pymc-extras 0.2.5__py3-none-any.whl → 0.2.7__py3-none-any.whl

tests/model/test_model_api.py

@@ -1,38 +0,0 @@
-import numpy as np
-import pymc as pm
-
-import pymc_extras as pmx
-
-
-def test_logp():
-    """Compare standard PyMC `with pm.Model()` context API against `pmx.model` decorator
-    and a functional syntax. Checks whether the kwarg `coords` can be passed.
-    """
-    coords = {"obs": ["a", "b"]}
-
-    with pm.Model(coords=coords) as model:
-        pm.Normal("x", 0.0, 1.0, dims="obs")
-
-    @pmx.as_model(coords=coords)
-    def model_wrapped():
-        pm.Normal("x", 0.0, 1.0, dims="obs")
-
-    mw = model_wrapped()
-
-    @pmx.as_model()
-    def model_wrapped2():
-        pm.Normal("x", 0.0, 1.0, dims="obs")
-
-    mw2 = model_wrapped2(coords=coords)
-
-    @pmx.as_model()
-    def model_wrapped3(mu):
-        pm.Normal("x", mu, 1.0, dims="obs")
-
-    mw3 = model_wrapped3(0.0, coords=coords)
-    mw4 = model_wrapped3(np.array([np.nan]), coords=coords)
-
-    np.testing.assert_equal(model.point_logps(), mw.point_logps())
-    np.testing.assert_equal(mw.point_logps(), mw2.point_logps())
-    assert mw3["mu"] in mw3.data_vars
-    assert "mu" not in mw4

tests/statespace/test_ETS.py

@@ -1,411 +0,0 @@
-import numpy as np
-import pytensor
-import pytest
-import statsmodels.api as sm
-
-from numpy.testing import assert_allclose
-from pytensor.graph.basic import explicit_graph_inputs
-from scipy import linalg
-
-from pymc_extras.statespace.models.ETS import BayesianETS
-from pymc_extras.statespace.utils.constants import LONG_MATRIX_NAMES
-from tests.statespace.utilities.shared_fixtures import rng
-from tests.statespace.utilities.test_helpers import load_nile_test_data
-
-
-@pytest.fixture(scope="session")
-def data():
-    return load_nile_test_data()
-
-
-def tests_invalid_order_raises():
-    # Order must be length 3
-    with pytest.raises(ValueError, match="Order must be a tuple of three strings"):
-        BayesianETS(order=("A", "N"))
-
-        # Order must be strings
-    with pytest.raises(ValueError, match="Order must be a tuple of three strings"):
-        BayesianETS(order=(2, 1, 1))
-
-    # Only additive errors allowed
-    with pytest.raises(ValueError, match="Only additive errors are supported"):
-        BayesianETS(order=("M", "N", "N"))
-
-    # Trend must be A or Ad
-    with pytest.raises(ValueError, match="Invalid trend specification"):
-        BayesianETS(order=("A", "P", "N"))
-
-    # Seasonal must be A or N
-    with pytest.raises(ValueError, match="Invalid seasonal specification"):
-        BayesianETS(order=("A", "Ad", "M"))
-
-    # seasonal_periods must be provided if seasonal is requested
-    with pytest.raises(ValueError, match="If seasonal is True, seasonal_periods must be provided."):
-        BayesianETS(order=("A", "Ad", "A"))
-
-
-orders = (
-    ("A", "N", "N"),
-    ("A", "A", "N"),
-    ("A", "Ad", "N"),
-    ("A", "N", "A"),
-    ("A", "A", "A"),
-    ("A", "Ad", "A"),
-)
-order_names = (
-    "Basic",
-    "Trend",
-    "Damped Trend",
-    "Seasonal",
-    "Trend and Seasonal",
-    "Trend, Damped Trend, Seasonal",
-)
-
-order_expected_flags = (
-    {"trend": False, "damped_trend": False, "seasonal": False},
-    {"trend": True, "damped_trend": False, "seasonal": False},
-    {"trend": True, "damped_trend": True, "seasonal": False},
-    {"trend": False, "damped_trend": False, "seasonal": True},
-    {"trend": True, "damped_trend": False, "seasonal": True},
-    {"trend": True, "damped_trend": True, "seasonal": True},
-)
-
-order_params = (
-    ["alpha", "initial_level"],
-    ["alpha", "initial_level", "beta", "initial_trend"],
-    ["alpha", "initial_level", "beta", "initial_trend", "phi"],
-    ["alpha", "initial_level", "gamma", "initial_seasonal"],
-    ["alpha", "initial_level", "beta", "initial_trend", "gamma", "initial_seasonal"],
-    ["alpha", "initial_level", "beta", "initial_trend", "gamma", "initial_seasonal", "phi"],
-)
-
-
-@pytest.mark.parametrize(
-    "order, expected_flags", zip(orders, order_expected_flags), ids=order_names
-)
-def test_order_flags(order, expected_flags):
-    mod = BayesianETS(order=order, seasonal_periods=4)
-    for key, value in expected_flags.items():
-        assert getattr(mod, key) == value
-
-
-@pytest.mark.parametrize("order, expected_params", zip(orders, order_params), ids=order_names)
-def test_param_info(order: tuple[str, str, str], expected_params):
-    mod = BayesianETS(order=order, seasonal_periods=4)
-
-    all_expected_params = [*expected_params, "sigma_state", "P0"]
-    assert all(param in mod.param_names for param in all_expected_params)
-    assert all(param in all_expected_params for param in mod.param_names)
-    assert all(
-        mod.param_info[param]["dims"] is None
-        for param in expected_params
-        if "seasonal" not in param
-    )
-
-
-@pytest.mark.parametrize("order, expected_params", zip(orders, order_params), ids=order_names)
-@pytest.mark.parametrize("use_transformed", [True, False], ids=["transformed", "untransformed"])
-def test_statespace_matrices(
-    rng, order: tuple[str, str, str], expected_params: list[str], use_transformed: bool
-):
-    seasonal_periods = np.random.randint(3, 12)
-    mod = BayesianETS(
-        order=order,
-        seasonal_periods=seasonal_periods,
-        measurement_error=True,
-        use_transformed_parameterization=use_transformed,
-    )
-    expected_states = 2 + int(order[1] != "N") + int(order[2] != "N") * seasonal_periods
-
-    test_values = {
-        "alpha": rng.beta(1, 1),
-        "beta": rng.beta(1, 1),
-        "gamma": rng.beta(1, 1),
-        "phi": rng.beta(1, 1),
-        "sigma_state": rng.normal() ** 2,
-        "sigma_obs": rng.normal() ** 2,
-        "initial_level": rng.normal() ** 2,
-        "initial_trend": rng.normal() ** 2,
-        "initial_seasonal": np.ones(seasonal_periods),
-        "initial_state_cov": np.eye(expected_states),
-    }
-
-    matrices = x0, P0, c, d, T, Z, R, H, Q = mod._unpack_statespace_with_placeholders()
-
-    assert x0.type.shape == (expected_states,)
-    assert P0.type.shape == (expected_states, expected_states)
-    assert c.type.shape == (expected_states,)
-    assert d.type.shape == (1,)
-    assert T.type.shape == (expected_states, expected_states)
-    assert Z.type.shape == (1, expected_states)
-    assert R.type.shape == (expected_states, 1)
-    assert H.type.shape == (1, 1)
-    assert Q.type.shape == (1, 1)
-
-    inputs = list(explicit_graph_inputs(matrices))
-    input_names = [x.name for x in inputs]
-    assert all(name in input_names for name in expected_params)
-
-    f_matrices = pytensor.function(inputs, matrices)
-    [x0, P0, c, d, T, Z, R, H, Q] = f_matrices(**{name: test_values[name] for name in input_names})
-
-    assert_allclose(H, np.eye(1) * test_values["sigma_obs"] ** 2)
-    assert_allclose(Q, np.eye(1) * test_values["sigma_state"] ** 2)
-
-    R_val = np.zeros((expected_states, 1))
-    R_val[0] = 1.0 - test_values["alpha"]
-    R_val[1] = test_values["alpha"]
-
-    Z_val = np.zeros((1, expected_states))
-    Z_val[0, 0] = 1.0
-    Z_val[0, 1] = 1.0
-
-    x0_val = np.zeros((expected_states,))
-    x0_val[1] = test_values["initial_level"]
-
-    if order[1] == "N":
-        T_val = np.array([[0.0, 0.0], [0.0, 1.0]])
-    else:
-        x0_val[2] = test_values["initial_trend"]
-        R_val[2] = (
-            test_values["beta"] if use_transformed else test_values["beta"] * test_values["alpha"]
-        )
-        T_val = np.array([[0.0, 0.0, 0.0], [0.0, 1.0, 1.0], [0.0, 0.0, 1.0]])
-
-    if order[1] == "Ad":
-        T_val[1:, -1] *= test_values["phi"]
-
-    if order[2] == "A":
-        x0_val[2 + int(order[1] != "N") :] = test_values["initial_seasonal"]
-        gamma = (
-            test_values["gamma"]
-            if use_transformed
-            else (1 - test_values["alpha"]) * test_values["gamma"]
-        )
-        R_val[2 + int(order[1] != "N")] = gamma
-        R_val[0] = R_val[0] - gamma
-
-        S = np.eye(seasonal_periods, k=-1)
-        S[0, -1] = 1.0
-        Z_val[0, 2 + int(order[1] != "N")] = 1.0
-    else:
-        S = np.eye(0)
-
-    T_val = linalg.block_diag(T_val, S)
-
-    assert_allclose(x0, x0_val)
-    assert_allclose(T, T_val)
-    assert_allclose(R, R_val)
-    assert_allclose(Z, Z_val)
-
-
-@pytest.mark.parametrize("order, params", zip(orders, order_params), ids=order_names)
-def test_statespace_matches_statsmodels(rng, order: tuple[str, str, str], params):
-    seasonal_periods = rng.integers(3, 12)
-    data = rng.normal(size=(100,))
-    mod = BayesianETS(
-        order=order,
-        seasonal_periods=seasonal_periods,
-        measurement_error=False,
-        use_transformed_parameterization=True,
-    )
-    sm_mod = sm.tsa.statespace.ExponentialSmoothing(
-        data,
-        trend=mod.trend,
-        damped_trend=mod.damped_trend,
-        seasonal=seasonal_periods if mod.seasonal else None,
-    )
-
-    simplex_params = ["alpha", "beta", "gamma"]
-    test_values = dict(zip(simplex_params, rng.dirichlet(alpha=np.ones(3))))
-    test_values["phi"] = rng.beta(1, 1)
-
-    test_values["initial_level"] = rng.normal()
-    test_values["initial_trend"] = rng.normal()
-    test_values["initial_seasonal"] = rng.normal(size=seasonal_periods)
-    test_values["initial_state_cov"] = np.eye(mod.k_states)
-    test_values["sigma_state"] = 1.0
-
-    sm_test_values = test_values.copy()
-    sm_test_values["smoothing_level"] = test_values["alpha"]
-    sm_test_values["smoothing_trend"] = test_values["beta"]
-    sm_test_values["smoothing_seasonal"] = test_values["gamma"]
-    sm_test_values["damping_trend"] = test_values["phi"]
-    sm_test_values["initial_seasonal"] = test_values["initial_seasonal"][0]
-    for i in range(1, seasonal_periods):
-        sm_test_values[f"initial_seasonal.L{i}"] = test_values["initial_seasonal"][i]
-
-    vals = [
-        np.atleast_1d(test_values[name])
-        for name in ["initial_level", "initial_trend", "initial_seasonal"]
-    ]
-    x0 = np.concatenate([[0.0], *vals])
-
-    mask = [True, True, order[1] != "N", *(order[2] != "N",) * seasonal_periods]
-
-    sm_mod.initialize_known(initial_state=x0[mask], initial_state_cov=np.eye(mod.k_states))
-    sm_mod.fit_constrained({name: sm_test_values[name] for name in sm_mod.param_names})
-
-    matrices = mod._unpack_statespace_with_placeholders()
-    inputs = list(explicit_graph_inputs(matrices))
-    input_names = [x.name for x in inputs]
-
-    f_matrices = pytensor.function(inputs, matrices)
-    test_values_subset = {name: test_values[name] for name in input_names}
-
-    matrices = f_matrices(**test_values_subset)
-    sm_matrices = [sm_mod.ssm[name] for name in LONG_MATRIX_NAMES[2:]]
-
-    for matrix, sm_matrix, name in zip(matrices[2:], sm_matrices, LONG_MATRIX_NAMES[2:]):
-        assert_allclose(matrix, sm_matrix, err_msg=f"{name} does not match")
-
-
-@pytest.mark.parametrize("order, params", zip(orders, order_params), ids=order_names)
-@pytest.mark.parametrize("dense_cov", [True, False], ids=["dense", "diagonal"])
-def test_ETS_with_multiple_endog(rng, order, params, dense_cov):
-    seasonal_periods = 4
-    mod = BayesianETS(
-        order=order,
-        seasonal_periods=seasonal_periods,
-        measurement_error=False,
-        use_transformed_parameterization=True,
-        dense_innovation_covariance=dense_cov,
-        endog_names=["A", "B"],
-    )
-
-    single_mod = BayesianETS(
-        order=order,
-        seasonal_periods=seasonal_periods,
-        measurement_error=False,
-        use_transformed_parameterization=True,
-    )
-
-    simplex_params = ["alpha", "beta", "gamma"]
-    test_values = dict(zip(simplex_params, rng.dirichlet(alpha=np.ones(3), size=(mod.k_endog,)).T))
-    test_values["phi"] = rng.beta(1, 1, size=(mod.k_endog,))
-
-    test_values["initial_level"] = rng.normal(
-        size=mod.k_endog,
-    )
-    test_values["initial_trend"] = rng.normal(
-        size=mod.k_endog,
-    )
-    test_values["initial_seasonal"] = rng.normal(size=(mod.k_endog, seasonal_periods))
-    test_values["initial_state_cov"] = np.eye(mod.k_states)
-
-    if not dense_cov:
-        test_values["sigma_state"] = np.ones(
-            mod.k_endog,
-        )
-    else:
-        L = np.random.normal(size=(mod.k_endog, mod.k_endog))
-        test_values["state_cov"] = L @ L.T
-
-    # Compile functions for the joined model
-    matrices_pt = mod._unpack_statespace_with_placeholders()
-    inputs = list(explicit_graph_inputs(matrices_pt))
-    input_names = [x.name for x in inputs]
-
-    test_values_subset = {name: test_values[name] for name in input_names}
-    f_matrices = pytensor.function(inputs, matrices_pt)
-
-    matrices = f_matrices(**test_values_subset)
-
-    # Compile functions for the single model
-    single_matrices_pt = single_mod._unpack_statespace_with_placeholders()
-    single_inputs = list(explicit_graph_inputs(single_matrices_pt))
-    single_input_names = [x.name for x in single_inputs]
-
-    cursor = 0
-    single_test_values_subsets = []
-    for i in range(mod.k_endog):
-        single_slice = slice(cursor, cursor + single_mod.k_states)
-        d = {
-            name: (
-                test_values[name][i]
-                if name != "initial_state_cov"
-                else test_values_subset[name][single_slice, single_slice]
-            )
-            for name in single_input_names
-            if name != "sigma_state"
-        }
-        if dense_cov:
-            d["sigma_state"] = np.sqrt(test_values["state_cov"][i, i])
-        else:
-            d["sigma_state"] = test_values["sigma_state"][i]
-        single_test_values_subsets.append(d)
-        cursor += single_mod.k_states
-
-    f_single_matrices = pytensor.function(single_inputs, single_matrices_pt)
-    single_matrices = [f_single_matrices(**d) for d in single_test_values_subsets]
-    names = [x.name for x in matrices_pt]
-
-    for i, (x1, name) in enumerate(zip(matrices, names)):
-        cursor = 0
-        for j in range(mod.k_endog):
-            x2 = single_matrices[j][i]
-            state_slice = slice(cursor, cursor + single_mod.k_states)
-            obs_slice = slice(j, j + 1)  # Also endog_slice -- it's doing double duty
-            if name in ["state_intercept", "initial_state"]:
-                assert_allclose(x1[state_slice], x2, err_msg=f"{name} does not match for case {j}")
-            elif name in ["P0", "initial_state_cov", "transition"]:
-                assert_allclose(
-                    x1[state_slice, state_slice], x2, err_msg=f"{name} does not match for case {j}"
-                )
-            elif name == "selection":
-                assert_allclose(
-                    x1[state_slice, obs_slice], x2, err_msg=f"{name} does not match for case {j}"
-                )
-            elif name == "design":
-                assert_allclose(
-                    x1[obs_slice, state_slice], x2, err_msg=f"{name} does not match for case {j}"
-                )
-            elif name == "obs_intercept":
-                assert_allclose(x1[obs_slice], x2, err_msg=f"{name} does not match for case {j}")
-            elif name in ["obs_cov", "state_cov"]:
-                assert_allclose(
-                    x1[obs_slice, obs_slice], x2, err_msg=f"{name} does not match for case {j}"
-                )
-            else:
-                raise ValueError(f"You forgot {name} !")
-
-            cursor += single_mod.k_states
-
-
-def test_ETS_stationary_initialization():
-    mod = BayesianETS(
-        order=("A", "Ad", "A"),
-        seasonal_periods=4,
-        stationary_initialization=True,
-        initialization_dampening=0.66,
-    )
-
-    matrices = mod._unpack_statespace_with_placeholders()
-    inputs = list(explicit_graph_inputs(matrices))
-    input_names = [x.name for x in inputs]
-
-    # Make sure the stationary_dampening dummy variables was completely rewritten away
-    assert "stationary_dampening" not in input_names
-
-    # P0 should have been removed from param names
-    assert "P0" not in mod.param_names
-    assert "P0" not in mod.param_info.keys()
-
-    f = pytensor.function(inputs, matrices, mode="FAST_COMPILE")
-    test_values = f(**{x.name: np.full(x.type.shape, 0.5) for x in inputs})
-    outputs = {name: val for name, val in zip(LONG_MATRIX_NAMES, test_values)}
-
-    # Make sure that the transition matrix has ones in the expected positions, not the model dampening factor
-    assert outputs["transition"][1, 1] == 1.0
-    assert outputs["transition"][2, 2] == 0.5  # phi = 0.5 -- trend is dampened anyway
-    assert outputs["transition"][3, -1] == 1.0
-
-    # P0 should be equal to the solution to the Lyapunov equation using the dampening factors in the transition matrix
-    T_stationary = outputs["transition"].copy()
-    T_stationary[1, 1] = mod.initialization_dampening
-    T_stationary[3, -1] = mod.initialization_dampening
-
-    R, Q = outputs["selection"], outputs["state_cov"]
-    P0_expected = linalg.solve_discrete_lyapunov(T_stationary, R @ Q @ R.T)
-
-    assert_allclose(outputs["initial_state_cov"], P0_expected, rtol=1e-8, atol=1e-8)