel name does not cause a TypeError
clf = svm.SVC(kernel='linear', probability=True)
clf.fit(X, Y)
clf.predict_proba(T)