def test_extra_kwargs_2d(self):
sigma = np.random.random((25, 25))
sigma = sigma + sigma.T - np.diag(np.diag(sigma))
data = sm_data.handle_data(self.y, self.X, 'drop', sigma=sigma)
idx = ~np.isnan(np.c_[self.y, self.X]).any(axis=1)
sigma = sigma[idx][:,idx]
np.testing.assert_array_equal(data.sigma, sigma)
def setupClass(cls):
cls.endog = endog = pandas.DataFrame(np.random.random((10,4)),
columns=['y_1', 'y_2', 'y_3', 'y_4'])
exog = pandas.DataFrame(np.random.random((10,2)),
columns=['x_1','x_2'])
exog.insert(0, 'const', 1)
cls.exog = exog
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 3
neqs = 4
cls.col_input = np.random.random(nvars)
cls.col_result = pandas.Series(cls.col_input,
index=exog.columns)
cls.row_input = np.random.random(nrows)
cls.row_result = pandas.Series(cls.row_input,
index=exog.index)
cls.cov_input = np.random.random((nvars, nvars))
cls.cov_result = pandas.DataFrame(cls.cov_input,
index = exog.columns,
columns = exog.columns)
cls.cov_eq_input = np.random.random((neqs, neqs))
cls.cov_eq_result = pandas.DataFrame(cls.cov_eq_input,
index=endog.columns,
columns=endog.columns)
cls.col_eq_input = np.random.random((nvars, neqs))
cls.col_eq_result = pandas.DataFrame(cls.col_eq_input,
index=exog.columns,
columns=endog.columns)
cls.xnames = ['const', 'x_1', 'x_2']
cls.ynames = ['y_1', 'y_2', 'y_3', 'y_4']
cls.row_labels = cls.exog.index
def setupClass(cls):
super(TestArrays1dExog, cls).setupClass()
cls.endog = np.random.random(10)
exog = np.random.random(10)
cls.data = sm_data.handle_data(cls.endog, exog)
cls.exog = exog[:,None]
cls.xnames = ['x1']
cls.ynames = 'y'
def setupClass(cls):
super(TestStructarrays, cls).setupClass()
cls.endog = np.random.random(9).view([("y_1", "f8")]).view(np.recarray)
exog = np.random.random(9 * 3).view([("const", "f8"), ("x_1", "f8"), ("x_2", "f8")]).view(np.recarray)
exog["const"] = 1
cls.exog = exog
cls.data = sm_data.handle_data(cls.endog, cls.exog)
cls.xnames = ["const", "x_1", "x_2"]
cls.ynames = "y_1"
def test_drop(self):
y = self.y
X = self.X
combined = np.c_[y, X]
idx = ~np.isnan(combined).any(axis=1)
y = y[idx]
X = X[idx]
data = sm_data.handle_data(self.y, self.X, 'drop')
np.testing.assert_array_equal(data.endog, y)
np.testing.assert_array_equal(data.exog, X)
def setupClass(cls):
super(TestStructarrays, cls).setupClass()
cls.endog = np.random.random(9).view([('y_1',
'f8')]).view(np.recarray)
exog = np.random.random(9*3).view([('const', 'f8'),('x_1', 'f8'),
('x_2', 'f8')]).view(np.recarray)
exog['const'] = 1
cls.exog = exog
cls.data = sm_data.handle_data(cls.endog, cls.exog)
cls.xnames = ['const', 'x_1', 'x_2']
cls.ynames = 'y_1'
def setupClass(cls):
cls.endog = np.random.random(10)
cls.exog = np.c_[np.ones(10), np.random.random((10,2))]
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 3
cls.col_result = cls.col_input = np.random.random(nvars)
cls.row_result = cls.row_input = np.random.random(nrows)
cls.cov_result = cls.cov_input = np.random.random((nvars, nvars))
cls.xnames = ['const', 'x1', 'x2']
cls.ynames = 'y'
cls.row_labels = None
def setup_class(cls):
cls.endog = np.random.random(10)
cls.exog = np.c_[np.ones(10), np.random.random((10,2))]
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 3
cls.col_result = cls.col_input = np.random.random(nvars)
cls.row_result = cls.row_input = np.random.random(nrows)
cls.cov_result = cls.cov_input = np.random.random((nvars, nvars))
cls.xnames = ['const', 'x1', 'x2']
cls.ynames = 'y'
cls.row_labels = None
def test_drop(self):
y = self.y
X = self.X
combined = np.c_[y, X]
idx = ~np.isnan(combined).any(axis=1)
y = y.ix[idx]
X = X.ix[idx]
data = sm_data.handle_data(self.y, self.X, 'drop')
np.testing.assert_array_equal(data.endog, y.values)
ptesting.assert_series_equal(data._orig_endog, self.y.ix[idx])
np.testing.assert_array_equal(data.exog, X.values)
ptesting.assert_frame_equal(data._orig_exog, self.X.ix[idx])
def test_drop(self):
y = self.y
X = self.X
combined = np.c_[y, X]
idx = ~np.isnan(combined).any(axis=1)
y = y.ix[idx]
X = X.ix[idx]
data = sm_data.handle_data(self.y, self.X, 'drop')
np.testing.assert_array_equal(data.endog, y.values)
ptesting.assert_series_equal(data.orig_endog, self.y.ix[idx])
np.testing.assert_array_equal(data.exog, X.values)
ptesting.assert_frame_equal(data.orig_exog, self.X.ix[idx])
def setupClass(cls):
cls.endog = np.random.random((10,4))
cls.exog = np.c_[np.ones(10), np.random.random((10,2))]
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 3
neqs = 4
cls.col_result = cls.col_input = np.random.random(nvars)
cls.row_result = cls.row_input = np.random.random(nrows)
cls.cov_result = cls.cov_input = np.random.random((nvars, nvars))
cls.cov_eq_result = cls.cov_eq_input = np.random.random((neqs,neqs))
cls.col_eq_result = cls.col_eq_input = np.array((neqs, nvars))
cls.xnames = ['const', 'x1', 'x2']
cls.ynames = ['y1', 'y2', 'y3', 'y4']
cls.row_labels = None
def setupClass(cls):
cls.endog = np.random.random((10, 4))
cls.exog = np.c_[np.ones(10), np.random.random((10, 2))]
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 3
neqs = 4
cls.col_result = cls.col_input = np.random.random(nvars)
cls.row_result = cls.row_input = np.random.random(nrows)
cls.cov_result = cls.cov_input = np.random.random((nvars, nvars))
cls.cov_eq_result = cls.cov_eq_input = np.random.random((neqs, neqs))
cls.col_eq_result = cls.col_eq_input = np.array((neqs, nvars))
cls.xnames = ["const", "x1", "x2"]
cls.ynames = ["y1", "y2", "y3", "y4"]
cls.row_labels = None
def setupClass(cls):
cls.endog = np.random.random((10, 4))
cls.exog = np.c_[np.ones(10), np.random.random((10, 2))]
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 3
neqs = 4
cls.col_result = cls.col_input = np.random.random(nvars)
cls.row_result = cls.row_input = np.random.random(nrows)
cls.cov_result = cls.cov_input = np.random.random((nvars, nvars))
cls.cov_eq_result = cls.cov_eq_input = np.random.random((neqs, neqs))
cls.col_eq_result = cls.col_eq_input = np.array((neqs, nvars))
cls.xnames = ['const', 'x1', 'x2']
cls.ynames = ['y1', 'y2', 'y3', 'y4']
cls.row_labels = None
def setupClass(cls):
cls.endog = pandas.DataFrame(np.random.random(10), columns=["y_1"])
exog = pandas.DataFrame(np.random.random((10, 2)), columns=["x_1", "x_2"])
exog.insert(0, "const", 1)
cls.exog = exog
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 3
cls.col_input = np.random.random(nvars)
cls.col_result = pandas.Series(cls.col_input, index=exog.columns)
cls.row_input = np.random.random(nrows)
cls.row_result = pandas.Series(cls.row_input, index=exog.index)
cls.cov_input = np.random.random((nvars, nvars))
cls.cov_result = pandas.DataFrame(cls.cov_input, index=exog.columns, columns=exog.columns)
cls.xnames = ["const", "x_1", "x_2"]
cls.ynames = "y_1"
cls.row_labels = cls.exog.index
def setupClass(cls):
cls.endog = pandas.Series(np.random.random(10), name="y_1")
exog = pandas.Series(np.random.random(10), name="x_1")
cls.exog = exog
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 1
cls.col_input = np.random.random(nvars)
cls.col_result = pandas.Series(cls.col_input, index=[exog.name])
cls.row_input = np.random.random(nrows)
cls.row_result = pandas.Series(cls.row_input, index=exog.index)
cls.cov_input = np.random.random((nvars, nvars))
cls.cov_result = pandas.DataFrame(cls.cov_input, index=[exog.name], columns=[exog.name])
cls.xnames = ["x_1"]
cls.ynames = "y_1"
cls.row_labels = cls.exog.index
def setup_class(cls):
cls.endog = pd.DataFrame(np.random.random(10), columns=['y_1'])
exog = pd.DataFrame(np.random.random((10, 2)), columns=['x_1', 'x_2'])
exog.insert(0, 'const', 1)
cls.exog = exog
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 3
cls.col_input = np.random.random(nvars)
cls.col_result = pd.Series(cls.col_input, index=exog.columns)
cls.row_input = np.random.random(nrows)
cls.row_result = pd.Series(cls.row_input, index=exog.index)
cls.cov_input = np.random.random((nvars, nvars))
cls.cov_result = pd.DataFrame(cls.cov_input,
index=exog.columns,
columns=exog.columns)
cls.xnames = ['const', 'x_1', 'x_2']
cls.ynames = 'y_1'
cls.row_labels = cls.exog.index
def setupClass(cls):
cls.endog = pandas.Series(np.random.random(10), name='y_1')
exog = pandas.Series(np.random.random(10), name='x_1')
cls.exog = exog
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 1
cls.col_input = np.random.random(nvars)
cls.col_result = pandas.Series(cls.col_input, index=[exog.name])
cls.row_input = np.random.random(nrows)
cls.row_result = pandas.Series(cls.row_input, index=exog.index)
cls.cov_input = np.random.random((nvars, nvars))
cls.cov_result = pandas.DataFrame(cls.cov_input,
index=[exog.name],
columns=[exog.name])
cls.xnames = ['x_1']
cls.ynames = 'y_1'
cls.row_labels = cls.exog.index
def setup_class(cls):
cls.endog = pd.DataFrame(np.random.random(10), columns=['y_1'])
mi = pd.MultiIndex.from_product([['x'], ['1', '2']])
exog = pd.DataFrame(np.random.random((10, 2)), columns=mi)
exog_flattened_idx = pd.Index(['const', 'x_1', 'x_2'])
exog.insert(0, 'const', 1)
cls.exog = exog
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 3
cls.col_input = np.random.random(nvars)
cls.col_result = pd.Series(cls.col_input, index=exog_flattened_idx)
cls.row_input = np.random.random(nrows)
cls.row_result = pd.Series(cls.row_input, index=exog.index)
cls.cov_input = np.random.random((nvars, nvars))
cls.cov_result = pd.DataFrame(cls.cov_input,
index=exog_flattened_idx,
columns=exog_flattened_idx)
cls.xnames = ['const', 'x_1', 'x_2']
cls.ynames = 'y_1'
cls.row_labels = cls.exog.index
def setup_class(cls):
cls.endog = pandas.DataFrame(np.random.random(10), columns=['y_1'])
mi = pandas.MultiIndex.from_product([['x'], ['1', '2']])
exog = pandas.DataFrame(np.random.random((10, 2)), columns=mi)
exog_flattened_idx = pandas.Index(['const', 'x_1', 'x_2'])
exog.insert(0, 'const', 1)
cls.exog = exog
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 3
cls.col_input = np.random.random(nvars)
cls.col_result = pandas.Series(cls.col_input, index=exog_flattened_idx)
cls.row_input = np.random.random(nrows)
cls.row_result = pandas.Series(cls.row_input, index=exog.index)
cls.cov_input = np.random.random((nvars, nvars))
cls.cov_result = pandas.DataFrame(cls.cov_input,
index=exog_flattened_idx,
columns=exog_flattened_idx)
cls.xnames = ['const', 'x_1', 'x_2']
cls.ynames = 'y_1'
cls.row_labels = cls.exog.index
def setup_class(cls):
cls.endog = np.random.random(10).tolist()
exog = pandas.DataFrame(np.random.random((10,2)),
columns=['x_1','x_2'])
exog.insert(0, 'const', 1)
cls.exog = exog
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 3
cls.col_input = np.random.random(nvars)
cls.col_result = pandas.Series(cls.col_input,
index=exog.columns)
cls.row_input = np.random.random(nrows)
cls.row_result = pandas.Series(cls.row_input,
index=exog.index)
cls.cov_input = np.random.random((nvars, nvars))
cls.cov_result = pandas.DataFrame(cls.cov_input,
index = exog.columns,
columns = exog.columns)
cls.xnames = ['const', 'x_1', 'x_2']
cls.ynames = 'y'
cls.row_labels = cls.exog.index
def setupClass(cls):
cls.endog = pandas.DataFrame(np.random.random(10), columns=['y_1'])
exog = pandas.DataFrame(np.random.random((10,2)),
columns=['x1','x2']) # names mimic defaults
exog.insert(0, 'const', 1)
cls.exog = exog.values
cls.data = sm_data.handle_data(cls.endog, cls.exog)
nrows = 10
nvars = 3
cls.col_input = np.random.random(nvars)
cls.col_result = pandas.Series(cls.col_input,
index=exog.columns)
cls.row_input = np.random.random(nrows)
cls.row_result = pandas.Series(cls.row_input,
index=exog.index)
cls.cov_input = np.random.random((nvars, nvars))
cls.cov_result = pandas.DataFrame(cls.cov_input,
index = exog.columns,
columns = exog.columns)
cls.xnames = ['const', 'x1', 'x2']
cls.ynames = 'y_1'
cls.row_labels = cls.endog.index
def test_endog_only_drop(self):
y = self.y
y = y.dropna()
data = sm_data.handle_data(self.y, None, 'drop')
np.testing.assert_array_equal(data.endog, y.values)
def test_none(self):
data = sm_data.handle_data(self.y, self.X, 'none')
np.testing.assert_array_equal(data.endog, self.y.values)
np.testing.assert_array_equal(data.exog, self.X.values)
def test_none(self):
data = sm_data.handle_data(self.y, self.X, 'none', hasconst=False)
np.testing.assert_array_equal(data.endog, self.y)
np.testing.assert_array_equal(data.exog, self.X)
assert data.k_constant == 0
def test_mv_endog(self):
y = self.X
y = y.loc[~np.isnan(y.values).any(axis=1)]
data = sm_data.handle_data(self.X, None, 'drop')
np.testing.assert_array_equal(data.endog, y.values)
def test_none(self):
data = sm_data.handle_data(self.y, self.X, 'none', hasconst=False)
np.testing.assert_array_equal(data.endog, self.y.values)
np.testing.assert_array_equal(data.exog, self.X.values)
def test_endog_only_raise(self):
with pytest.raises(Exception):
# TODO: be more specific about exception
sm_data.handle_data(self.y, None, 'raise')
def setupClass(cls):
super(TestArrays2dEndog, cls).setupClass()
cls.endog = np.random.random((10,1))
cls.exog = np.c_[np.ones(10), np.random.random((10,2))]
cls.data = sm_data.handle_data(cls.endog, cls.exog)
def test_raise_no_missing(self):
# GH#1700
sm_data.handle_data(pd.Series(np.random.random(20)),
pd.DataFrame(np.random.random((20, 2))), 'raise')
def __init__(self, endog, exog, constraints=None, **kwargs):
# Standardize data
endog_using_pandas = _is_using_pandas(endog, None)
if not endog_using_pandas:
endog = np.asanyarray(endog)
exog_is_using_pandas = _is_using_pandas(exog, None)
if not exog_is_using_pandas:
exog = np.asarray(exog)
# Make sure we have 2-dimensional array
if exog.ndim == 1:
if not exog_is_using_pandas:
exog = exog[:, None]
else:
exog = pd.DataFrame(exog)
self.k_exog = exog.shape[1]
# Handle constraints
self.k_constraints = 0
self._r_matrix = self._q_matrix = None
if constraints is not None:
from patsy import DesignInfo
from statsmodels.base.data import handle_data
data = handle_data(endog, exog, **kwargs)
names = data.param_names
LC = DesignInfo(names).linear_constraint(constraints)
self._r_matrix, self._q_matrix = LC.coefs, LC.constants
self.k_constraints = self._r_matrix.shape[0]
constraint_endog = np.zeros((len(endog), len(self._r_matrix)))
if endog_using_pandas:
constraint_endog = pd.DataFrame(constraint_endog,
index=endog.index)
endog = concat([endog, constraint_endog], axis=1)
endog.values[:, 1:] = self._q_matrix[:, 0]
else:
endog[:, 1:] = self._q_matrix[:, 0]
# Handle coefficient initialization
kwargs.setdefault('initialization', 'diffuse')
# Initialize the state space representation
super(RecursiveLS, self).__init__(
endog, k_states=self.k_exog, exog=exog, **kwargs)
# Use univariate filtering by default
self.ssm.filter_univariate = True
# Concentrate the scale out of the likelihood function
self.ssm.filter_concentrated = True
# Setup the state space representation
self['design'] = np.zeros((self.k_endog, self.k_states, self.nobs))
self['design', 0] = self.exog[:, :, None].T
if self._r_matrix is not None:
self['design', 1:, :] = self._r_matrix[:, :, None]
self['transition'] = np.eye(self.k_states)
# Notice that the filter output does not depend on the measurement
# variance, so we set it here to 1
self['obs_cov', 0, 0] = 1.
self['transition'] = np.eye(self.k_states)
# Linear constraints are technically imposed by adding "fake" endog
# variables that are used during filtering, but for all model- and
# results-based purposes we want k_endog = 1.
if self._r_matrix is not None:
self.k_endog = 1
def test_raise_no_missing(self):
# smoke test for #1700
sm_data.handle_data(pandas.Series(np.random.random(20)),
pandas.DataFrame(np.random.random((20, 2))),
'raise')
def test_pandas_constant(self):
exog = self.data.exog.copy()
exog['const'] = 1
data = sm_data.handle_data(self.data.endog, exog)
np.testing.assert_equal(data.k_constant, 1)
np.testing.assert_equal(data.const_idx, 6)
def test_pandas_noconstant(self):
exog = self.data.exog.copy()
data = sm_data.handle_data(self.data.endog, exog)
np.testing.assert_equal(data.k_constant, 0)
np.testing.assert_equal(data.const_idx, None)
def setupClass(cls):
super(TestLists, cls).setupClass()
cls.endog = np.random.random(10).tolist()
cls.exog = np.c_[np.ones(10), np.random.random((10,2))].tolist()
cls.data = sm_data.handle_data(cls.endog, cls.exog)
def test_mv_endog(self):
y = self.X
y = y.ix[~np.isnan(y.values).any(axis=1)]
data = sm_data.handle_data(self.X, None, 'drop')
np.testing.assert_array_equal(data.endog, y.values)
def test_raise_no_missing(self):
# smoke test for #1700
sm_data.handle_data(np.random.random(20), np.random.random((20, 2)),
'raise')
def test_labels(self):
2, 10, 14
labels = pandas.Index([0, 1, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24])
data = sm_data.handle_data(self.y, self.X, 'drop')
np.testing.assert_(data.row_labels.equals(labels))
def test_extra_kwargs_1d(self):
weights = np.random.random(25)
data = sm_data.handle_data(self.y, self.X, 'drop', weights=weights)
idx = ~np.isnan(np.c_[self.y, self.X]).any(axis=1)
weights = weights[idx]
np.testing.assert_array_equal(data.weights, weights)
def setupClass(cls):
super(TestArrays2dEndog, cls).setupClass()
cls.endog = np.random.random((10, 1))
cls.exog = np.c_[np.ones(10), np.random.random((10, 2))]
cls.data = sm_data.handle_data(cls.endog, cls.exog)
def test_raise(self):
with pytest.raises(Exception):
# TODO: be more specific about exception
sm_data.handle_data(self.y, self.X, 'raise')
def setupClass(cls):
super(TestLists, cls).setupClass()
cls.endog = np.random.random(10).tolist()
cls.exog = np.c_[np.ones(10), np.random.random((10, 2))].tolist()
cls.data = sm_data.handle_data(cls.endog, cls.exog)
def test_pandas_noconstant(self):
exog = self.data.exog.copy()
data = sm_data.handle_data(self.data.endog, exog)
np.testing.assert_equal(data.k_constant, 0)
np.testing.assert_equal(data.const_idx, None)
def test_raise_no_missing(self):
# smoke test for #1700
sm_data.handle_data(np.random.random(20), np.random.random((20, 2)),
'raise')
def test_endog_only_drop(self):
y = self.y
y = y[~np.isnan(y)]
data = sm_data.handle_data(self.y, None, 'drop')
np.testing.assert_array_equal(data.endog, y)
def test_endog_only_drop(self):
y = self.y
y = y[~np.isnan(y)]
data = sm_data.handle_data(self.y, None, 'drop')
np.testing.assert_array_equal(data.endog, y)
def test_formula_missing_extra_arrays():
np.random.seed(1)
# because patsy can't turn off missing data-handling as of 0.3.0, we need
# separate tests to make sure that missing values are handled correctly
# when going through formulas
# there is a handle_formula_data step
# then there is the regular handle_data step
# see 2083
# the untested cases are endog/exog have missing. extra has missing.
# endog/exog are fine. extra has missing.
# endog/exog do or do not have missing and extra has wrong dimension
y = np.random.randn(10)
y_missing = y.copy()
y_missing[[2, 5]] = np.nan
X = np.random.randn(10)
X_missing = X.copy()
X_missing[[1, 3]] = np.nan
weights = np.random.uniform(size=10)
weights_missing = weights.copy()
weights_missing[[6]] = np.nan
weights_wrong_size = np.random.randn(12)
data = {'y': y,
'X': X,
'y_missing': y_missing,
'X_missing': X_missing,
'weights': weights,
'weights_missing': weights_missing}
data = pandas.DataFrame.from_dict(data)
data['constant'] = 1
formula = 'y_missing ~ X_missing'
((endog, exog),
missing_idx, design_info) = handle_formula_data(data, None, formula,
depth=2,
missing='drop')
kwargs = {'missing_idx': missing_idx, 'missing': 'drop',
'weights': data['weights_missing']}
model_data = sm_data.handle_data(endog, exog, **kwargs)
data_nona = data.dropna()
assert_equal(data_nona['y'].values, model_data.endog)
assert_equal(data_nona[['constant', 'X']].values, model_data.exog)
assert_equal(data_nona['weights'].values, model_data.weights)
tmp = handle_formula_data(data, None, formula, depth=2, missing='drop')
(endog, exog), missing_idx, design_info = tmp
weights_2d = np.random.randn(10, 10)
weights_2d[[8, 7], [7, 8]] = np.nan #symmetric missing values
kwargs.update({'weights': weights_2d,
'missing_idx': missing_idx})
model_data2 = sm_data.handle_data(endog, exog, **kwargs)
good_idx = [0, 4, 6, 9]
assert_equal(data.loc[good_idx, 'y'], model_data2.endog)
assert_equal(data.loc[good_idx, ['constant', 'X']], model_data2.exog)
assert_equal(weights_2d[good_idx][:, good_idx], model_data2.weights)
tmp = handle_formula_data(data, None, formula, depth=2, missing='drop')
(endog, exog), missing_idx, design_info = tmp
kwargs.update({'weights': weights_wrong_size,
'missing_idx': missing_idx})
assert_raises(ValueError, sm_data.handle_data, endog, exog, **kwargs)
def test_raise_no_missing(self):
# smoke test for #1700
sm_data.handle_data(pandas.Series(np.random.random(20)),
pandas.DataFrame(np.random.random((20, 2))),
'raise')
def test_extra_kwargs_1d(self):
weights = np.random.random(25)
data = sm_data.handle_data(self.y, self.X, 'drop', weights=weights)
idx = ~np.isnan(np.c_[self.y, self.X]).any(axis=1)
weights = weights[idx]
np.testing.assert_array_equal(data.weights, weights)
def test_endog_only_drop(self):
y = self.y
y = y.dropna()
data = sm_data.handle_data(self.y, None, 'drop')
np.testing.assert_array_equal(data.endog, y.values)
def test_none(self):
data = sm_data.handle_data(self.y, self.X, 'none', hasconst=False)
np.testing.assert_array_equal(data.endog, self.y)
np.testing.assert_array_equal(data.exog, self.X)
def test_pandas_constant(self):
exog = self.data.exog.copy()
exog['const'] = 1
data = sm_data.handle_data(self.data.endog, exog)
np.testing.assert_equal(data.k_constant, 1)
np.testing.assert_equal(data.const_idx, 6)
def test_array_noconstant(self):
exog = self.data.exog.copy()
data = sm_data.handle_data(self.data.endog.values, exog.values)
np.testing.assert_equal(data.k_constant, 0)
np.testing.assert_equal(data.const_idx, None)
def test_array_noconstant(self):
exog = self.data.exog.copy()
data = sm_data.handle_data(self.data.endog.values, exog.values)
np.testing.assert_equal(data.k_constant, 0)
np.testing.assert_equal(data.const_idx, None)
def test_none(self):
data = sm_data.handle_data(self.y, self.X, 'none')
np.testing.assert_array_equal(data.endog, self.y)
np.testing.assert_array_equal(data.exog, self.X)
def test_formula_missing_extra_arrays():
np.random.seed(1)
# because patsy can't turn off missing data-handling as of 0.3.0, we need
# separate tests to make sure that missing values are handled correctly
# when going through formulas
# there is a handle_formula_data step
# then there is the regular handle_data step
# see 2083
# the untested cases are endog/exog have missing. extra has missing.
# endog/exog are fine. extra has missing.
# endog/exog do or do not have missing and extra has wrong dimension
y = np.random.randn(10)
y_missing = y.copy()
y_missing[[2, 5]] = np.nan
X = np.random.randn(10)
X_missing = X.copy()
X_missing[[1, 3]] = np.nan
weights = np.random.uniform(size=10)
weights_missing = weights.copy()
weights_missing[[6]] = np.nan
weights_wrong_size = np.random.randn(12)
data = {
'y': y,
'X': X,
'y_missing': y_missing,
'X_missing': X_missing,
'weights': weights,
'weights_missing': weights_missing
}
data = pandas.DataFrame.from_dict(data)
data['constant'] = 1
formula = 'y_missing ~ X_missing'
((endog, exog), missing_idx,
design_info) = handle_formula_data(data,
None,
formula,
depth=2,
missing='drop')
kwargs = {
'missing_idx': missing_idx,
'missing': 'drop',
'weights': data['weights_missing']
}
model_data = sm_data.handle_data(endog, exog, **kwargs)
data_nona = data.dropna()
assert_equal(data_nona['y'].values, model_data.endog)
assert_equal(data_nona[['constant', 'X']].values, model_data.exog)
assert_equal(data_nona['weights'].values, model_data.weights)
tmp = handle_formula_data(data, None, formula, depth=2, missing='drop')
(endog, exog), missing_idx, design_info = tmp
weights_2d = np.random.randn(10, 10)
weights_2d[[8, 7], [7, 8]] = np.nan #symmetric missing values
kwargs.update({'weights': weights_2d, 'missing_idx': missing_idx})
model_data2 = sm_data.handle_data(endog, exog, **kwargs)
good_idx = [0, 4, 6, 9]
assert_equal(data.loc[good_idx, 'y'], model_data2.endog)
assert_equal(data.loc[good_idx, ['constant', 'X']], model_data2.exog)
assert_equal(weights_2d[good_idx][:, good_idx], model_data2.weights)
tmp = handle_formula_data(data, None, formula, depth=2, missing='drop')
(endog, exog), missing_idx, design_info = tmp
kwargs.update({'weights': weights_wrong_size, 'missing_idx': missing_idx})
assert_raises(ValueError, sm_data.handle_data, endog, exog, **kwargs)
def _handle_data(self, X, missing='none'):
data = handle_data(X, None, missing, 0)
self.exog = None #TODO: remove this when we don't inherit from LLM
self.endog = data.endog #TODO: ditto
return data