pymc-extras 0.2.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- pymc_extras/__init__.py +29 -0
- pymc_extras/distributions/__init__.py +40 -0
- pymc_extras/distributions/continuous.py +351 -0
- pymc_extras/distributions/discrete.py +399 -0
- pymc_extras/distributions/histogram_utils.py +163 -0
- pymc_extras/distributions/multivariate/__init__.py +3 -0
- pymc_extras/distributions/multivariate/r2d2m2cp.py +446 -0
- pymc_extras/distributions/timeseries.py +356 -0
- pymc_extras/gp/__init__.py +18 -0
- pymc_extras/gp/latent_approx.py +183 -0
- pymc_extras/inference/__init__.py +18 -0
- pymc_extras/inference/find_map.py +431 -0
- pymc_extras/inference/fit.py +44 -0
- pymc_extras/inference/laplace.py +570 -0
- pymc_extras/inference/pathfinder.py +134 -0
- pymc_extras/inference/smc/__init__.py +13 -0
- pymc_extras/inference/smc/sampling.py +451 -0
- pymc_extras/linearmodel.py +130 -0
- pymc_extras/model/__init__.py +0 -0
- pymc_extras/model/marginal/__init__.py +0 -0
- pymc_extras/model/marginal/distributions.py +276 -0
- pymc_extras/model/marginal/graph_analysis.py +372 -0
- pymc_extras/model/marginal/marginal_model.py +595 -0
- pymc_extras/model/model_api.py +56 -0
- pymc_extras/model/transforms/__init__.py +0 -0
- pymc_extras/model/transforms/autoreparam.py +434 -0
- pymc_extras/model_builder.py +759 -0
- pymc_extras/preprocessing/__init__.py +0 -0
- pymc_extras/preprocessing/standard_scaler.py +17 -0
- pymc_extras/printing.py +182 -0
- pymc_extras/statespace/__init__.py +13 -0
- pymc_extras/statespace/core/__init__.py +7 -0
- pymc_extras/statespace/core/compile.py +48 -0
- pymc_extras/statespace/core/representation.py +438 -0
- pymc_extras/statespace/core/statespace.py +2268 -0
- pymc_extras/statespace/filters/__init__.py +15 -0
- pymc_extras/statespace/filters/distributions.py +453 -0
- pymc_extras/statespace/filters/kalman_filter.py +820 -0
- pymc_extras/statespace/filters/kalman_smoother.py +126 -0
- pymc_extras/statespace/filters/utilities.py +59 -0
- pymc_extras/statespace/models/ETS.py +670 -0
- pymc_extras/statespace/models/SARIMAX.py +536 -0
- pymc_extras/statespace/models/VARMAX.py +393 -0
- pymc_extras/statespace/models/__init__.py +6 -0
- pymc_extras/statespace/models/structural.py +1651 -0
- pymc_extras/statespace/models/utilities.py +387 -0
- pymc_extras/statespace/utils/__init__.py +0 -0
- pymc_extras/statespace/utils/constants.py +74 -0
- pymc_extras/statespace/utils/coord_tools.py +0 -0
- pymc_extras/statespace/utils/data_tools.py +182 -0
- pymc_extras/utils/__init__.py +23 -0
- pymc_extras/utils/linear_cg.py +290 -0
- pymc_extras/utils/pivoted_cholesky.py +69 -0
- pymc_extras/utils/prior.py +200 -0
- pymc_extras/utils/spline.py +131 -0
- pymc_extras/version.py +11 -0
- pymc_extras/version.txt +1 -0
- pymc_extras-0.2.0.dist-info/LICENSE +212 -0
- pymc_extras-0.2.0.dist-info/METADATA +99 -0
- pymc_extras-0.2.0.dist-info/RECORD +101 -0
- pymc_extras-0.2.0.dist-info/WHEEL +5 -0
- pymc_extras-0.2.0.dist-info/top_level.txt +2 -0
- tests/__init__.py +13 -0
- tests/distributions/__init__.py +19 -0
- tests/distributions/test_continuous.py +185 -0
- tests/distributions/test_discrete.py +210 -0
- tests/distributions/test_discrete_markov_chain.py +258 -0
- tests/distributions/test_multivariate.py +304 -0
- tests/model/__init__.py +0 -0
- tests/model/marginal/__init__.py +0 -0
- tests/model/marginal/test_distributions.py +131 -0
- tests/model/marginal/test_graph_analysis.py +182 -0
- tests/model/marginal/test_marginal_model.py +867 -0
- tests/model/test_model_api.py +29 -0
- tests/statespace/__init__.py +0 -0
- tests/statespace/test_ETS.py +411 -0
- tests/statespace/test_SARIMAX.py +405 -0
- tests/statespace/test_VARMAX.py +184 -0
- tests/statespace/test_coord_assignment.py +116 -0
- tests/statespace/test_distributions.py +270 -0
- tests/statespace/test_kalman_filter.py +326 -0
- tests/statespace/test_representation.py +175 -0
- tests/statespace/test_statespace.py +818 -0
- tests/statespace/test_statespace_JAX.py +156 -0
- tests/statespace/test_structural.py +829 -0
- tests/statespace/utilities/__init__.py +0 -0
- tests/statespace/utilities/shared_fixtures.py +9 -0
- tests/statespace/utilities/statsmodel_local_level.py +42 -0
- tests/statespace/utilities/test_helpers.py +310 -0
- tests/test_blackjax_smc.py +222 -0
- tests/test_find_map.py +98 -0
- tests/test_histogram_approximation.py +109 -0
- tests/test_laplace.py +238 -0
- tests/test_linearmodel.py +208 -0
- tests/test_model_builder.py +306 -0
- tests/test_pathfinder.py +45 -0
- tests/test_pivoted_cholesky.py +24 -0
- tests/test_printing.py +98 -0
- tests/test_prior_from_trace.py +172 -0
- tests/test_splines.py +77 -0
- tests/utils.py +31 -0
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import logging
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from collections.abc import Callable, Sequence
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from typing import Any
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import numpy as np
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import pandas as pd
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import pymc as pm
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import pytensor
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import pytensor.tensor as pt
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from arviz import InferenceData
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from pymc.model import modelcontext
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from pymc.model.transform.optimization import freeze_dims_and_data
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from pymc.util import RandomState
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from pytensor import Variable, graph_replace
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from pytensor.compile import get_mode
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from pymc_extras.statespace.core.representation import PytensorRepresentation
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from pymc_extras.statespace.filters import (
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KalmanSmoother,
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SquareRootFilter,
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StandardFilter,
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UnivariateFilter,
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)
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from pymc_extras.statespace.filters.distributions import (
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LinearGaussianStateSpace,
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MvNormalSVD,
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SequenceMvNormal,
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)
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from pymc_extras.statespace.filters.utilities import stabilize
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from pymc_extras.statespace.utils.constants import (
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ALL_STATE_AUX_DIM,
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ALL_STATE_DIM,
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FILTER_OUTPUT_DIMS,
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FILTER_OUTPUT_TYPES,
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JITTER_DEFAULT,
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MATRIX_DIMS,
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MATRIX_NAMES,
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OBS_STATE_DIM,
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SHOCK_DIM,
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SHORT_NAME_TO_LONG,
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TIME_DIM,
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VECTOR_VALUED,
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)
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from pymc_extras.statespace.utils.data_tools import register_data_with_pymc
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_log = logging.getLogger("pymc.experimental.statespace")
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floatX = pytensor.config.floatX
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FILTER_FACTORY = {
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"standard": StandardFilter,
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"univariate": UnivariateFilter,
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"cholesky": SquareRootFilter,
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}
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def _validate_filter_arg(filter_arg):
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if filter_arg.lower() not in FILTER_OUTPUT_TYPES:
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raise ValueError(
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f'filter_output should be one of {", ".join(FILTER_OUTPUT_TYPES)}, received {filter_arg}'
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)
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def _verify_group(group):
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if group not in ["prior", "posterior"]:
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raise ValueError(f'Argument "group" must be one of "prior" or "posterior", found {group}')
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class PyMCStateSpace:
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r"""
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Base class for Linear Gaussian Statespace models in PyMC.
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Holds a ``PytensorRepresentation`` and ``KalmanFilter``, and provides a mapping between a PyMC model and the
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statespace model.
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Parameters
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----------
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k_endog : int
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The number of endogenous variables (observed time series).
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k_states : int
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The number of state variables.
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k_posdef : int
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The number of shocks in the model
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filter_type : str, optional
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The type of Kalman filter to use. Valid options are "standard", "univariate", "single", "cholesky", and
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"steady_state". For more information, see the docs for each filter. Default is "standard".
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verbose : bool, optional
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If True, displays information about the initialized model. Defaults to True.
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measurement_error : bool, optional
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If true, the model contains measurement error. Needed by post-estimation sampling methods to decide how to
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compute the observation errors. If False, these errors are deterministically zero; if True, they are sampled
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from a multivariate normal.
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Notes
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-----
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Based on the statsmodels statespace implementation https://github.com/statsmodels/statsmodels/blob/main/statsmodels/tsa/statespace/representation.py,
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described in [1].
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All statespace models inherit from this base class, which is responsible for providing an interface between a
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PyMC model and a PytensorRepresentation of a linear statespace model. This is done via the ``update`` method,
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which takes as input a vector of PyMC random variables and assigns them to their correct positions inside the
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underlying ``PytensorRepresentation``. Construction of the parameter vector, called ``theta``, is done
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automatically, but depend on the names provided in the ``param_names`` property.
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To implement a new statespace model, one needs to:
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1. Overload the ``param_names`` property to return a list of parameter names.
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2. Overload the ``update`` method to put these parameters into their respective statespace matrices
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In addition, a number of additional properties can be overloaded to provide users with additional resources
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when writing their PyMC models. For details, see the attributes section of the docs for this class.
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Finally, this class holds post-estimation methods common to all statespace models, which do not need to be
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overloaded when writing a custom statespace model.
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Examples
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--------
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The local level model is a simple statespace model. It is a Gaussian random walk with a drift term that itself also
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follows a Gaussian random walk, as described by the following two equations:
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.. math::
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\begin{align}
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y_{t} &= y_{t-1} + x_t + \nu_t \tag{1} \\
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x_{t} &= x_{t-1} + \eta_t \tag{2}
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\end{align}
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Where :math:`y_t` is the observed data, and :math:`x_t` is an unobserved trend term. The model has two unknown
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parameters, the variances on the two innovations, :math:`sigma_\nu` and :math:`sigma_\eta`. Take the hidden state
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vector to be :math:`\begin{bmatrix} y_t & x_t \end{bmatrix}^T` and the shock vector
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:math:`\varepsilon_t = \begin{bmatrix} \nu_t & \eta_t \end{bmatrix}^T`. Then this model can be cast into state-space
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form with the following matrices:
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.. math::
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\begin{align}
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T &= \begin{bmatrix}1 & 1 \\ 0 & 1 \end{bmatrix} &
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R &= \begin{bmatrix}1 & 0 \\ 0 & 1 \end{bmatrix} &
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Q &= \begin{bmatrix} \sigma_\nu & 0 \\ 0 & \sigma_\eta \end{bmatrix} &
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Z &= \begin{bmatrix} 1 & 0 \end{bmatrix}
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\end{align}
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With the remaining statespace matrices as zero matrices of the appropriate sizes. The model has two states,
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two shocks, and one observed state. Knowing all this, a very simple local level model can be implemented as
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follows:
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.. code:: python
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from pymc_extras.statespace.core import PyMCStateSpace
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import numpy as np
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class LocalLevel(PyMCStateSpace):
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def __init__():
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# Initialize the superclass. This creates the PytensorRepresentation and the Kalman Filter
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super().__init__(k_endog=1, k_states=2, k_posdef=2)
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# Declare the non-zero, non-parameterized matrices
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self.ssm['transition', :, :] = np.array([[1.0, 1.0], [0.0, 1.0]])
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self.ssm['selection', :, :] = np.eye(2)
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self.ssm['design', :, :] = np.array([[1.0, 0.0]])
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@property
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def param_names(self):
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return ['x0', 'P0', 'sigma_nu', 'sigma_eta']
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def make_symbolic_graph(self):
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# Declare symbolic variables that represent parameters of the model
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# In this case, we have 4: x0 (initial state), P0 (initial state covariance), sigma_nu, and sigma_eta
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x0 = self.make_and_register_variable('x0', shape=(2,))
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P0 = self.make_and_register_variable('P0', shape=(2,2))
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sigma_mu = self.make_and_register_variable('sigma_nu')
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sigma_eta = self.make_and_register_variable('sigma_eta')
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# Next, use these symbolic variables to build the statespace matrices by assigning each parameter
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# to its correct location in the correct matrix
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self.ssm['initial_state', :] = x0
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self.ssm['initial_state_cov', :, :] = P0
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self.ssm['state_cov', 0, 0] = sigma_nu
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self.ssm['state_cov', 1, 1] = sigma_eta
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After defining priors over the named parameters ``P0``, ``x0``, ``sigma_eta``, and ``sigma_nu``, we can sample
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from this model:
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.. code:: python
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import pymc as pm
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ll = LocalLevel()
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with pm.Model() as mod:
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x0 = pm.Normal('x0', shape=(2,))
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P0_diag = pm.Exponential('P0_diag', 1, shape=(2,))
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P0 = pm.Deterministic('P0', pt.diag(P0_diag))
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sigma_nu = pm.Exponential('sigma_nu', 1)
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sigma_eta = pm.Exponential('sigma_eta', 1)
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ll.build_statespace_graph(data = data)
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idata = pm.sample()
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References
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----------
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.. [1] Fulton, Chad. "Estimating time series models by state space methods in Python: Statsmodels." (2015).
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http://www.chadfulton.com/files/fulton_statsmodels_2017_v1.pdf
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"""
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def __init__(
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self,
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k_endog: int,
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k_states: int,
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k_posdef: int,
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filter_type: str = "standard",
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verbose: bool = True,
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measurement_error: bool = False,
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):
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self._fit_mode: str | None = None
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self._fit_coords: dict[str, Sequence[str]] | None = None
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self._fit_dims: dict[str, Sequence[str]] | None = None
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self._fit_data: pt.TensorVariable | None = None
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self._needs_exog_data = None
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self._exog_names = []
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self._exog_data_info = {}
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self._name_to_variable = {}
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self._name_to_data = {}
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self.k_endog = k_endog
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self.k_states = k_states
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self.k_posdef = k_posdef
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self.measurement_error = measurement_error
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# All models contain a state space representation and a Kalman filter
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self.ssm = PytensorRepresentation(k_endog, k_states, k_posdef)
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+
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# This will be populated with PyMC random matrices after calling _insert_random_variables
|
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self.subbed_ssm: list[pt.TensorVariable] | None = None
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+
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if filter_type.lower() not in FILTER_FACTORY.keys():
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raise NotImplementedError(
|
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"The following are valid filter types: " + ", ".join(list(FILTER_FACTORY.keys()))
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+
)
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+
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+
if filter_type == "single" and self.k_endog > 1:
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raise ValueError('Cannot use filter_type = "single" with multiple observed time series')
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+
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+
self.kalman_filter = FILTER_FACTORY[filter_type.lower()]()
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self.kalman_smoother = KalmanSmoother()
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self.make_symbolic_graph()
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+
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if verbose:
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# These are split into separate try-except blocks, because it will be quite rare of models to implement
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# _print_data_requirements, but we still want to print the prior requirements.
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try:
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self._print_prior_requirements()
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except NotImplementedError:
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pass
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try:
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self._print_data_requirements()
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except NotImplementedError:
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pass
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+
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+
def _print_prior_requirements(self) -> None:
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"""
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Prints a short report to the terminal about the priors needed for the model, including their names,
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shapes, named dimensions, and any parameter constraints.
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"""
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out = ""
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for param, info in self.param_info.items():
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out += f'\t{param} -- shape: {info["shape"]}, constraints: {info["constraints"]}, dims: {info["dims"]}\n'
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out = out.rstrip()
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+
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_log.info(
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"The following parameters should be assigned priors inside a PyMC "
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f"model block: \n"
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+
f"{out}"
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)
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+
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+
def _print_data_requirements(self) -> None:
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+
"""
|
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+
Prints a short report to the terminal about the data needed for the model, including their names, shapes,
|
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|
+
and named dimensions.
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+
"""
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+
if not self.data_info:
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+
return
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+
|
|
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+
out = ""
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|
+
for data, info in self.data_info.items():
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|
+
out += f'\t{data} -- shape: {info["shape"]}, dims: {info["dims"]}\n'
|
|
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|
+
out = out.rstrip()
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297
|
+
|
|
298
|
+
_log.info(
|
|
299
|
+
"The following Data variables should be assigned to the model inside a PyMC "
|
|
300
|
+
f"model block: \n"
|
|
301
|
+
f"{out}"
|
|
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|
+
)
|
|
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|
+
|
|
304
|
+
def _unpack_statespace_with_placeholders(
|
|
305
|
+
self,
|
|
306
|
+
) -> tuple[
|
|
307
|
+
pt.TensorVariable,
|
|
308
|
+
pt.TensorVariable,
|
|
309
|
+
pt.TensorVariable,
|
|
310
|
+
pt.TensorVariable,
|
|
311
|
+
pt.TensorVariable,
|
|
312
|
+
pt.TensorVariable,
|
|
313
|
+
pt.TensorVariable,
|
|
314
|
+
pt.TensorVariable,
|
|
315
|
+
pt.TensorVariable,
|
|
316
|
+
]:
|
|
317
|
+
"""
|
|
318
|
+
Helper function to quickly obtain all statespace matrices in the standard order. Matrices returned by this
|
|
319
|
+
method will include pytensor placeholders.
|
|
320
|
+
"""
|
|
321
|
+
|
|
322
|
+
a0 = self.ssm["initial_state"]
|
|
323
|
+
P0 = self.ssm["initial_state_cov"]
|
|
324
|
+
c = self.ssm["state_intercept"]
|
|
325
|
+
d = self.ssm["obs_intercept"]
|
|
326
|
+
T = self.ssm["transition"]
|
|
327
|
+
Z = self.ssm["design"]
|
|
328
|
+
R = self.ssm["selection"]
|
|
329
|
+
H = self.ssm["obs_cov"]
|
|
330
|
+
Q = self.ssm["state_cov"]
|
|
331
|
+
|
|
332
|
+
return a0, P0, c, d, T, Z, R, H, Q
|
|
333
|
+
|
|
334
|
+
def unpack_statespace(self) -> list[pt.TensorVariable]:
|
|
335
|
+
"""
|
|
336
|
+
Helper function to quickly obtain all statespace matrices in the standard order.
|
|
337
|
+
"""
|
|
338
|
+
|
|
339
|
+
if self.subbed_ssm is None:
|
|
340
|
+
raise ValueError(
|
|
341
|
+
"Cannot unpack the complete statespace system until PyMC model variables have been "
|
|
342
|
+
"inserted. To build the random statespace matrices, call build_statespace_graph() inside"
|
|
343
|
+
"a PyMC model context. "
|
|
344
|
+
)
|
|
345
|
+
|
|
346
|
+
return self.subbed_ssm
|
|
347
|
+
|
|
348
|
+
@property
|
|
349
|
+
def param_names(self) -> list[str]:
|
|
350
|
+
"""
|
|
351
|
+
Names of model parameters
|
|
352
|
+
|
|
353
|
+
A list of all parameters expected by the model. Each parameter will be sought inside the active PyMC model
|
|
354
|
+
context when ``build_statespace_graph`` is invoked.
|
|
355
|
+
"""
|
|
356
|
+
raise NotImplementedError("The param_names property has not been implemented!")
|
|
357
|
+
|
|
358
|
+
@property
|
|
359
|
+
def data_names(self) -> list[str]:
|
|
360
|
+
"""
|
|
361
|
+
Names of data variables expected by the model.
|
|
362
|
+
|
|
363
|
+
This does not include the observed data series, which is automatically handled by PyMC. This property only
|
|
364
|
+
needs to be implemented for models that expect exogenous data.
|
|
365
|
+
"""
|
|
366
|
+
return []
|
|
367
|
+
|
|
368
|
+
@property
|
|
369
|
+
def param_info(self) -> dict[str, dict[str, Any]]:
|
|
370
|
+
"""
|
|
371
|
+
Information about parameters needed to declare priors
|
|
372
|
+
|
|
373
|
+
A dictionary of param_name: dictionary key-value pairs. The return value is used by the
|
|
374
|
+
``_print_prior_requirements`` method, to print a message telling users how to define the necessary priors for
|
|
375
|
+
the model. Each dictionary should have the following key-value pairs:
|
|
376
|
+
* key: "shape", value: a tuple of integers
|
|
377
|
+
* key: "constraints", value: a string describing the support of the prior (positive,
|
|
378
|
+
positive semi-definite, etc)
|
|
379
|
+
* key: "dims", value: tuple of strings
|
|
380
|
+
"""
|
|
381
|
+
raise NotImplementedError("The params_info property has not been implemented!")
|
|
382
|
+
|
|
383
|
+
@property
|
|
384
|
+
def data_info(self) -> dict[str, dict[str, Any]]:
|
|
385
|
+
"""
|
|
386
|
+
Information about Data variables that need to be declared in the PyMC model block.
|
|
387
|
+
|
|
388
|
+
Returns a dictionary of data_name: dictionary of property-name:property description pairs. The return value is
|
|
389
|
+
used by the ``_print_data_requirements`` method, to print a message telling users how to define the necessary
|
|
390
|
+
data for the model. Each dictionary should have the following key-value pairs:
|
|
391
|
+
* key: "shape", value: a tuple of integers
|
|
392
|
+
* key: "dims", value: tuple of strings
|
|
393
|
+
"""
|
|
394
|
+
raise NotImplementedError("The data_info property has not been implemented!")
|
|
395
|
+
|
|
396
|
+
@property
|
|
397
|
+
def state_names(self) -> list[str]:
|
|
398
|
+
"""
|
|
399
|
+
A k_states length list of strings, associated with the model's hidden states
|
|
400
|
+
|
|
401
|
+
"""
|
|
402
|
+
|
|
403
|
+
raise NotImplementedError("The state_names property has not been implemented!")
|
|
404
|
+
|
|
405
|
+
@property
|
|
406
|
+
def observed_states(self) -> list[str]:
|
|
407
|
+
"""
|
|
408
|
+
A k_endog length list of strings, associated with the model's observed states
|
|
409
|
+
"""
|
|
410
|
+
raise NotImplementedError("The observed_states property has not been implemented!")
|
|
411
|
+
|
|
412
|
+
@property
|
|
413
|
+
def shock_names(self) -> list[str]:
|
|
414
|
+
"""
|
|
415
|
+
A k_posdef length list of strings, associated with the model's shock processes
|
|
416
|
+
|
|
417
|
+
"""
|
|
418
|
+
raise NotImplementedError("The shock_names property has not been implemented!")
|
|
419
|
+
|
|
420
|
+
@property
|
|
421
|
+
def default_priors(self) -> dict[str, Callable]:
|
|
422
|
+
"""
|
|
423
|
+
Dictionary of parameter names and callable functions to construct default priors for the model
|
|
424
|
+
|
|
425
|
+
Returns a dictionary with param_name: Callable key-value pairs. Used by the ``add_default_priors()`` method
|
|
426
|
+
to automatically add priors to the PyMC model.
|
|
427
|
+
"""
|
|
428
|
+
raise NotImplementedError("The default_priors property has not been implemented!")
|
|
429
|
+
|
|
430
|
+
@property
|
|
431
|
+
def coords(self) -> dict[str, Sequence[str]]:
|
|
432
|
+
"""
|
|
433
|
+
PyMC model coordinates
|
|
434
|
+
|
|
435
|
+
Returns a dictionary of dimension: coordinate key-value pairs, to be provided to ``pm.Model``. Dimensions
|
|
436
|
+
should come from the default names defined in ``statespace.utils.constants`` for them to be detected by
|
|
437
|
+
sampling methods.
|
|
438
|
+
"""
|
|
439
|
+
raise NotImplementedError("The coords property has not been implemented!")
|
|
440
|
+
|
|
441
|
+
@property
|
|
442
|
+
def param_dims(self) -> dict[str, Sequence[str]]:
|
|
443
|
+
"""
|
|
444
|
+
Dictionary of named dimensions for each model parameter
|
|
445
|
+
|
|
446
|
+
Returns a dictionary of param_name: dimension key-value pairs, to be provided to the ``dims`` argument of a
|
|
447
|
+
PyMC random variable. Dimensions should come from the default names defined in ``statespace.utils.constants``
|
|
448
|
+
for them to be detected by sampling methods.
|
|
449
|
+
|
|
450
|
+
"""
|
|
451
|
+
raise NotImplementedError("The param_dims property has not been implemented!")
|
|
452
|
+
|
|
453
|
+
def add_default_priors(self) -> None:
|
|
454
|
+
"""
|
|
455
|
+
Add default priors to the active PyMC model context
|
|
456
|
+
"""
|
|
457
|
+
raise NotImplementedError("The add_default_priors property has not been implemented!")
|
|
458
|
+
|
|
459
|
+
def make_and_register_variable(
|
|
460
|
+
self, name, shape: int | tuple[int, ...] | None = None, dtype=floatX
|
|
461
|
+
) -> pt.TensorVariable:
|
|
462
|
+
"""
|
|
463
|
+
Helper function to create a pytensor symbolic variable and register it in the _name_to_variable dictionary
|
|
464
|
+
|
|
465
|
+
Parameters
|
|
466
|
+
----------
|
|
467
|
+
name : str
|
|
468
|
+
The name of the placeholder variable. Must be the name of a model parameter.
|
|
469
|
+
shape : int or tuple of int
|
|
470
|
+
Shape of the parameter
|
|
471
|
+
dtype : str, default pytensor.config.floatX
|
|
472
|
+
dtype of the parameter
|
|
473
|
+
|
|
474
|
+
Notes
|
|
475
|
+
-----
|
|
476
|
+
Symbolic pytensor variables are used in the ``make_symbolic_graph`` method as placeholders for PyMC random
|
|
477
|
+
variables. The change is made in the ``_insert_random_variables`` method via ``pytensor.graph_replace``. To
|
|
478
|
+
make the change, a dictionary mapping pytensor variables to PyMC random variables needs to be constructed.
|
|
479
|
+
|
|
480
|
+
The purpose of this method is to:
|
|
481
|
+
1. Create the placeholder symbolic variables
|
|
482
|
+
2. Register the placeholder variable in the ``_name_to_variable`` dictionary
|
|
483
|
+
|
|
484
|
+
The shape provided here will define the shape of the prior that will need to be provided by the user.
|
|
485
|
+
|
|
486
|
+
An error is raised if the provided name has already been registered, or if the name is not present in the
|
|
487
|
+
``param_names`` property.
|
|
488
|
+
"""
|
|
489
|
+
if name not in self.param_names:
|
|
490
|
+
raise ValueError(
|
|
491
|
+
f"{name} is not a model parameter. All placeholder variables should correspond to model "
|
|
492
|
+
f"parameters."
|
|
493
|
+
)
|
|
494
|
+
|
|
495
|
+
if name in self._name_to_variable.keys():
|
|
496
|
+
raise ValueError(
|
|
497
|
+
f"{name} is already a registered placeholder variable with shape "
|
|
498
|
+
f"{self._name_to_variable[name].type.shape}"
|
|
499
|
+
)
|
|
500
|
+
|
|
501
|
+
placeholder = pt.tensor(name, shape=shape, dtype=dtype)
|
|
502
|
+
self._name_to_variable[name] = placeholder
|
|
503
|
+
return placeholder
|
|
504
|
+
|
|
505
|
+
def make_and_register_data(
|
|
506
|
+
self, name: str, shape: int | tuple[int], dtype: str = floatX
|
|
507
|
+
) -> Variable:
|
|
508
|
+
r"""
|
|
509
|
+
Helper function to create a pytensor symbolic variable and register it in the _name_to_data dictionary
|
|
510
|
+
|
|
511
|
+
Parameters
|
|
512
|
+
----------
|
|
513
|
+
name : str
|
|
514
|
+
The name of the placeholder data. Must be the name of an expected data variable.
|
|
515
|
+
shape : int or tuple of int
|
|
516
|
+
Shape of the parameter
|
|
517
|
+
dtype : str, default pytensor.config.floatX
|
|
518
|
+
dtype of the parameter
|
|
519
|
+
|
|
520
|
+
Notes
|
|
521
|
+
-----
|
|
522
|
+
See docstring for make_and_register_variable for more details. This function is similar, but handles data
|
|
523
|
+
inputs instead of model parameters.
|
|
524
|
+
|
|
525
|
+
An error is raised if the provided name has already been registered, or if the name is not present in the
|
|
526
|
+
``data_names`` property.
|
|
527
|
+
"""
|
|
528
|
+
if name not in self.data_names:
|
|
529
|
+
raise ValueError(
|
|
530
|
+
f"{name} is not a model parameter. All placeholder variables should correspond to model "
|
|
531
|
+
f"parameters."
|
|
532
|
+
)
|
|
533
|
+
|
|
534
|
+
if name in self._name_to_data.keys():
|
|
535
|
+
raise ValueError(
|
|
536
|
+
f"{name} is already a registered placeholder variable with shape "
|
|
537
|
+
f"{self._name_to_data[name].type.shape}"
|
|
538
|
+
)
|
|
539
|
+
|
|
540
|
+
placeholder = pt.tensor(name, shape=shape, dtype=dtype)
|
|
541
|
+
self._name_to_data[name] = placeholder
|
|
542
|
+
return placeholder
|
|
543
|
+
|
|
544
|
+
def make_symbolic_graph(self) -> None:
|
|
545
|
+
"""
|
|
546
|
+
The purpose of the make_symbolic_graph function is to hide tedious parameter allocations from the user.
|
|
547
|
+
In statespace models, it is extremely rare for an entire matrix to be defined by a single prior distribution.
|
|
548
|
+
Instead, users expect to place priors over single entries of the matrix. The purpose of this function is to
|
|
549
|
+
meet that expectation.
|
|
550
|
+
|
|
551
|
+
Every statespace model needs to implement this function.
|
|
552
|
+
|
|
553
|
+
Examples
|
|
554
|
+
--------
|
|
555
|
+
As an example, consider an ARMA(2,2) model, which has five parameters (excluding the initial state distribution):
|
|
556
|
+
2 AR parameters (:math:`\rho_1` and :math:`\rho_2`), 2 MA parameters (:math:`\theta_1` and :math:`theta_2`),
|
|
557
|
+
and a single innovation covariance (:math:`\\sigma`). A common way of writing this statespace is:
|
|
558
|
+
|
|
559
|
+
..math::
|
|
560
|
+
|
|
561
|
+
\begin{align}
|
|
562
|
+
T &= \begin{bmatrix} \rho_1 & 1 & 0 \\
|
|
563
|
+
\rho_2 & 0 & 1 \\
|
|
564
|
+
0 & 0 & 0
|
|
565
|
+
\\end{bmatrix} \\
|
|
566
|
+
R & = \begin{bmatrix} 1 \\ \theta_1 \\ \theta_2 \\end{bmatrix} \\
|
|
567
|
+
Q &= \begin{bmatrix} \\sigma \\end{bmatrix}
|
|
568
|
+
\\end{align}
|
|
569
|
+
|
|
570
|
+
To implement this model, we begin by creating the required matrices, and fill in the "fixed" values -- the ones
|
|
571
|
+
at position (0, 1) and (0, 2) in the T matrix, and at position (0, 0) in the R matrix. These are then saved
|
|
572
|
+
to the class's PytensorRepresentation -- called ``ssm``.
|
|
573
|
+
|
|
574
|
+
.. code:: python
|
|
575
|
+
|
|
576
|
+
T = np.eye(2, k=1)
|
|
577
|
+
R = np.concatenate([np.ones(1,1), np.zeros((2, 1))], axis=0)
|
|
578
|
+
|
|
579
|
+
self.ssm['transition'] = T
|
|
580
|
+
self.ssm['selection'] = R
|
|
581
|
+
|
|
582
|
+
Next, placeholders need to be inserted for the random variables rho_1, rho_2, theta_1, theta_2, and sigma.
|
|
583
|
+
This can be done many ways: we could define two vectors, rho and theta, and a scalar for sigma, or five
|
|
584
|
+
scalars. Whatever is chosen, the choice needs to be consistent with the ``param_names`` property.
|
|
585
|
+
|
|
586
|
+
Suppose the ``param_names`` are ``[rho, theta, sigma]``, then we make one placeholder for each, and insert it
|
|
587
|
+
into the correct ``ssm`` matrix, at the correct location. To create placeholders, use the
|
|
588
|
+
``make_and_register_variable`` helper method, which will maintain an internal registry of variables.
|
|
589
|
+
|
|
590
|
+
.. code:: python
|
|
591
|
+
rho_parmas = self.make_and_register_variable(name='rho', shape=(2,))
|
|
592
|
+
theta_params = self.make_and_register_variable(name='theta', shape=(2,))
|
|
593
|
+
sigma = self.make_and_register_variable(name='sigma', shape=(1,))
|
|
594
|
+
|
|
595
|
+
self.ssm['transition', :, 0] = rho_params
|
|
596
|
+
self.ssm['selection', 1:, 0] = theta_params
|
|
597
|
+
self.ssm['state_cov', 0, 0] = sigma
|
|
598
|
+
"""
|
|
599
|
+
raise NotImplementedError("The make_symbolic_statespace method has not been implemented!")
|
|
600
|
+
|
|
601
|
+
def _get_matrix_shape_and_dims(self, name: str) -> tuple[tuple[int] | None, tuple[str] | None]:
|
|
602
|
+
"""
|
|
603
|
+
Get the shape and dimensions of a matrix associated with the specified name.
|
|
604
|
+
|
|
605
|
+
This method retrieves the shape and dimensions of a matrix associated with the given name. Importantly,
|
|
606
|
+
it will only find named dimension if they are the "default" dimension names defined in the
|
|
607
|
+
statespace.utils.constant.py file.
|
|
608
|
+
|
|
609
|
+
Parameters
|
|
610
|
+
----------
|
|
611
|
+
name : str
|
|
612
|
+
The name of the matrix whose shape and dimensions need to be retrieved.
|
|
613
|
+
|
|
614
|
+
Returns
|
|
615
|
+
-------
|
|
616
|
+
shape: tuple or None
|
|
617
|
+
If no named dimension are found, the shape of the requested matrix, otherwise None.
|
|
618
|
+
|
|
619
|
+
dims: tuple or None
|
|
620
|
+
If named dimensions are found, a tuple of strings, otherwise None
|
|
621
|
+
"""
|
|
622
|
+
|
|
623
|
+
pm_mod = modelcontext(None)
|
|
624
|
+
dims = MATRIX_DIMS.get(name, None)
|
|
625
|
+
dims = dims if all([dim in pm_mod.coords.keys() for dim in dims]) else None
|
|
626
|
+
data_len = len(self._fit_data)
|
|
627
|
+
|
|
628
|
+
if name in self.kalman_filter.seq_names:
|
|
629
|
+
shape = (data_len, *self.ssm[SHORT_NAME_TO_LONG[name]].type.shape)
|
|
630
|
+
dims = (TIME_DIM, *dims)
|
|
631
|
+
else:
|
|
632
|
+
shape = self.ssm[SHORT_NAME_TO_LONG[name]].type.shape
|
|
633
|
+
|
|
634
|
+
shape = shape if dims is None else None
|
|
635
|
+
|
|
636
|
+
return shape, dims
|
|
637
|
+
|
|
638
|
+
def _save_exogenous_data_info(self):
|
|
639
|
+
"""
|
|
640
|
+
Store exogenous data required by posterior sampling functions
|
|
641
|
+
"""
|
|
642
|
+
pymc_mod = modelcontext(None)
|
|
643
|
+
for data_name in self.data_names:
|
|
644
|
+
data = pymc_mod[data_name]
|
|
645
|
+
self._exog_data_info[data_name] = {
|
|
646
|
+
"name": data_name,
|
|
647
|
+
"value": data.get_value(),
|
|
648
|
+
"dims": pymc_mod.named_vars_to_dims.get(data_name, None),
|
|
649
|
+
}
|
|
650
|
+
|
|
651
|
+
def _insert_random_variables(self):
|
|
652
|
+
"""
|
|
653
|
+
Replace pytensor symbolic variables with PyMC random variables.
|
|
654
|
+
|
|
655
|
+
Examples
|
|
656
|
+
--------
|
|
657
|
+
.. code:: python
|
|
658
|
+
|
|
659
|
+
ss_mod = pmss.BayesianSARIMA(order=(2, 0, 2), verbose=False, stationary_initialization=True)
|
|
660
|
+
with pm.Model():
|
|
661
|
+
x0 = pm.Normal('x0', size=ss_mod.k_states)
|
|
662
|
+
ar_params = pm.Normal('ar_params', size=ss_mod.p)
|
|
663
|
+
ma_parama = pm.Normal('ma_params', size=ss_mod.q)
|
|
664
|
+
sigma_state = pm.Normal('sigma_state')
|
|
665
|
+
|
|
666
|
+
ss_mod._insert_random_variables()
|
|
667
|
+
matrics = ss_mod.unpack_statespace()
|
|
668
|
+
|
|
669
|
+
pm.draw(matrices['transition'], random_seed=RANDOM_SEED)
|
|
670
|
+
>>> array([[-0.90590386, 1. , 0. ],
|
|
671
|
+
>>> [ 1.25190143, 0. , 1. ],
|
|
672
|
+
>>> [ 0. , 0. , 0. ]])
|
|
673
|
+
|
|
674
|
+
pm.draw(matrices['selection'], random_seed=RANDOM_SEED)
|
|
675
|
+
>>> array([[ 1. ],
|
|
676
|
+
>>> [-2.46741039],
|
|
677
|
+
>>> [-0.28947689]])
|
|
678
|
+
|
|
679
|
+
pm.draw(matrices['state_cov'], random_seed=RANDOM_SEED)
|
|
680
|
+
>>> array([[-1.69353533]])
|
|
681
|
+
"""
|
|
682
|
+
|
|
683
|
+
pymc_model = modelcontext(None)
|
|
684
|
+
found_params = []
|
|
685
|
+
with pymc_model:
|
|
686
|
+
for param_name in self.param_names:
|
|
687
|
+
param = getattr(pymc_model, param_name, None)
|
|
688
|
+
if param:
|
|
689
|
+
found_params.append(param.name)
|
|
690
|
+
|
|
691
|
+
missing_params = list(set(self.param_names) - set(found_params))
|
|
692
|
+
if len(missing_params) > 0:
|
|
693
|
+
raise ValueError(
|
|
694
|
+
"The following required model parameters were not found in the PyMC model: "
|
|
695
|
+
+ ", ".join(missing_params)
|
|
696
|
+
)
|
|
697
|
+
|
|
698
|
+
excess_params = list(set(found_params) - set(self.param_names))
|
|
699
|
+
if len(excess_params) > 0:
|
|
700
|
+
raise ValueError(
|
|
701
|
+
"The following parameters were found in the PyMC model but are not required by the statespace model: "
|
|
702
|
+
+ ", ".join(excess_params)
|
|
703
|
+
)
|
|
704
|
+
|
|
705
|
+
matrices = list(self._unpack_statespace_with_placeholders())
|
|
706
|
+
|
|
707
|
+
replacement_dict = {var: pymc_model[name] for name, var in self._name_to_variable.items()}
|
|
708
|
+
self.subbed_ssm = graph_replace(matrices, replace=replacement_dict, strict=True)
|
|
709
|
+
|
|
710
|
+
def _insert_data_variables(self):
|
|
711
|
+
"""
|
|
712
|
+
Replace symbolic pytensor variables with PyMC data containers.
|
|
713
|
+
|
|
714
|
+
Only used when models require exogenous data. The observed data is not added to the model using this method!
|
|
715
|
+
"""
|
|
716
|
+
|
|
717
|
+
try:
|
|
718
|
+
data_names = self.data_names
|
|
719
|
+
except NotImplementedError:
|
|
720
|
+
return
|
|
721
|
+
|
|
722
|
+
pymc_model = modelcontext(None)
|
|
723
|
+
found_data = []
|
|
724
|
+
with pymc_model:
|
|
725
|
+
for data_name in data_names:
|
|
726
|
+
data = getattr(pymc_model, data_name, None)
|
|
727
|
+
if data:
|
|
728
|
+
found_data.append(data.name)
|
|
729
|
+
|
|
730
|
+
missing_data = list(set(data_names) - set(found_data))
|
|
731
|
+
if len(missing_data) > 0:
|
|
732
|
+
raise ValueError(
|
|
733
|
+
"The following required exogenous data were not found in the PyMC model: "
|
|
734
|
+
+ ", ".join(missing_data)
|
|
735
|
+
)
|
|
736
|
+
|
|
737
|
+
replacement_dict = {data: pymc_model[name] for name, data in self._name_to_data.items()}
|
|
738
|
+
self.subbed_ssm = graph_replace(self.subbed_ssm, replace=replacement_dict, strict=True)
|
|
739
|
+
|
|
740
|
+
def _register_matrices_with_pymc_model(self) -> list[pt.TensorVariable]:
|
|
741
|
+
"""
|
|
742
|
+
Add all statespace matrices to the PyMC model currently on the context stack as pm.Deterministic nodes, and
|
|
743
|
+
adds named dimensions if they are found.
|
|
744
|
+
|
|
745
|
+
Returns
|
|
746
|
+
-------
|
|
747
|
+
registered_matrices: list of pt.TensorVariable
|
|
748
|
+
list of statespace matrices, wrapped in pm.Deterministic
|
|
749
|
+
"""
|
|
750
|
+
|
|
751
|
+
pm_mod = modelcontext(None)
|
|
752
|
+
matrices = self.unpack_statespace()
|
|
753
|
+
|
|
754
|
+
registered_matrices = []
|
|
755
|
+
for i, (matrix, name) in enumerate(zip(matrices, MATRIX_NAMES)):
|
|
756
|
+
time_varying_ndim = 2 if name in VECTOR_VALUED else 3
|
|
757
|
+
if not getattr(pm_mod, name, None):
|
|
758
|
+
shape, dims = self._get_matrix_shape_and_dims(name)
|
|
759
|
+
has_dims = dims is not None
|
|
760
|
+
|
|
761
|
+
if matrix.ndim == time_varying_ndim and has_dims:
|
|
762
|
+
dims = (TIME_DIM, *dims)
|
|
763
|
+
|
|
764
|
+
x = pm.Deterministic(name, matrix, dims=dims)
|
|
765
|
+
registered_matrices.append(x)
|
|
766
|
+
else:
|
|
767
|
+
registered_matrices.append(matrices[i])
|
|
768
|
+
|
|
769
|
+
return registered_matrices
|
|
770
|
+
|
|
771
|
+
@staticmethod
|
|
772
|
+
def _register_kalman_filter_outputs_with_pymc_model(outputs: tuple[pt.TensorVariable]) -> None:
|
|
773
|
+
mod = modelcontext(None)
|
|
774
|
+
coords = mod.coords
|
|
775
|
+
|
|
776
|
+
states, covs = outputs[:4], outputs[4:]
|
|
777
|
+
|
|
778
|
+
state_names = [
|
|
779
|
+
"filtered_state",
|
|
780
|
+
"predicted_state",
|
|
781
|
+
"predicted_observed_state",
|
|
782
|
+
"smoothed_state",
|
|
783
|
+
]
|
|
784
|
+
cov_names = [
|
|
785
|
+
"filtered_covariance",
|
|
786
|
+
"predicted_covariance",
|
|
787
|
+
"predicted_observed_covariance",
|
|
788
|
+
"smoothed_covariance",
|
|
789
|
+
]
|
|
790
|
+
|
|
791
|
+
with mod:
|
|
792
|
+
for var, name in zip(states + covs, state_names + cov_names):
|
|
793
|
+
dim_names = FILTER_OUTPUT_DIMS.get(name, None)
|
|
794
|
+
dims = tuple([dim if dim in coords.keys() else None for dim in dim_names])
|
|
795
|
+
pm.Deterministic(name, var, dims=dims)
|
|
796
|
+
|
|
797
|
+
def build_statespace_graph(
|
|
798
|
+
self,
|
|
799
|
+
data: np.ndarray | pd.DataFrame | pt.TensorVariable,
|
|
800
|
+
register_data: bool = True,
|
|
801
|
+
mode: str | None = None,
|
|
802
|
+
missing_fill_value: float | None = None,
|
|
803
|
+
cov_jitter: float | None = JITTER_DEFAULT,
|
|
804
|
+
save_kalman_filter_outputs_in_idata: bool = False,
|
|
805
|
+
) -> None:
|
|
806
|
+
"""
|
|
807
|
+
Given a parameter vector `theta`, constructs the full computational graph describing the state space model and
|
|
808
|
+
the associated log probability of the data. Hidden states and log probabilities are computed via the Kalman
|
|
809
|
+
Filter.
|
|
810
|
+
|
|
811
|
+
Parameters
|
|
812
|
+
----------
|
|
813
|
+
data : Union[np.ndarray, pd.DataFrame, pt.TensorVariable]
|
|
814
|
+
The observed data used to fit the state space model. It can be a NumPy array, a Pandas DataFrame,
|
|
815
|
+
or a Pytensor tensor variable.
|
|
816
|
+
|
|
817
|
+
register_data : bool, optional, default=True
|
|
818
|
+
If True, the observed data will be registered with PyMC as a pm.Data variable. In addition,
|
|
819
|
+
a "time" dim will be created an added to the model's coords.
|
|
820
|
+
|
|
821
|
+
mode : Optional[str], optional, default=None
|
|
822
|
+
The Pytensor mode used for the computation graph construction. If None, the default mode will be used.
|
|
823
|
+
Other options include "JAX" and "NUMBA".
|
|
824
|
+
|
|
825
|
+
missing_fill_value: float, optional, default=-9999
|
|
826
|
+
A value to mask in missing values. NaN values in the data need to be filled with an arbitrary value to
|
|
827
|
+
avoid triggering PyMC's automatic imputation machinery (missing values are instead filled by treating them
|
|
828
|
+
as hidden states during Kalman filtering).
|
|
829
|
+
|
|
830
|
+
In general this never needs to be set. But if by a wild coincidence your data includes the value -9999.0,
|
|
831
|
+
you will need to change the missing_fill_value to something else, to avoid incorrectly mark in
|
|
832
|
+
data as missing.
|
|
833
|
+
|
|
834
|
+
cov_jitter: float, default 1e-8 or 1e-6 if pytensor.config.floatX is float32
|
|
835
|
+
The Kalman filter is known to be numerically unstable, especially at half precision. This value is added to
|
|
836
|
+
the diagonal of every covariance matrix -- predicted, filtered, and smoothed -- at every step, to ensure
|
|
837
|
+
all matrices are strictly positive semi-definite.
|
|
838
|
+
|
|
839
|
+
Obviously, if this can be zero, that's best. In general:
|
|
840
|
+
- Having measurement error makes Kalman Filters more robust. A large source of numerical errors come
|
|
841
|
+
from the Filtered and Smoothed covariance matrices having a zero in the (0, 0) position, which always
|
|
842
|
+
occurs when there is no measurement error. You can lower this value in the presence of measurement
|
|
843
|
+
error.
|
|
844
|
+
|
|
845
|
+
- The Univariate Filter is more robust than other filters, and can tolerate a lower jitter value
|
|
846
|
+
|
|
847
|
+
save_kalman_filter_outputs_in_idata: bool, optional, default=False
|
|
848
|
+
If True, Kalman Filter outputs will be saved in the model as deterministics. Useful for debugging, but
|
|
849
|
+
should not be necessary for the majority of users.
|
|
850
|
+
"""
|
|
851
|
+
pm_mod = modelcontext(None)
|
|
852
|
+
|
|
853
|
+
self._insert_random_variables()
|
|
854
|
+
self._save_exogenous_data_info()
|
|
855
|
+
self._insert_data_variables()
|
|
856
|
+
|
|
857
|
+
obs_coords = pm_mod.coords.get(OBS_STATE_DIM, None)
|
|
858
|
+
self._fit_data = data
|
|
859
|
+
|
|
860
|
+
data, nan_mask = register_data_with_pymc(
|
|
861
|
+
data,
|
|
862
|
+
n_obs=self.ssm.k_endog,
|
|
863
|
+
obs_coords=obs_coords,
|
|
864
|
+
register_data=register_data,
|
|
865
|
+
missing_fill_value=missing_fill_value,
|
|
866
|
+
)
|
|
867
|
+
|
|
868
|
+
filter_outputs = self.kalman_filter.build_graph(
|
|
869
|
+
pt.as_tensor_variable(data),
|
|
870
|
+
*self.unpack_statespace(),
|
|
871
|
+
mode=mode,
|
|
872
|
+
missing_fill_value=missing_fill_value,
|
|
873
|
+
cov_jitter=cov_jitter,
|
|
874
|
+
)
|
|
875
|
+
|
|
876
|
+
logp = filter_outputs.pop(-1)
|
|
877
|
+
states, covs = filter_outputs[:3], filter_outputs[3:]
|
|
878
|
+
filtered_states, predicted_states, observed_states = states
|
|
879
|
+
filtered_covariances, predicted_covariances, observed_covariances = covs
|
|
880
|
+
if save_kalman_filter_outputs_in_idata:
|
|
881
|
+
smooth_states, smooth_covariances = self._build_smoother_graph(
|
|
882
|
+
filtered_states, filtered_covariances, self.unpack_statespace(), mode=mode
|
|
883
|
+
)
|
|
884
|
+
all_kf_outputs = [*states, smooth_states, *covs, smooth_covariances]
|
|
885
|
+
self._register_kalman_filter_outputs_with_pymc_model(all_kf_outputs)
|
|
886
|
+
|
|
887
|
+
obs_dims = FILTER_OUTPUT_DIMS["predicted_observed_state"]
|
|
888
|
+
obs_dims = obs_dims if all([dim in pm_mod.coords.keys() for dim in obs_dims]) else None
|
|
889
|
+
|
|
890
|
+
SequenceMvNormal(
|
|
891
|
+
"obs",
|
|
892
|
+
mus=observed_states,
|
|
893
|
+
covs=observed_covariances,
|
|
894
|
+
logp=logp,
|
|
895
|
+
observed=data,
|
|
896
|
+
dims=obs_dims,
|
|
897
|
+
)
|
|
898
|
+
|
|
899
|
+
self._fit_coords = pm_mod.coords.copy()
|
|
900
|
+
self._fit_dims = pm_mod.named_vars_to_dims.copy()
|
|
901
|
+
self._fit_mode = mode
|
|
902
|
+
|
|
903
|
+
def _build_smoother_graph(
|
|
904
|
+
self,
|
|
905
|
+
filtered_states: pt.TensorVariable,
|
|
906
|
+
filtered_covariances: pt.TensorVariable,
|
|
907
|
+
matrices,
|
|
908
|
+
mode: str | None = None,
|
|
909
|
+
cov_jitter=JITTER_DEFAULT,
|
|
910
|
+
):
|
|
911
|
+
"""
|
|
912
|
+
Build the computation graph for the Kalman smoother.
|
|
913
|
+
|
|
914
|
+
This method constructs the computation graph for applying the Kalman smoother to the filtered states
|
|
915
|
+
and covariances obtained from the Kalman filter. The Kalman smoother is used to generate smoothed
|
|
916
|
+
estimates of the latent states and their covariances in a state space model.
|
|
917
|
+
|
|
918
|
+
The Kalman smoother provides a more accurate estimate of the latent states by incorporating future
|
|
919
|
+
information in the backward pass, resulting in smoothed state trajectories.
|
|
920
|
+
|
|
921
|
+
Parameters
|
|
922
|
+
----------
|
|
923
|
+
filtered_states : pytensor.tensor.TensorVariable
|
|
924
|
+
The filtered states obtained from the Kalman filter. Returned by the `build_statespace_graph` method.
|
|
925
|
+
|
|
926
|
+
filtered_covariances : pytensor.tensor.TensorVariable
|
|
927
|
+
The filtered state covariances obtained from the Kalman filter. Returned by the `build_statespace_graph`
|
|
928
|
+
method.
|
|
929
|
+
|
|
930
|
+
mode : Optional[str], default=None
|
|
931
|
+
The mode used by pytensor for the construction of the logp graph. If None, the mode provided to
|
|
932
|
+
`build_statespace_graph` will be used.
|
|
933
|
+
|
|
934
|
+
Returns
|
|
935
|
+
-------
|
|
936
|
+
Tuple[pytensor.tensor.TensorVariable, pytensor.tensor.TensorVariable]
|
|
937
|
+
A tuple containing TensorVariables representing the smoothed states and smoothed state covariances
|
|
938
|
+
obtained from the Kalman smoother.
|
|
939
|
+
"""
|
|
940
|
+
|
|
941
|
+
pymc_model = modelcontext(None)
|
|
942
|
+
with pymc_model:
|
|
943
|
+
*_, T, Z, R, H, Q = matrices
|
|
944
|
+
|
|
945
|
+
smooth_states, smooth_covariances = self.kalman_smoother.build_graph(
|
|
946
|
+
T, R, Q, filtered_states, filtered_covariances, mode=mode, cov_jitter=cov_jitter
|
|
947
|
+
)
|
|
948
|
+
smooth_states.name = "smooth_states"
|
|
949
|
+
smooth_covariances.name = "smooth_covariances"
|
|
950
|
+
|
|
951
|
+
return smooth_states, smooth_covariances
|
|
952
|
+
|
|
953
|
+
def _build_dummy_graph(self) -> None:
|
|
954
|
+
"""
|
|
955
|
+
Build a dummy computation graph for the state space model matrices.
|
|
956
|
+
|
|
957
|
+
This method creates "dummy" pm.Flat variables representing the deep parameters used in the state space model.
|
|
958
|
+
|
|
959
|
+
Returns
|
|
960
|
+
-------
|
|
961
|
+
list[pm.Flat]
|
|
962
|
+
A list of pm.Flat variables representing all parameters estimated by the model.
|
|
963
|
+
"""
|
|
964
|
+
for name in self.param_names:
|
|
965
|
+
pm.Flat(
|
|
966
|
+
name,
|
|
967
|
+
shape=self._name_to_variable[name].type.shape,
|
|
968
|
+
dims=self._fit_dims.get(name, None),
|
|
969
|
+
)
|
|
970
|
+
|
|
971
|
+
def _kalman_filter_outputs_from_dummy_graph(
|
|
972
|
+
self,
|
|
973
|
+
data: pt.TensorLike | None = None,
|
|
974
|
+
data_dims: str | tuple[str] | list[str] | None = None,
|
|
975
|
+
scenario: dict[str, pd.DataFrame] | pd.DataFrame | None = None,
|
|
976
|
+
) -> tuple[list[pt.TensorVariable], list[tuple[pt.TensorVariable, pt.TensorVariable]]]:
|
|
977
|
+
"""
|
|
978
|
+
Builds a Kalman filter graph using "dummy" pm.Flat distributions for the model variables and sorts the returns
|
|
979
|
+
into (mean, covariance) pairs for each of filtered, predicted, and smoothed output.
|
|
980
|
+
|
|
981
|
+
Parameters
|
|
982
|
+
----------
|
|
983
|
+
data: pt.TensorLike, optional
|
|
984
|
+
Observed data on which to condition the model. If not provided, the function will use the data that was
|
|
985
|
+
provided when the model was built.
|
|
986
|
+
data_dims: str or tuple of str, optional
|
|
987
|
+
Dimension names associated with the model data. If None, defaults to ("time", "obs_state")
|
|
988
|
+
|
|
989
|
+
Returns
|
|
990
|
+
-------
|
|
991
|
+
matrices: list of tensors
|
|
992
|
+
Statespace matrices with dummy parameters.
|
|
993
|
+
|
|
994
|
+
grouped_outputs: list of tuple of tensors
|
|
995
|
+
A list of tuples, each containing the mean and covariance of the filtered, predicted, and smoothed states.
|
|
996
|
+
"""
|
|
997
|
+
if scenario is None:
|
|
998
|
+
scenario = dict()
|
|
999
|
+
|
|
1000
|
+
pm_mod = modelcontext(None)
|
|
1001
|
+
self._build_dummy_graph()
|
|
1002
|
+
self._insert_random_variables()
|
|
1003
|
+
|
|
1004
|
+
for name in self.data_names:
|
|
1005
|
+
if name not in pm_mod:
|
|
1006
|
+
pm.Data(**self._exog_data_info[name])
|
|
1007
|
+
|
|
1008
|
+
self._insert_data_variables()
|
|
1009
|
+
|
|
1010
|
+
for name in self.data_names:
|
|
1011
|
+
if name in scenario.keys():
|
|
1012
|
+
pm.set_data({name: scenario[name]})
|
|
1013
|
+
|
|
1014
|
+
x0, P0, c, d, T, Z, R, H, Q = self.unpack_statespace()
|
|
1015
|
+
|
|
1016
|
+
if data is None:
|
|
1017
|
+
data = self._fit_data
|
|
1018
|
+
|
|
1019
|
+
obs_coords = pm_mod.coords.get(OBS_STATE_DIM, None)
|
|
1020
|
+
|
|
1021
|
+
data, nan_mask = register_data_with_pymc(
|
|
1022
|
+
data,
|
|
1023
|
+
n_obs=self.ssm.k_endog,
|
|
1024
|
+
obs_coords=obs_coords,
|
|
1025
|
+
data_dims=data_dims,
|
|
1026
|
+
register_data=True,
|
|
1027
|
+
)
|
|
1028
|
+
|
|
1029
|
+
filter_outputs = self.kalman_filter.build_graph(
|
|
1030
|
+
data,
|
|
1031
|
+
x0,
|
|
1032
|
+
P0,
|
|
1033
|
+
c,
|
|
1034
|
+
d,
|
|
1035
|
+
T,
|
|
1036
|
+
Z,
|
|
1037
|
+
R,
|
|
1038
|
+
H,
|
|
1039
|
+
Q,
|
|
1040
|
+
mode=self._fit_mode,
|
|
1041
|
+
)
|
|
1042
|
+
|
|
1043
|
+
filter_outputs.pop(-1)
|
|
1044
|
+
states, covariances = filter_outputs[:3], filter_outputs[3:]
|
|
1045
|
+
|
|
1046
|
+
filtered_states, predicted_states, _ = states
|
|
1047
|
+
filtered_covariances, predicted_covariances, _ = covariances
|
|
1048
|
+
|
|
1049
|
+
[smoothed_states, smoothed_covariances] = self.kalman_smoother.build_graph(
|
|
1050
|
+
T, R, Q, filtered_states, filtered_covariances, mode=self._fit_mode
|
|
1051
|
+
)
|
|
1052
|
+
|
|
1053
|
+
grouped_outputs = [
|
|
1054
|
+
(filtered_states, filtered_covariances),
|
|
1055
|
+
(predicted_states, predicted_covariances),
|
|
1056
|
+
(smoothed_states, smoothed_covariances),
|
|
1057
|
+
]
|
|
1058
|
+
|
|
1059
|
+
return [x0, P0, c, d, T, Z, R, H, Q], grouped_outputs
|
|
1060
|
+
|
|
1061
|
+
def _sample_conditional(
|
|
1062
|
+
self,
|
|
1063
|
+
idata: InferenceData,
|
|
1064
|
+
group: str,
|
|
1065
|
+
random_seed: RandomState | None = None,
|
|
1066
|
+
data: pt.TensorLike | None = None,
|
|
1067
|
+
**kwargs,
|
|
1068
|
+
):
|
|
1069
|
+
"""
|
|
1070
|
+
Common functionality shared between `sample_conditional_prior` and `sample_conditional_posterior`. See those
|
|
1071
|
+
methods for details.
|
|
1072
|
+
|
|
1073
|
+
Parameters
|
|
1074
|
+
----------
|
|
1075
|
+
idata : InferenceData
|
|
1076
|
+
An Arviz InferenceData object containing the posterior distribution over model parameters.
|
|
1077
|
+
|
|
1078
|
+
group : str
|
|
1079
|
+
InferenceData group from which to draw samples. Should be one of "prior" or "posterior".
|
|
1080
|
+
|
|
1081
|
+
random_seed : int, RandomState or Generator, optional
|
|
1082
|
+
Seed for the random number generator.
|
|
1083
|
+
|
|
1084
|
+
data: pt.TensorLike, optional
|
|
1085
|
+
Observed data on which to condition the model. If not provided, the function will use the data that was
|
|
1086
|
+
provided when the model was built.
|
|
1087
|
+
|
|
1088
|
+
kwargs:
|
|
1089
|
+
Additional keyword arguments are passed to pymc.sample_posterior_predictive
|
|
1090
|
+
|
|
1091
|
+
Returns
|
|
1092
|
+
-------
|
|
1093
|
+
InferenceData
|
|
1094
|
+
An Arviz InferenceData object containing sampled trajectories from the requested conditional distribution,
|
|
1095
|
+
with data variables "filtered_{group}", "predicted_{group}", and "smoothed_{group}".
|
|
1096
|
+
"""
|
|
1097
|
+
if data is None and self._fit_data is None:
|
|
1098
|
+
raise ValueError("No data provided to condition the model")
|
|
1099
|
+
|
|
1100
|
+
_verify_group(group)
|
|
1101
|
+
group_idata = getattr(idata, group)
|
|
1102
|
+
|
|
1103
|
+
with pm.Model(coords=self._fit_coords) as forward_model:
|
|
1104
|
+
(
|
|
1105
|
+
[
|
|
1106
|
+
x0,
|
|
1107
|
+
P0,
|
|
1108
|
+
c,
|
|
1109
|
+
d,
|
|
1110
|
+
T,
|
|
1111
|
+
Z,
|
|
1112
|
+
R,
|
|
1113
|
+
H,
|
|
1114
|
+
Q,
|
|
1115
|
+
],
|
|
1116
|
+
grouped_outputs,
|
|
1117
|
+
) = self._kalman_filter_outputs_from_dummy_graph(data=data)
|
|
1118
|
+
|
|
1119
|
+
for name, (mu, cov) in zip(FILTER_OUTPUT_TYPES, grouped_outputs):
|
|
1120
|
+
dummy_ll = pt.zeros_like(mu)
|
|
1121
|
+
|
|
1122
|
+
state_dims = (
|
|
1123
|
+
(TIME_DIM, ALL_STATE_DIM)
|
|
1124
|
+
if all([dim in self._fit_coords for dim in [TIME_DIM, ALL_STATE_DIM]])
|
|
1125
|
+
else (None, None)
|
|
1126
|
+
)
|
|
1127
|
+
obs_dims = (
|
|
1128
|
+
(TIME_DIM, OBS_STATE_DIM)
|
|
1129
|
+
if all([dim in self._fit_coords for dim in [TIME_DIM, OBS_STATE_DIM]])
|
|
1130
|
+
else (None, None)
|
|
1131
|
+
)
|
|
1132
|
+
|
|
1133
|
+
SequenceMvNormal(
|
|
1134
|
+
f"{name}_{group}",
|
|
1135
|
+
mus=mu,
|
|
1136
|
+
covs=cov,
|
|
1137
|
+
logp=dummy_ll,
|
|
1138
|
+
dims=state_dims,
|
|
1139
|
+
)
|
|
1140
|
+
|
|
1141
|
+
obs_mu = (Z @ mu[..., None]).squeeze(-1)
|
|
1142
|
+
obs_cov = Z @ cov @ pt.swapaxes(Z, -2, -1) + H
|
|
1143
|
+
|
|
1144
|
+
SequenceMvNormal(
|
|
1145
|
+
f"{name}_{group}_observed",
|
|
1146
|
+
mus=obs_mu,
|
|
1147
|
+
covs=obs_cov,
|
|
1148
|
+
logp=dummy_ll,
|
|
1149
|
+
dims=obs_dims,
|
|
1150
|
+
)
|
|
1151
|
+
|
|
1152
|
+
# TODO: Remove this after pm.Flat initial values are fixed
|
|
1153
|
+
forward_model.rvs_to_initial_values = {
|
|
1154
|
+
rv: None for rv in forward_model.rvs_to_initial_values.keys()
|
|
1155
|
+
}
|
|
1156
|
+
|
|
1157
|
+
frozen_model = freeze_dims_and_data(forward_model)
|
|
1158
|
+
with frozen_model:
|
|
1159
|
+
idata_conditional = pm.sample_posterior_predictive(
|
|
1160
|
+
group_idata,
|
|
1161
|
+
var_names=[
|
|
1162
|
+
f"{name}_{group}{suffix}"
|
|
1163
|
+
for name in FILTER_OUTPUT_TYPES
|
|
1164
|
+
for suffix in ["", "_observed"]
|
|
1165
|
+
],
|
|
1166
|
+
compile_kwargs={"mode": get_mode(self._fit_mode)},
|
|
1167
|
+
random_seed=random_seed,
|
|
1168
|
+
**kwargs,
|
|
1169
|
+
)
|
|
1170
|
+
|
|
1171
|
+
return idata_conditional.posterior_predictive
|
|
1172
|
+
|
|
1173
|
+
def _sample_unconditional(
|
|
1174
|
+
self,
|
|
1175
|
+
idata: InferenceData,
|
|
1176
|
+
group: str,
|
|
1177
|
+
steps: int | None = None,
|
|
1178
|
+
use_data_time_dim: bool = False,
|
|
1179
|
+
random_seed: RandomState | None = None,
|
|
1180
|
+
**kwargs,
|
|
1181
|
+
):
|
|
1182
|
+
"""
|
|
1183
|
+
Draw unconditional sample trajectories according to state space dynamics, using random samples from the
|
|
1184
|
+
a provided trace. The state space update equations are:
|
|
1185
|
+
|
|
1186
|
+
X[t+1] = T @ X[t] + R @ eta[t], eta ~ N(0, Q)
|
|
1187
|
+
Y[t] = Z @ X[t] + nu[t], nu ~ N(0, H)
|
|
1188
|
+
x[0] ~ N(a0, P0)
|
|
1189
|
+
|
|
1190
|
+
Parameters
|
|
1191
|
+
----------
|
|
1192
|
+
idata : InferenceData
|
|
1193
|
+
An Arviz InferenceData object with a posterior group containing samples from the
|
|
1194
|
+
posterior distribution over model parameters.
|
|
1195
|
+
|
|
1196
|
+
steps : Optional[int], default=None
|
|
1197
|
+
The number of time steps to sample for the unconditional trajectories. If not provided (None),
|
|
1198
|
+
the function will sample trajectories for the entire available time dimension in the posterior.
|
|
1199
|
+
Otherwise, it will generate trajectories for the specified number of steps.
|
|
1200
|
+
|
|
1201
|
+
use_data_time_dim : bool, default=False
|
|
1202
|
+
If True, the function uses the time dimension present in the provided `idata` object to sample
|
|
1203
|
+
unconditional trajectories. If False, a custom time dimension is created based on the number of steps
|
|
1204
|
+
specified, or if steps is None, it uses the entire available time dimension in the posterior.
|
|
1205
|
+
|
|
1206
|
+
random_seed : int, RandomState or Generator, optional
|
|
1207
|
+
Seed for the random number generator.
|
|
1208
|
+
|
|
1209
|
+
kwargs:
|
|
1210
|
+
Additional keyword arguments are passed to pymc.sample_posterior_predictive
|
|
1211
|
+
|
|
1212
|
+
Returns
|
|
1213
|
+
-------
|
|
1214
|
+
InferenceData
|
|
1215
|
+
An Arviz InfereceData with two groups, posterior_latent and posterior_observed
|
|
1216
|
+
|
|
1217
|
+
- posterior_latent represents the latent state trajectories `X[t]`, which follows the dynamics:
|
|
1218
|
+
`x[t+1] = T @ x[t] + R @ eta[t]`, where `eta ~ N(0, Q)`.
|
|
1219
|
+
|
|
1220
|
+
- posterior_observed represents the observed state trajectories `Y[t]`, which is obtained from
|
|
1221
|
+
the latent state trajectories: `y[t] = Z @ x[t] + nu[t]`, where `nu ~ N(0, H)`.
|
|
1222
|
+
"""
|
|
1223
|
+
_verify_group(group)
|
|
1224
|
+
group_idata = getattr(idata, group)
|
|
1225
|
+
dims = None
|
|
1226
|
+
temp_coords = self._fit_coords.copy()
|
|
1227
|
+
|
|
1228
|
+
if not use_data_time_dim and steps is not None:
|
|
1229
|
+
temp_coords.update({TIME_DIM: np.arange(1 + steps, dtype="int")})
|
|
1230
|
+
steps = len(temp_coords[TIME_DIM]) - 1
|
|
1231
|
+
elif steps is not None:
|
|
1232
|
+
n_dimsteps = len(temp_coords[TIME_DIM])
|
|
1233
|
+
if n_dimsteps != steps:
|
|
1234
|
+
raise ValueError(
|
|
1235
|
+
f"Length of time dimension does not match specified number of steps, expected"
|
|
1236
|
+
f" {n_dimsteps} steps, or steps=None."
|
|
1237
|
+
)
|
|
1238
|
+
else:
|
|
1239
|
+
steps = len(temp_coords[TIME_DIM]) - 1
|
|
1240
|
+
|
|
1241
|
+
if all([dim in self._fit_coords for dim in [TIME_DIM, ALL_STATE_DIM, OBS_STATE_DIM]]):
|
|
1242
|
+
dims = [TIME_DIM, ALL_STATE_DIM, OBS_STATE_DIM]
|
|
1243
|
+
|
|
1244
|
+
with pm.Model(coords=temp_coords if dims is not None else None) as forward_model:
|
|
1245
|
+
self._build_dummy_graph()
|
|
1246
|
+
self._insert_random_variables()
|
|
1247
|
+
|
|
1248
|
+
for name in self.data_names:
|
|
1249
|
+
pm.Data(**self._exog_data_info[name])
|
|
1250
|
+
|
|
1251
|
+
self._insert_data_variables()
|
|
1252
|
+
|
|
1253
|
+
matrices = [x0, P0, c, d, T, Z, R, H, Q] = self.unpack_statespace()
|
|
1254
|
+
|
|
1255
|
+
if not self.measurement_error:
|
|
1256
|
+
H_jittered = pm.Deterministic(
|
|
1257
|
+
"H_jittered", pt.specify_shape(stabilize(H), (self.k_endog, self.k_endog))
|
|
1258
|
+
)
|
|
1259
|
+
matrices = [x0, P0, c, d, T, Z, R, H_jittered, Q]
|
|
1260
|
+
|
|
1261
|
+
LinearGaussianStateSpace(
|
|
1262
|
+
group,
|
|
1263
|
+
*matrices,
|
|
1264
|
+
steps=steps,
|
|
1265
|
+
dims=dims,
|
|
1266
|
+
mode=self._fit_mode,
|
|
1267
|
+
sequence_names=self.kalman_filter.seq_names,
|
|
1268
|
+
k_endog=self.k_endog,
|
|
1269
|
+
)
|
|
1270
|
+
|
|
1271
|
+
# TODO: Remove this after pm.Flat has its initial_value fixed
|
|
1272
|
+
forward_model.rvs_to_initial_values = {
|
|
1273
|
+
rv: None for rv in forward_model.rvs_to_initial_values.keys()
|
|
1274
|
+
}
|
|
1275
|
+
frozen_model = freeze_dims_and_data(forward_model)
|
|
1276
|
+
|
|
1277
|
+
with frozen_model:
|
|
1278
|
+
idata_unconditional = pm.sample_posterior_predictive(
|
|
1279
|
+
group_idata,
|
|
1280
|
+
var_names=[f"{group}_latent", f"{group}_observed"],
|
|
1281
|
+
compile_kwargs={"mode": self._fit_mode},
|
|
1282
|
+
random_seed=random_seed,
|
|
1283
|
+
**kwargs,
|
|
1284
|
+
)
|
|
1285
|
+
|
|
1286
|
+
return idata_unconditional.posterior_predictive
|
|
1287
|
+
|
|
1288
|
+
def sample_conditional_prior(
|
|
1289
|
+
self, idata: InferenceData, random_seed: RandomState | None = None, **kwargs
|
|
1290
|
+
) -> InferenceData:
|
|
1291
|
+
"""
|
|
1292
|
+
Sample from the conditional prior; that is, given parameter draws from the prior distribution,
|
|
1293
|
+
compute Kalman filtered trajectories. Trajectories are drawn from a single multivariate normal with mean and
|
|
1294
|
+
covariance computed via either the Kalman filter, smoother, or predictions.
|
|
1295
|
+
|
|
1296
|
+
Parameters
|
|
1297
|
+
----------
|
|
1298
|
+
idata : InferenceData
|
|
1299
|
+
Arviz InferenceData with prior samples for state space matrices x0, P0, c, d, T, Z, R, H, Q.
|
|
1300
|
+
Obtained from `pm.sample_prior_predictive` after calling PyMCStateSpace.build_statespace_graph().
|
|
1301
|
+
|
|
1302
|
+
random_seed : int, RandomState or Generator, optional
|
|
1303
|
+
Seed for the random number generator.
|
|
1304
|
+
|
|
1305
|
+
kwargs:
|
|
1306
|
+
Additional keyword arguments are passed to pymc.sample_posterior_predictive
|
|
1307
|
+
|
|
1308
|
+
Returns
|
|
1309
|
+
-------
|
|
1310
|
+
InferenceData
|
|
1311
|
+
An Arviz InferenceData object containing sampled trajectories from the conditional prior.
|
|
1312
|
+
The trajectories are stored in the posterior_predictive group with names "filtered_prior",
|
|
1313
|
+
"predicted_prior", and "smoothed_prior".
|
|
1314
|
+
"""
|
|
1315
|
+
|
|
1316
|
+
return self._sample_conditional(idata, "prior", random_seed, **kwargs)
|
|
1317
|
+
|
|
1318
|
+
def sample_conditional_posterior(
|
|
1319
|
+
self, idata: InferenceData, random_seed: RandomState | None = None, **kwargs
|
|
1320
|
+
):
|
|
1321
|
+
"""
|
|
1322
|
+
Sample from the conditional posterior; that is, given parameter draws from the posterior distribution,
|
|
1323
|
+
compute Kalman filtered trajectories. Trajectories are drawn from a single multivariate normal with mean and
|
|
1324
|
+
covariance computed via either the Kalman filter, smoother, or predictions.
|
|
1325
|
+
|
|
1326
|
+
Parameters
|
|
1327
|
+
----------
|
|
1328
|
+
idata : InferenceData
|
|
1329
|
+
An Arviz InferenceData object containing the posterior distribution over model parameters.
|
|
1330
|
+
|
|
1331
|
+
random_seed : int, RandomState or Generator, optional
|
|
1332
|
+
Seed for the random number generator.
|
|
1333
|
+
|
|
1334
|
+
kwargs:
|
|
1335
|
+
Additional keyword arguments are passed to pymc.sample_posterior_predictive
|
|
1336
|
+
|
|
1337
|
+
Returns
|
|
1338
|
+
-------
|
|
1339
|
+
InferenceData
|
|
1340
|
+
An Arviz InferenceData object containing sampled trajectories from the conditional posterior.
|
|
1341
|
+
The trajectories are stored in the posterior_predictive group with names "filtered_posterior",
|
|
1342
|
+
"predicted_posterior", and "smoothed_posterior".
|
|
1343
|
+
"""
|
|
1344
|
+
|
|
1345
|
+
return self._sample_conditional(idata, "posterior", random_seed, **kwargs)
|
|
1346
|
+
|
|
1347
|
+
def sample_unconditional_prior(
|
|
1348
|
+
self,
|
|
1349
|
+
idata: InferenceData,
|
|
1350
|
+
steps: int | None = None,
|
|
1351
|
+
use_data_time_dim: bool = False,
|
|
1352
|
+
random_seed: RandomState | None = None,
|
|
1353
|
+
**kwargs,
|
|
1354
|
+
) -> InferenceData:
|
|
1355
|
+
"""
|
|
1356
|
+
Draw unconditional sample trajectories according to state space dynamics, using random samples from the prior
|
|
1357
|
+
distribution over model parameters. The state space update equations are:
|
|
1358
|
+
|
|
1359
|
+
X[t+1] = T @ X[t] + R @ eta[t], eta ~ N(0, Q)
|
|
1360
|
+
Y[t] = Z @ X[t] + nu[t], nu ~ N(0, H)
|
|
1361
|
+
|
|
1362
|
+
Parameters
|
|
1363
|
+
----------
|
|
1364
|
+
idata: InferenceData
|
|
1365
|
+
Arviz InferenceData with prior samples for state space matrices x0, P0, c, d, T, Z, R, H, Q.
|
|
1366
|
+
Obtained from `pm.sample_prior_predictive` after calling PyMCStateSpace.build_statespace_graph().
|
|
1367
|
+
|
|
1368
|
+
steps : Optional[int], default=None
|
|
1369
|
+
The number of time steps to sample for the unconditional trajectories. If not provided (None),
|
|
1370
|
+
the function will sample trajectories for the entire available time dimension in the posterior.
|
|
1371
|
+
Otherwise, it will generate trajectories for the specified number of steps.
|
|
1372
|
+
|
|
1373
|
+
use_data_time_dim : bool, default=False
|
|
1374
|
+
If True, the function uses the time dimension present in the provided `idata` object to sample
|
|
1375
|
+
unconditional trajectories. If False, a custom time dimension is created based on the number of steps
|
|
1376
|
+
specified, or if steps is None, it uses the entire available time dimension in the posterior.
|
|
1377
|
+
|
|
1378
|
+
random_seed : int, RandomState or Generator, optional
|
|
1379
|
+
Seed for the random number generator.
|
|
1380
|
+
|
|
1381
|
+
kwargs:
|
|
1382
|
+
Additional keyword arguments are passed to pymc.sample_posterior_predictive
|
|
1383
|
+
|
|
1384
|
+
Returns
|
|
1385
|
+
-------
|
|
1386
|
+
InferenceData
|
|
1387
|
+
An Arviz InfereceData with two data variables, prior_latent and prior_observed
|
|
1388
|
+
|
|
1389
|
+
- prior_latent represents the latent state trajectories `X[t]`, which follows the dynamics:
|
|
1390
|
+
`x[t+1] = T @ x[t] + R @ eta[t]`, where `eta ~ N(0, Q)`.
|
|
1391
|
+
|
|
1392
|
+
- prior_observed represents the observed state trajectories `Y[t]`, which is obtained from
|
|
1393
|
+
the observation equation: `y[t] = Z @ x[t] + nu[t]`, where `nu ~ N(0, H)`.
|
|
1394
|
+
"""
|
|
1395
|
+
|
|
1396
|
+
return self._sample_unconditional(
|
|
1397
|
+
idata, "prior", steps, use_data_time_dim, random_seed, **kwargs
|
|
1398
|
+
)
|
|
1399
|
+
|
|
1400
|
+
def sample_unconditional_posterior(
|
|
1401
|
+
self,
|
|
1402
|
+
idata: InferenceData,
|
|
1403
|
+
steps: int | None = None,
|
|
1404
|
+
use_data_time_dim: bool = False,
|
|
1405
|
+
random_seed: RandomState | None = None,
|
|
1406
|
+
**kwargs,
|
|
1407
|
+
) -> InferenceData:
|
|
1408
|
+
"""
|
|
1409
|
+
Draw unconditional sample trajectories according to state space dynamics, using random samples from the
|
|
1410
|
+
posterior distribution over model parameters. The state space update equations are:
|
|
1411
|
+
|
|
1412
|
+
X[t+1] = T @ X[t] + R @ eta[t], eta ~ N(0, Q)
|
|
1413
|
+
Y[t] = Z @ X[t] + nu[t], nu ~ N(0, H)
|
|
1414
|
+
x[0] ~ N(a0, P0)
|
|
1415
|
+
|
|
1416
|
+
Parameters
|
|
1417
|
+
----------
|
|
1418
|
+
idata : InferenceData
|
|
1419
|
+
An Arviz InferenceData object with a posterior group containing samples from the
|
|
1420
|
+
posterior distribution over model parameters.
|
|
1421
|
+
|
|
1422
|
+
steps : Optional[int], default=None
|
|
1423
|
+
The number of time steps to sample for the unconditional trajectories. If not provided (None),
|
|
1424
|
+
the function will sample trajectories for the entire available time dimension in the posterior.
|
|
1425
|
+
Otherwise, it will generate trajectories for the specified number of steps.
|
|
1426
|
+
|
|
1427
|
+
use_data_time_dim : bool, default=False
|
|
1428
|
+
If True, the function uses the time dimension present in the provided `idata` object to sample
|
|
1429
|
+
unconditional trajectories. If False, a custom time dimension is created based on the number of steps
|
|
1430
|
+
specified, or if steps is None, it uses the entire available time dimension in the posterior.
|
|
1431
|
+
|
|
1432
|
+
random_seed : int, RandomState or Generator, optional
|
|
1433
|
+
Seed for the random number generator.
|
|
1434
|
+
|
|
1435
|
+
Returns
|
|
1436
|
+
-------
|
|
1437
|
+
InferenceData
|
|
1438
|
+
An Arviz InfereceData with two groups, posterior_latent and posterior_observed
|
|
1439
|
+
|
|
1440
|
+
- posterior_latent represents the latent state trajectories `X[t]`, which follows the dynamics:
|
|
1441
|
+
`x[t+1] = T @ x[t] + R @ eta[t]`, where `eta ~ N(0, Q)`.
|
|
1442
|
+
|
|
1443
|
+
- posterior_observed represents the observed state trajectories `Y[t]`, which is obtained from
|
|
1444
|
+
the latent state trajectories: `y[t] = Z @ x[t] + nu[t]`, where `nu ~ N(0, H)`.
|
|
1445
|
+
"""
|
|
1446
|
+
|
|
1447
|
+
return self._sample_unconditional(
|
|
1448
|
+
idata, "posterior", steps, use_data_time_dim, random_seed, **kwargs
|
|
1449
|
+
)
|
|
1450
|
+
|
|
1451
|
+
def sample_statespace_matrices(
|
|
1452
|
+
self, idata, matrix_names: str | list[str] | None, group: str = "posterior"
|
|
1453
|
+
):
|
|
1454
|
+
"""
|
|
1455
|
+
Draw samples of requested statespace matrices from provided idata
|
|
1456
|
+
|
|
1457
|
+
Parameters
|
|
1458
|
+
----------
|
|
1459
|
+
matrix_names: str, list[str], optional
|
|
1460
|
+
Statespace matrices to be sampled. Valid names are short names: x0, P0, c, d, T, Z, R, H, Q, or
|
|
1461
|
+
"formal" names: initial_state, initial_state_cov, state_intercept, obs_intercept, transition, design,
|
|
1462
|
+
selection, obs_cov, state_cov
|
|
1463
|
+
idata: az.InferenceData
|
|
1464
|
+
InferenceData from which to sample
|
|
1465
|
+
|
|
1466
|
+
group: str, one of "posterior" or "prior"
|
|
1467
|
+
Whether to sample from priors or posteriors
|
|
1468
|
+
|
|
1469
|
+
Returns
|
|
1470
|
+
-------
|
|
1471
|
+
idata_matrices: az.InterenceData
|
|
1472
|
+
"""
|
|
1473
|
+
_verify_group(group)
|
|
1474
|
+
|
|
1475
|
+
if matrix_names is None:
|
|
1476
|
+
matrix_names = MATRIX_NAMES
|
|
1477
|
+
elif isinstance(matrix_names, str):
|
|
1478
|
+
matrix_names = [matrix_names]
|
|
1479
|
+
|
|
1480
|
+
with pm.Model(coords=self._fit_coords) as forward_model:
|
|
1481
|
+
self._build_dummy_graph()
|
|
1482
|
+
self._insert_random_variables()
|
|
1483
|
+
|
|
1484
|
+
for name in self.data_names:
|
|
1485
|
+
pm.Data(**self._exog_data_info[name])
|
|
1486
|
+
|
|
1487
|
+
self._insert_data_variables()
|
|
1488
|
+
matrices = self.unpack_statespace()
|
|
1489
|
+
for short_name, matrix in zip(MATRIX_NAMES, matrices):
|
|
1490
|
+
long_name = SHORT_NAME_TO_LONG[short_name]
|
|
1491
|
+
if (long_name in matrix_names) or (short_name in matrix_names):
|
|
1492
|
+
name = long_name if long_name in matrix_names else short_name
|
|
1493
|
+
dims = [x if x in self._fit_coords else None for x in MATRIX_DIMS[short_name]]
|
|
1494
|
+
pm.Deterministic(name, matrix, dims=dims)
|
|
1495
|
+
|
|
1496
|
+
# TODO: Remove this after pm.Flat has its initial_value fixed
|
|
1497
|
+
forward_model.rvs_to_initial_values = {
|
|
1498
|
+
rv: None for rv in forward_model.rvs_to_initial_values.keys()
|
|
1499
|
+
}
|
|
1500
|
+
frozen_model = freeze_dims_and_data(forward_model)
|
|
1501
|
+
with frozen_model:
|
|
1502
|
+
matrix_idata = pm.sample_posterior_predictive(
|
|
1503
|
+
idata if group == "posterior" else idata.prior,
|
|
1504
|
+
var_names=matrix_names,
|
|
1505
|
+
compile_kwargs={"mode": self._fit_mode},
|
|
1506
|
+
extend_inferencedata=False,
|
|
1507
|
+
)
|
|
1508
|
+
|
|
1509
|
+
return matrix_idata
|
|
1510
|
+
|
|
1511
|
+
@staticmethod
|
|
1512
|
+
def _validate_forecast_args(
|
|
1513
|
+
time_index: pd.RangeIndex | pd.DatetimeIndex,
|
|
1514
|
+
start: int | pd.Timestamp,
|
|
1515
|
+
periods: int | None = None,
|
|
1516
|
+
end: int | pd.Timestamp = None,
|
|
1517
|
+
scenario: pd.DataFrame | np.ndarray | None = None,
|
|
1518
|
+
use_scenario_index: bool = False,
|
|
1519
|
+
verbose: bool = True,
|
|
1520
|
+
):
|
|
1521
|
+
if isinstance(start, pd.Timestamp) and start not in time_index:
|
|
1522
|
+
raise ValueError("Datetime start must be in the data index used to fit the model.")
|
|
1523
|
+
elif isinstance(start, int):
|
|
1524
|
+
if abs(start) > len(time_index):
|
|
1525
|
+
raise ValueError(
|
|
1526
|
+
"Integer start must be within the range of the data index used to fit the model."
|
|
1527
|
+
)
|
|
1528
|
+
if periods is None and end is None:
|
|
1529
|
+
raise ValueError("Must specify one of either periods or end")
|
|
1530
|
+
if periods is not None and end is not None:
|
|
1531
|
+
raise ValueError("Must specify exactly one of either periods or end")
|
|
1532
|
+
if scenario is None and use_scenario_index:
|
|
1533
|
+
raise ValueError("use_scenario_index=True requires a scenario to be provided.")
|
|
1534
|
+
if scenario is not None and use_scenario_index:
|
|
1535
|
+
if isinstance(scenario, dict):
|
|
1536
|
+
first_df = next(
|
|
1537
|
+
(df for df in scenario.values() if isinstance(df, pd.DataFrame | pd.Series)),
|
|
1538
|
+
None,
|
|
1539
|
+
)
|
|
1540
|
+
if first_df is None:
|
|
1541
|
+
raise ValueError(
|
|
1542
|
+
"use_scenario_index=True requires a scenario to be a DataFrame or Series."
|
|
1543
|
+
)
|
|
1544
|
+
elif not isinstance(scenario, pd.DataFrame | pd.Series):
|
|
1545
|
+
raise ValueError(
|
|
1546
|
+
"use_scenario_index=True requires a scenario to be a DataFrame or Series."
|
|
1547
|
+
)
|
|
1548
|
+
if use_scenario_index and any(arg is not None for arg in [start, end, periods]) and verbose:
|
|
1549
|
+
_log.warning(
|
|
1550
|
+
"start, end, and periods arguments are ignored when use_scenario_index is True. Pass only "
|
|
1551
|
+
"one or the other to avoid this warning, or pass verbose = False."
|
|
1552
|
+
)
|
|
1553
|
+
|
|
1554
|
+
def _get_fit_time_index(self) -> pd.RangeIndex | pd.DatetimeIndex:
|
|
1555
|
+
time_index = self._fit_coords.get(TIME_DIM, None) if self._fit_coords is not None else None
|
|
1556
|
+
if time_index is None:
|
|
1557
|
+
raise ValueError(
|
|
1558
|
+
"No time dimension found on coordinates used to fit the model. Has this model been fit?"
|
|
1559
|
+
)
|
|
1560
|
+
|
|
1561
|
+
if isinstance(time_index[0], pd.Timestamp):
|
|
1562
|
+
time_index = pd.DatetimeIndex(time_index)
|
|
1563
|
+
time_index.freq = time_index.inferred_freq
|
|
1564
|
+
else:
|
|
1565
|
+
time_index = np.array(time_index)
|
|
1566
|
+
|
|
1567
|
+
return time_index
|
|
1568
|
+
|
|
1569
|
+
def _validate_scenario_data(
|
|
1570
|
+
self,
|
|
1571
|
+
scenario: pd.DataFrame | np.ndarray | dict[str, pd.DataFrame | np.ndarray] | None,
|
|
1572
|
+
name: str | None = None,
|
|
1573
|
+
verbose=True,
|
|
1574
|
+
):
|
|
1575
|
+
"""
|
|
1576
|
+
Validate the scenario data provided to the forecast method by checking that it has the correct shape and
|
|
1577
|
+
dimensions.
|
|
1578
|
+
|
|
1579
|
+
Parameters
|
|
1580
|
+
----------
|
|
1581
|
+
scenario
|
|
1582
|
+
name
|
|
1583
|
+
verbose
|
|
1584
|
+
|
|
1585
|
+
Returns
|
|
1586
|
+
-------
|
|
1587
|
+
scenario: pd.DataFrame | np.ndarray | dict[str, pd.DataFrame | np.ndarray]
|
|
1588
|
+
Scenario data, validated and potentially modified.
|
|
1589
|
+
|
|
1590
|
+
"""
|
|
1591
|
+
if not self._needs_exog_data:
|
|
1592
|
+
return scenario
|
|
1593
|
+
|
|
1594
|
+
var_to_dims = {key: info["dims"][1:] for key, info in self.data_info.items()}
|
|
1595
|
+
|
|
1596
|
+
if any(len(dims) > 1 for dims in var_to_dims.values()):
|
|
1597
|
+
raise NotImplementedError(">2d exogenous data is not yet supported.")
|
|
1598
|
+
coords = {
|
|
1599
|
+
var: self._fit_coords[dim[0]]
|
|
1600
|
+
for var, dim in var_to_dims.items()
|
|
1601
|
+
if dim[0] in self._fit_coords
|
|
1602
|
+
}
|
|
1603
|
+
|
|
1604
|
+
if self._needs_exog_data and scenario is None:
|
|
1605
|
+
exog_str = ",".join(self._exog_names)
|
|
1606
|
+
suffix = "s" if len(exog_str) > 1 else ""
|
|
1607
|
+
raise ValueError(
|
|
1608
|
+
f"This model was fit using exogenous data. Forecasting cannot be performed without "
|
|
1609
|
+
f"providing scenario data for the following variable{suffix}: {exog_str}"
|
|
1610
|
+
)
|
|
1611
|
+
|
|
1612
|
+
if isinstance(scenario, dict):
|
|
1613
|
+
for name, data in scenario.items():
|
|
1614
|
+
if name not in self._exog_names:
|
|
1615
|
+
raise ValueError(
|
|
1616
|
+
f"Scenario data provided for variable '{name}', which is not an exogenous variable "
|
|
1617
|
+
f"used to fit the model."
|
|
1618
|
+
)
|
|
1619
|
+
|
|
1620
|
+
# Recursively call this function to trigger the non-dictionary branch of the checks on each object
|
|
1621
|
+
# inside the dictionary
|
|
1622
|
+
scenario[name] = self._validate_scenario_data(data, name)
|
|
1623
|
+
|
|
1624
|
+
# The provided dictionary might be a mix of numpy arrays and dataframes if the user is truly horrible.
|
|
1625
|
+
# For checking shapes, the first object will always be good enough. But we also need to make sure all the
|
|
1626
|
+
# indices agree, so we grab the first dataframe (which might not exist, but that's OK)
|
|
1627
|
+
first_scenario = next(iter(scenario.values()))
|
|
1628
|
+
first_df = next((df for df in scenario.values() if isinstance(df, pd.DataFrame)), None)
|
|
1629
|
+
|
|
1630
|
+
if not all(data.shape[0] == first_scenario.shape[0] for data in scenario.values()):
|
|
1631
|
+
raise ValueError(
|
|
1632
|
+
"Scenario data must have the same number of time steps for all variables."
|
|
1633
|
+
)
|
|
1634
|
+
|
|
1635
|
+
if first_df is not None and not all(
|
|
1636
|
+
df.index.equals(first_df.index)
|
|
1637
|
+
for df in scenario.values()
|
|
1638
|
+
if isinstance(df, pd.DataFrame)
|
|
1639
|
+
):
|
|
1640
|
+
raise ValueError("Scenario data must have the same index for all variables.")
|
|
1641
|
+
|
|
1642
|
+
return scenario
|
|
1643
|
+
|
|
1644
|
+
elif isinstance(scenario, pd.Series | pd.DataFrame | np.ndarray | list | tuple):
|
|
1645
|
+
# A user might be lazy and pass a simple list when there is only one exogenous variable.
|
|
1646
|
+
if isinstance(scenario, list | tuple) or (
|
|
1647
|
+
isinstance(scenario, np.ndarray) and scenario.ndim == 1
|
|
1648
|
+
):
|
|
1649
|
+
scenario = np.array(scenario).reshape(-1, 1)
|
|
1650
|
+
|
|
1651
|
+
if name is None:
|
|
1652
|
+
# name should only be None on the first non-recursive call. We only arrive to this branch in that case
|
|
1653
|
+
# if a non-dictionary was passed, which in turn should only happen if only a single exogenous data
|
|
1654
|
+
# needs to be set.
|
|
1655
|
+
if len(self._exog_names) > 1:
|
|
1656
|
+
raise ValueError(
|
|
1657
|
+
"Multiple exogenous variables were used to fit the model. Provide a dictionary of "
|
|
1658
|
+
"scenario data instead."
|
|
1659
|
+
)
|
|
1660
|
+
name = self._exog_names[0]
|
|
1661
|
+
|
|
1662
|
+
# Omit dataframe from this basic shape check so we can give more detailed information about missing columns
|
|
1663
|
+
# in the next check
|
|
1664
|
+
if not isinstance(scenario, pd.DataFrame | pd.Series) and scenario.shape[1] != len(
|
|
1665
|
+
coords[name]
|
|
1666
|
+
):
|
|
1667
|
+
raise ValueError(
|
|
1668
|
+
f"Scenario data for variable '{name}' has the wrong number of columns. Expected "
|
|
1669
|
+
f"{len(coords[name])}, got {scenario.shape[1]}"
|
|
1670
|
+
)
|
|
1671
|
+
|
|
1672
|
+
if isinstance(scenario, pd.Series):
|
|
1673
|
+
if len(coords[name]) > 1:
|
|
1674
|
+
raise ValueError(
|
|
1675
|
+
f"Scenario data for variable '{name}' has the wrong number of columns. Expected "
|
|
1676
|
+
f"{len(coords[name])}, got 1"
|
|
1677
|
+
)
|
|
1678
|
+
|
|
1679
|
+
if isinstance(scenario, pd.DataFrame):
|
|
1680
|
+
expected_cols = coords[name]
|
|
1681
|
+
cols = scenario.columns
|
|
1682
|
+
missing_columns = sorted(list(set(expected_cols) - set(cols)))
|
|
1683
|
+
if len(missing_columns) > 0:
|
|
1684
|
+
suffix = "s" if len(missing_columns) > 1 else ""
|
|
1685
|
+
raise ValueError(
|
|
1686
|
+
f"Scenario data for variable '{name}' is missing the following column{suffix}: "
|
|
1687
|
+
f"{', '.join(missing_columns)}"
|
|
1688
|
+
)
|
|
1689
|
+
|
|
1690
|
+
extra_columns = sorted(list(set(cols) - set(expected_cols)))
|
|
1691
|
+
if len(extra_columns) > 0:
|
|
1692
|
+
suffix = "s" if len(extra_columns) > 1 else ""
|
|
1693
|
+
verb = "is" if len(extra_columns) == 1 else "are"
|
|
1694
|
+
raise ValueError(
|
|
1695
|
+
f"Scenario data for variable '{name}' contains the following extra column{suffix} "
|
|
1696
|
+
f"that {verb} not used by the model: "
|
|
1697
|
+
f"{', '.join(extra_columns)}"
|
|
1698
|
+
)
|
|
1699
|
+
|
|
1700
|
+
if not (a == b for a, b in zip(expected_cols, cols)) and verbose:
|
|
1701
|
+
_log.warning(
|
|
1702
|
+
f"Scenario data for {name} has a different column order than the data used to fit the "
|
|
1703
|
+
f"model. Columns will be automatically re-ordered. Ensure consistent ordering to avoid "
|
|
1704
|
+
f"silent errors."
|
|
1705
|
+
)
|
|
1706
|
+
scenario = scenario[expected_cols]
|
|
1707
|
+
|
|
1708
|
+
return scenario
|
|
1709
|
+
|
|
1710
|
+
@staticmethod
|
|
1711
|
+
def _build_forecast_index(
|
|
1712
|
+
time_index: pd.RangeIndex | pd.DatetimeIndex,
|
|
1713
|
+
start: int | pd.Timestamp | None = None,
|
|
1714
|
+
end: int | pd.Timestamp = None,
|
|
1715
|
+
periods: int | None = None,
|
|
1716
|
+
use_scenario_index: bool = False,
|
|
1717
|
+
scenario: pd.DataFrame | np.ndarray | None = None,
|
|
1718
|
+
) -> tuple[int | pd.Timestamp, pd.RangeIndex | pd.DatetimeIndex]:
|
|
1719
|
+
"""
|
|
1720
|
+
Construct a pandas Index for the requested forecast horizon.
|
|
1721
|
+
|
|
1722
|
+
Parameters
|
|
1723
|
+
----------
|
|
1724
|
+
time_index: pd.RangeIndex or pd.DatetimeIndex
|
|
1725
|
+
Index of the data used to fit the model
|
|
1726
|
+
start: int or pd.Timestamp, optional
|
|
1727
|
+
Date from which to begin forecasting. If using a datetime index, integer start will be interpreted
|
|
1728
|
+
as a positional index. Otherwise, start must be found inside the time_index
|
|
1729
|
+
end: int or pd.Timestamp, optional
|
|
1730
|
+
Date at which to end forecasting. If using a datetime index, end must be a timestamp.
|
|
1731
|
+
periods: int, optional
|
|
1732
|
+
Number of periods to forecast
|
|
1733
|
+
scenario: pd.DataFrame, np.ndarray, optional
|
|
1734
|
+
Scenario data to use for forecasting. If provided, the index of the scenario data will be used as the
|
|
1735
|
+
forecast index. If provided, start, end, and periods will be ignored.
|
|
1736
|
+
use_scenario_index: bool, default False
|
|
1737
|
+
If True, the index of the scenario data will be used as the forecast index.
|
|
1738
|
+
|
|
1739
|
+
|
|
1740
|
+
Returns
|
|
1741
|
+
-------
|
|
1742
|
+
start: int | pd.TimeStamp
|
|
1743
|
+
The starting date index or time step from which to generate the forecasts.
|
|
1744
|
+
|
|
1745
|
+
forecast_index: pd.DatetimeIndex or pd.RangeIndex
|
|
1746
|
+
Index for the forecast results
|
|
1747
|
+
"""
|
|
1748
|
+
|
|
1749
|
+
def get_or_create_index(x, time_index, start=None):
|
|
1750
|
+
if isinstance(x, pd.DataFrame | pd.Series):
|
|
1751
|
+
return x.index
|
|
1752
|
+
elif isinstance(x, dict):
|
|
1753
|
+
return get_or_create_index(next(iter(x.values())), time_index, start)
|
|
1754
|
+
elif isinstance(x, np.ndarray | list | tuple):
|
|
1755
|
+
if start is None:
|
|
1756
|
+
raise ValueError(
|
|
1757
|
+
"Provided scenario has no index and no start date was provided. This combination "
|
|
1758
|
+
"is ambiguous. Please provide a start date, or add an index to the scenario."
|
|
1759
|
+
)
|
|
1760
|
+
is_datetime_index = isinstance(time_index, pd.DatetimeIndex)
|
|
1761
|
+
n = x.shape[0] if isinstance(x, np.ndarray) else len(x)
|
|
1762
|
+
|
|
1763
|
+
if isinstance(start, int):
|
|
1764
|
+
start = time_index[start]
|
|
1765
|
+
if is_datetime_index:
|
|
1766
|
+
return pd.date_range(start, periods=n, freq=time_index.freq)
|
|
1767
|
+
return pd.RangeIndex(start, n + start, step=1, dtype="int")
|
|
1768
|
+
|
|
1769
|
+
else:
|
|
1770
|
+
raise ValueError(f"{type(x)} is not a valid type for scenario data.")
|
|
1771
|
+
|
|
1772
|
+
x0_idx = None
|
|
1773
|
+
|
|
1774
|
+
if use_scenario_index:
|
|
1775
|
+
forecast_index = get_or_create_index(scenario, time_index, start)
|
|
1776
|
+
is_datetime = isinstance(forecast_index, pd.DatetimeIndex)
|
|
1777
|
+
|
|
1778
|
+
# If the user provided an index, we want to take it as-is (without removing the start value). Instead,
|
|
1779
|
+
# step one back and use this as the start value.
|
|
1780
|
+
delta = forecast_index.freq if is_datetime else 1
|
|
1781
|
+
x0_idx = forecast_index[0] - delta
|
|
1782
|
+
|
|
1783
|
+
else:
|
|
1784
|
+
# Otherwise, build an index. It will be a DateTime index if we have all the necessary information, otherwise
|
|
1785
|
+
# use a range index.
|
|
1786
|
+
is_datetime = isinstance(time_index, pd.DatetimeIndex)
|
|
1787
|
+
forecast_index = None
|
|
1788
|
+
|
|
1789
|
+
if is_datetime:
|
|
1790
|
+
freq = time_index.freq
|
|
1791
|
+
if isinstance(start, int):
|
|
1792
|
+
start = time_index[start]
|
|
1793
|
+
if isinstance(end, int):
|
|
1794
|
+
raise ValueError(
|
|
1795
|
+
"end must be a timestamp if using a datetime index. To specify a number of "
|
|
1796
|
+
"timesteps from the start date, use the periods argument instead."
|
|
1797
|
+
)
|
|
1798
|
+
if end is not None:
|
|
1799
|
+
forecast_index = pd.date_range(start, end=end, freq=freq)
|
|
1800
|
+
if periods is not None:
|
|
1801
|
+
# date_range includes both the start and end date, but we're going to pop off the start later
|
|
1802
|
+
# (it will be interpreted as x0). So we need to add 1 to the periods so the user gets "periods"
|
|
1803
|
+
# number of forecasts back
|
|
1804
|
+
forecast_index = pd.date_range(start, periods=periods + 1, freq=freq)
|
|
1805
|
+
|
|
1806
|
+
else:
|
|
1807
|
+
# If the user provided a positive integer as start, directly interpret it as the start time. If its
|
|
1808
|
+
# negative, interpret it as a positional index.
|
|
1809
|
+
if start < 0:
|
|
1810
|
+
start = time_index[start]
|
|
1811
|
+
if end is not None:
|
|
1812
|
+
forecast_index = pd.RangeIndex(start, end, step=1, dtype="int")
|
|
1813
|
+
if periods is not None:
|
|
1814
|
+
forecast_index = pd.RangeIndex(start, start + periods + 1, step=1, dtype="int")
|
|
1815
|
+
|
|
1816
|
+
if is_datetime:
|
|
1817
|
+
if forecast_index.freq != time_index.freq:
|
|
1818
|
+
raise ValueError(
|
|
1819
|
+
"The frequency of the forecast index must match the frequency on the data used "
|
|
1820
|
+
f"to fit the model. Got {forecast_index.freq}, expected {time_index.freq}"
|
|
1821
|
+
)
|
|
1822
|
+
|
|
1823
|
+
if x0_idx is None:
|
|
1824
|
+
x0_idx, forecast_index = forecast_index[0], forecast_index[1:]
|
|
1825
|
+
if x0_idx in forecast_index:
|
|
1826
|
+
raise ValueError("x0_idx should not be in the forecast index")
|
|
1827
|
+
if x0_idx not in time_index:
|
|
1828
|
+
raise ValueError("start must be in the data index used to fit the model.")
|
|
1829
|
+
|
|
1830
|
+
# The starting value should not be included in the forecast index. It will be used only to define x0 and P0,
|
|
1831
|
+
# and no forecast will be associated with it.
|
|
1832
|
+
return x0_idx, forecast_index
|
|
1833
|
+
|
|
1834
|
+
def _finalize_scenario_initialization(
|
|
1835
|
+
self,
|
|
1836
|
+
scenario: pd.DataFrame | np.ndarray | dict[str, pd.DataFrame | np.ndarray] | None,
|
|
1837
|
+
forecast_index: pd.RangeIndex | pd.DatetimeIndex,
|
|
1838
|
+
name=None,
|
|
1839
|
+
):
|
|
1840
|
+
try:
|
|
1841
|
+
var_to_dims = {key: info["dims"][1:] for key, info in self.data_info.items()}
|
|
1842
|
+
except NotImplementedError:
|
|
1843
|
+
return scenario
|
|
1844
|
+
|
|
1845
|
+
if any(len(dims) > 1 for dims in var_to_dims.values()):
|
|
1846
|
+
raise NotImplementedError(">2d exogenous data is not yet supported.")
|
|
1847
|
+
coords = {
|
|
1848
|
+
var: self._fit_coords[dim[0]]
|
|
1849
|
+
for var, dim in var_to_dims.items()
|
|
1850
|
+
if dim[0] in self._fit_coords
|
|
1851
|
+
}
|
|
1852
|
+
|
|
1853
|
+
if scenario is None:
|
|
1854
|
+
return scenario
|
|
1855
|
+
|
|
1856
|
+
if isinstance(scenario, dict):
|
|
1857
|
+
for name, data in scenario.items():
|
|
1858
|
+
scenario[name] = self._finalize_scenario_initialization(data, forecast_index, name)
|
|
1859
|
+
return scenario
|
|
1860
|
+
|
|
1861
|
+
# This was already checked as valid
|
|
1862
|
+
name = self._exog_names[0] if name is None else name
|
|
1863
|
+
|
|
1864
|
+
# Small tidying up in the case we just have a single scenario that's already a dataframe.
|
|
1865
|
+
if isinstance(scenario, pd.DataFrame | pd.Series):
|
|
1866
|
+
if isinstance(scenario, pd.Series):
|
|
1867
|
+
scenario = scenario.to_frame(name=coords[name][0])
|
|
1868
|
+
if not scenario.index.equals(forecast_index):
|
|
1869
|
+
scenario.index = forecast_index
|
|
1870
|
+
|
|
1871
|
+
# lists and tuples were handled during validation, along with shape check, so just cast arrays to dataframes
|
|
1872
|
+
# with the correct index and columns
|
|
1873
|
+
if isinstance(scenario, np.ndarray):
|
|
1874
|
+
scenario = pd.DataFrame(scenario, index=forecast_index, columns=coords[name])
|
|
1875
|
+
|
|
1876
|
+
return scenario
|
|
1877
|
+
|
|
1878
|
+
def forecast(
|
|
1879
|
+
self,
|
|
1880
|
+
idata: InferenceData,
|
|
1881
|
+
start: int | pd.Timestamp | None = None,
|
|
1882
|
+
periods: int | None = None,
|
|
1883
|
+
end: int | pd.Timestamp = None,
|
|
1884
|
+
scenario: pd.DataFrame | np.ndarray | dict[str, pd.DataFrame | np.ndarray] | None = None,
|
|
1885
|
+
use_scenario_index: bool = False,
|
|
1886
|
+
filter_output="smoothed",
|
|
1887
|
+
random_seed: RandomState | None = None,
|
|
1888
|
+
verbose: bool = True,
|
|
1889
|
+
**kwargs,
|
|
1890
|
+
) -> InferenceData:
|
|
1891
|
+
"""
|
|
1892
|
+
Generate forecasts of state space model trajectories into the future.
|
|
1893
|
+
|
|
1894
|
+
This function combines posterior parameter samples in the provided idata with model dynamics to generate
|
|
1895
|
+
forecasts for out-of-sample data. The trajectory is initialized using the filter output specified in
|
|
1896
|
+
the filter_output argument.
|
|
1897
|
+
|
|
1898
|
+
Parameters
|
|
1899
|
+
----------
|
|
1900
|
+
idata : InferenceData
|
|
1901
|
+
An Arviz InferenceData object containing the posterior distribution over model parameters.
|
|
1902
|
+
|
|
1903
|
+
start : int or pd.Timestamp, optional
|
|
1904
|
+
The starting date index or time step from which to generate the forecasts. If the data provided to
|
|
1905
|
+
`PyMCStateSpace.build_statespace_graph` had a datetime index, `start` should be a datetime.
|
|
1906
|
+
If using integer time series, `start` should be an integer indicating the starting time step. In either
|
|
1907
|
+
case, `start` should be in the data index used to build the statespace graph.
|
|
1908
|
+
|
|
1909
|
+
If start is None, the last value on the data's index will be used.
|
|
1910
|
+
|
|
1911
|
+
periods : int, optional
|
|
1912
|
+
The number of time steps to forecast into the future. If `periods` is specified, the `end`
|
|
1913
|
+
parameter will be ignored. If `None`, then the `end` parameter must be provided.
|
|
1914
|
+
|
|
1915
|
+
end : int or pd.Timestamp, optional
|
|
1916
|
+
The ending date index or time step up to which to generate the forecasts. If the data provided to
|
|
1917
|
+
`PyMCStateSpace.build_statespace_graph` had a datetime index, `start` should be a datetime.
|
|
1918
|
+
If using integer time series, `end` should be an integer indicating the ending time step.
|
|
1919
|
+
If `end` is provided, the `periods` parameter will be ignored.
|
|
1920
|
+
|
|
1921
|
+
scenario: pd.Dataframe or np.ndarray, optional
|
|
1922
|
+
Exogenous variables to use for scenario-based forecasting. Must be a 2d array-like, with second dimension
|
|
1923
|
+
equal to the number of exogenous variables. If start, end, or periods are specified, the first dimension
|
|
1924
|
+
must conform with these settings. Otherwise, the index of the scenario data will be used to set the
|
|
1925
|
+
number of forecast steps. If the index of the forecast scenairo is a pandas DateTimeIndex, its frequency
|
|
1926
|
+
must match the frequency of the data used to fit the model. Otherwise, dates will be based on the number
|
|
1927
|
+
of forecast steps and the data.
|
|
1928
|
+
|
|
1929
|
+
use_scenario_index: bool, default False
|
|
1930
|
+
If True, the index of the scenario data will be used to determine the forecast period. In this case,
|
|
1931
|
+
the start, end, and periods arguments will be ignored. If True, the scenario data must be a DataFrame,
|
|
1932
|
+
otherwise an error will be raised.
|
|
1933
|
+
|
|
1934
|
+
filter_output : str, default="smoothed"
|
|
1935
|
+
The type of Kalman Filter output used to initialize the forecasts. The 0th timestep of the forecast will
|
|
1936
|
+
be sampled from x[0] ~ N(filter_output_mean[start], filter_output_covariance[start]). Default is "smoothed",
|
|
1937
|
+
which uses past and future data to make the best possible hidden state estimate.
|
|
1938
|
+
|
|
1939
|
+
random_seed : int, RandomState or Generator, optional
|
|
1940
|
+
Seed for the random number generator.
|
|
1941
|
+
|
|
1942
|
+
verbose: bool, default=True
|
|
1943
|
+
Whether to print diagnostic information about forecasting.
|
|
1944
|
+
|
|
1945
|
+
kwargs:
|
|
1946
|
+
Additional keyword arguments are passed to pymc.sample_posterior_predictive
|
|
1947
|
+
|
|
1948
|
+
Returns
|
|
1949
|
+
-------
|
|
1950
|
+
InferenceData
|
|
1951
|
+
An Arviz InferenceData object containing forecast samples for the latent and observed state
|
|
1952
|
+
trajectories of the state space model, named "forecast_latent" and "forecast_observed".
|
|
1953
|
+
|
|
1954
|
+
- forecast_latent represents the latent state trajectories `X[t]`, which follows the dynamics:
|
|
1955
|
+
`x[t+1] = T @ x[t] + R @ eta[t]`, where `eta ~ N(0, Q)`.
|
|
1956
|
+
|
|
1957
|
+
- forecast_observed represents the observed state trajectories `Y[t]`, which is obtained from
|
|
1958
|
+
the latent state trajectories: `y[t] = Z @ x[t] + nu[t]`, where `nu ~ N(0, H)`.
|
|
1959
|
+
|
|
1960
|
+
"""
|
|
1961
|
+
filter_time_dim = TIME_DIM
|
|
1962
|
+
|
|
1963
|
+
_validate_filter_arg(filter_output)
|
|
1964
|
+
time_index = self._get_fit_time_index()
|
|
1965
|
+
|
|
1966
|
+
if start is None and verbose:
|
|
1967
|
+
_log.warning(
|
|
1968
|
+
"No start date provided. Using the last date in the data index. To silence this warning, "
|
|
1969
|
+
"explicitly pass a start date or set verbose = False"
|
|
1970
|
+
)
|
|
1971
|
+
start = time_index[-1]
|
|
1972
|
+
|
|
1973
|
+
if self._needs_exog_data and not isinstance(scenario, dict):
|
|
1974
|
+
if len(self.data_names) > 1:
|
|
1975
|
+
raise ValueError(
|
|
1976
|
+
"Model needs more than one exogenous data to do forecasting. In this case, you must "
|
|
1977
|
+
"pass a dictionary of scenario data."
|
|
1978
|
+
)
|
|
1979
|
+
[data_name] = self.data_names
|
|
1980
|
+
scenario = {data_name: scenario}
|
|
1981
|
+
|
|
1982
|
+
scenario: dict = self._validate_scenario_data(scenario, verbose=verbose)
|
|
1983
|
+
|
|
1984
|
+
self._validate_forecast_args(
|
|
1985
|
+
time_index=time_index,
|
|
1986
|
+
start=start,
|
|
1987
|
+
end=end,
|
|
1988
|
+
periods=periods,
|
|
1989
|
+
scenario=scenario,
|
|
1990
|
+
use_scenario_index=use_scenario_index,
|
|
1991
|
+
verbose=verbose,
|
|
1992
|
+
)
|
|
1993
|
+
|
|
1994
|
+
t0, forecast_index = self._build_forecast_index(
|
|
1995
|
+
time_index=time_index,
|
|
1996
|
+
start=start,
|
|
1997
|
+
end=end,
|
|
1998
|
+
periods=periods,
|
|
1999
|
+
scenario=scenario,
|
|
2000
|
+
use_scenario_index=use_scenario_index,
|
|
2001
|
+
)
|
|
2002
|
+
scenario = self._finalize_scenario_initialization(scenario, forecast_index)
|
|
2003
|
+
temp_coords = self._fit_coords.copy()
|
|
2004
|
+
|
|
2005
|
+
dims = None
|
|
2006
|
+
if all([dim in temp_coords for dim in [filter_time_dim, ALL_STATE_DIM, OBS_STATE_DIM]]):
|
|
2007
|
+
dims = [TIME_DIM, ALL_STATE_DIM, OBS_STATE_DIM]
|
|
2008
|
+
|
|
2009
|
+
t0_idx = np.flatnonzero(time_index == t0)[0]
|
|
2010
|
+
|
|
2011
|
+
temp_coords["data_time"] = time_index
|
|
2012
|
+
temp_coords[TIME_DIM] = forecast_index
|
|
2013
|
+
|
|
2014
|
+
mu_dims, cov_dims = None, None
|
|
2015
|
+
if all([dim in self._fit_coords for dim in [TIME_DIM, ALL_STATE_DIM, ALL_STATE_AUX_DIM]]):
|
|
2016
|
+
mu_dims = ["data_time", ALL_STATE_DIM]
|
|
2017
|
+
cov_dims = ["data_time", ALL_STATE_DIM, ALL_STATE_AUX_DIM]
|
|
2018
|
+
|
|
2019
|
+
with pm.Model(coords=temp_coords) as forecast_model:
|
|
2020
|
+
(_, _, *matrices), grouped_outputs = self._kalman_filter_outputs_from_dummy_graph(
|
|
2021
|
+
data_dims=["data_time", OBS_STATE_DIM],
|
|
2022
|
+
)
|
|
2023
|
+
|
|
2024
|
+
group_idx = FILTER_OUTPUT_TYPES.index(filter_output)
|
|
2025
|
+
mu, cov = grouped_outputs[group_idx]
|
|
2026
|
+
|
|
2027
|
+
x0 = pm.Deterministic(
|
|
2028
|
+
"x0_slice", mu[t0_idx], dims=mu_dims[1:] if mu_dims is not None else None
|
|
2029
|
+
)
|
|
2030
|
+
P0 = pm.Deterministic(
|
|
2031
|
+
"P0_slice", cov[t0_idx], dims=cov_dims[1:] if cov_dims is not None else None
|
|
2032
|
+
)
|
|
2033
|
+
|
|
2034
|
+
if scenario is not None:
|
|
2035
|
+
sub_dict = {
|
|
2036
|
+
forecast_model[data_name]: pt.as_tensor_variable(
|
|
2037
|
+
scenario.get(data_name), name=data_name
|
|
2038
|
+
)
|
|
2039
|
+
for data_name in self.data_names
|
|
2040
|
+
}
|
|
2041
|
+
|
|
2042
|
+
matrices = graph_replace(matrices, replace=sub_dict, strict=True)
|
|
2043
|
+
[setattr(matrix, "name", name) for name, matrix in zip(MATRIX_NAMES[2:], matrices)]
|
|
2044
|
+
|
|
2045
|
+
_ = LinearGaussianStateSpace(
|
|
2046
|
+
"forecast",
|
|
2047
|
+
x0,
|
|
2048
|
+
P0,
|
|
2049
|
+
*matrices,
|
|
2050
|
+
steps=len(forecast_index),
|
|
2051
|
+
dims=dims,
|
|
2052
|
+
mode=self._fit_mode,
|
|
2053
|
+
sequence_names=self.kalman_filter.seq_names,
|
|
2054
|
+
k_endog=self.k_endog,
|
|
2055
|
+
append_x0=False,
|
|
2056
|
+
)
|
|
2057
|
+
|
|
2058
|
+
forecast_model.rvs_to_initial_values = {
|
|
2059
|
+
k: None for k in forecast_model.rvs_to_initial_values.keys()
|
|
2060
|
+
}
|
|
2061
|
+
frozen_model = freeze_dims_and_data(forecast_model)
|
|
2062
|
+
|
|
2063
|
+
with frozen_model:
|
|
2064
|
+
idata_forecast = pm.sample_posterior_predictive(
|
|
2065
|
+
idata,
|
|
2066
|
+
var_names=["forecast_latent", "forecast_observed"],
|
|
2067
|
+
compile_kwargs={"mode": self._fit_mode},
|
|
2068
|
+
random_seed=random_seed,
|
|
2069
|
+
**kwargs,
|
|
2070
|
+
)
|
|
2071
|
+
|
|
2072
|
+
return idata_forecast.posterior_predictive
|
|
2073
|
+
|
|
2074
|
+
def impulse_response_function(
|
|
2075
|
+
self,
|
|
2076
|
+
idata,
|
|
2077
|
+
n_steps: int = 40,
|
|
2078
|
+
use_posterior_cov: bool = True,
|
|
2079
|
+
shock_size: float | np.ndarray | None = None,
|
|
2080
|
+
shock_cov: np.ndarray | None = None,
|
|
2081
|
+
shock_trajectory: np.ndarray | None = None,
|
|
2082
|
+
orthogonalize_shocks: bool = False,
|
|
2083
|
+
random_seed: RandomState | None = None,
|
|
2084
|
+
**kwargs,
|
|
2085
|
+
):
|
|
2086
|
+
"""
|
|
2087
|
+
Generate impulse response functions (IRF) from state space model dynamics.
|
|
2088
|
+
|
|
2089
|
+
An impulse response function represents the dynamic response of the state space model
|
|
2090
|
+
to an instantaneous shock applied to the system. This function calculates the IRF
|
|
2091
|
+
based on either provided shock specifications or the posterior state covariance matrix.
|
|
2092
|
+
|
|
2093
|
+
Parameters
|
|
2094
|
+
----------
|
|
2095
|
+
idata : az.InferenceData
|
|
2096
|
+
An Arviz InferenceData object containing the posterior distribution over model parameters.
|
|
2097
|
+
|
|
2098
|
+
n_steps: int
|
|
2099
|
+
The number of time steps to calculate the impulse response. Default is 40.
|
|
2100
|
+
|
|
2101
|
+
If `shock_trajectory` is provided, the length of the shock trajectory will override this value.
|
|
2102
|
+
|
|
2103
|
+
use_posterior_cov: bool, default=True
|
|
2104
|
+
Whether to use the covariance matrix of the posterior distribution to generate the impulse response.
|
|
2105
|
+
|
|
2106
|
+
Only one of `use_posterior_cov`, `shock_cov`, `shock_size`, or `shock_trajectory` can be specified.
|
|
2107
|
+
|
|
2108
|
+
shock_size : Optional[Union[float, np.ndarray]], default=None
|
|
2109
|
+
The size of the shock applied to the system. If specified, it will create a covariance
|
|
2110
|
+
matrix for the shock with diagonal elements equal to `shock_size`. If float, the diagonal will be filled
|
|
2111
|
+
with `shock_size`. If an array, `shock_size` must match the number of shocks in the state space model.
|
|
2112
|
+
|
|
2113
|
+
Only one of `use_posterior_cov`, `shock_cov`, `shock_size`, or `shock_trajectory` can be specified.
|
|
2114
|
+
|
|
2115
|
+
shock_cov : Optional[np.ndarray], default=None
|
|
2116
|
+
A user-specified covariance matrix for the shocks. It should be a 2D numpy array with
|
|
2117
|
+
dimensions (n_shocks, n_shocks), where n_shocks is the number of shocks in the state space model.
|
|
2118
|
+
|
|
2119
|
+
Only one of `use_posterior_cov`, `shock_cov`, `shock_size`, or `shock_trajectory` can be specified.
|
|
2120
|
+
|
|
2121
|
+
shock_trajectory : Optional[np.ndarray], default=None
|
|
2122
|
+
A pre-defined trajectory of shocks applied to the system. It should be a 2D numpy array
|
|
2123
|
+
with dimensions (n, n_shocks), where n is the number of time steps and k_posdef is the
|
|
2124
|
+
number of shocks in the state space model.
|
|
2125
|
+
|
|
2126
|
+
Only one of `use_posterior_cov`, `shock_cov`, `shock_size`, or `shock_trajectory` can be specified.
|
|
2127
|
+
|
|
2128
|
+
orthogonalize_shocks : bool, default=False
|
|
2129
|
+
If True, orthogonalize the shocks using Cholesky decomposition when generating the impulse
|
|
2130
|
+
response. This option is ignored if `shock_trajectory` or `shock_size` are used.
|
|
2131
|
+
|
|
2132
|
+
random_seed : int, RandomState or Generator, optional
|
|
2133
|
+
Seed for the random number generator.
|
|
2134
|
+
|
|
2135
|
+
kwargs:
|
|
2136
|
+
Additional keyword arguments are passed to pymc.sample_posterior_predictive
|
|
2137
|
+
|
|
2138
|
+
Returns
|
|
2139
|
+
-------
|
|
2140
|
+
pm.InferenceData
|
|
2141
|
+
An Arviz InferenceData object containing impulse response function in a variable named "irf".
|
|
2142
|
+
"""
|
|
2143
|
+
options = [shock_size, shock_cov, shock_trajectory]
|
|
2144
|
+
n_options = sum(x is not None for x in options)
|
|
2145
|
+
Q = None # No covariance matrix needed if a trajectory is provided. Will be overwritten later if needed.
|
|
2146
|
+
|
|
2147
|
+
if n_options > 1:
|
|
2148
|
+
raise ValueError("Specify exactly 0 or 1 of shock_size, shock_cov, or shock_trajectory")
|
|
2149
|
+
elif n_options == 1:
|
|
2150
|
+
# If the user passed an alternative parameterization for the shocks of the IRF, don't use the posterior
|
|
2151
|
+
use_posterior_cov = False
|
|
2152
|
+
|
|
2153
|
+
if shock_trajectory is not None:
|
|
2154
|
+
# Validate the shock trajectory
|
|
2155
|
+
n, k = shock_trajectory.shape
|
|
2156
|
+
steps = n
|
|
2157
|
+
|
|
2158
|
+
if k != self.k_posdef:
|
|
2159
|
+
raise ValueError(
|
|
2160
|
+
"If shock_trajectory is provided, there must be a trajectory provided for each shock. "
|
|
2161
|
+
f"Model has {self.k_posdef} shocks, but shock_trajectory has only {k} columns"
|
|
2162
|
+
)
|
|
2163
|
+
if steps is not None and steps != n:
|
|
2164
|
+
_log.warning(
|
|
2165
|
+
"Both steps and shock_trajectory were provided but do not agree. Length of "
|
|
2166
|
+
"shock_trajectory will take priority, and steps will be ignored."
|
|
2167
|
+
)
|
|
2168
|
+
n_steps = n # Overwrite steps with the length of the shock trajectory
|
|
2169
|
+
shock_trajectory = pt.as_tensor_variable(shock_trajectory)
|
|
2170
|
+
|
|
2171
|
+
simulation_coords = self._fit_coords.copy()
|
|
2172
|
+
simulation_coords[TIME_DIM] = np.arange(n_steps, dtype="int")
|
|
2173
|
+
|
|
2174
|
+
with pm.Model(coords=simulation_coords):
|
|
2175
|
+
self._build_dummy_graph()
|
|
2176
|
+
self._insert_random_variables()
|
|
2177
|
+
|
|
2178
|
+
P0, _, c, d, T, Z, R, H, post_Q = self.unpack_statespace()
|
|
2179
|
+
x0 = pm.Deterministic("x0_new", pt.zeros(self.k_states), dims=[ALL_STATE_DIM])
|
|
2180
|
+
|
|
2181
|
+
if use_posterior_cov:
|
|
2182
|
+
Q = post_Q
|
|
2183
|
+
if orthogonalize_shocks:
|
|
2184
|
+
Q = pt.linalg.cholesky(Q) / pt.diag(Q)
|
|
2185
|
+
elif shock_cov is not None:
|
|
2186
|
+
Q = pt.as_tensor_variable(shock_cov)
|
|
2187
|
+
if orthogonalize_shocks:
|
|
2188
|
+
Q = pt.linalg.cholesky(Q) / pt.diag(Q)
|
|
2189
|
+
|
|
2190
|
+
if shock_trajectory is None:
|
|
2191
|
+
shock_trajectory = pt.zeros((n_steps, self.k_posdef))
|
|
2192
|
+
if Q is not None:
|
|
2193
|
+
init_shock = MvNormalSVD("initial_shock", mu=0, cov=Q, dims=[SHOCK_DIM])
|
|
2194
|
+
else:
|
|
2195
|
+
init_shock = pm.Deterministic(
|
|
2196
|
+
"initial_shock",
|
|
2197
|
+
pt.as_tensor_variable(np.atleast_1d(shock_size)),
|
|
2198
|
+
dims=[SHOCK_DIM],
|
|
2199
|
+
)
|
|
2200
|
+
shock_trajectory = pt.set_subtensor(shock_trajectory[0], init_shock)
|
|
2201
|
+
|
|
2202
|
+
else:
|
|
2203
|
+
shock_trajectory = pt.as_tensor_variable(shock_trajectory)
|
|
2204
|
+
|
|
2205
|
+
def irf_step(shock, x, c, T, R):
|
|
2206
|
+
next_x = c + T @ x + R @ shock
|
|
2207
|
+
return next_x
|
|
2208
|
+
|
|
2209
|
+
irf, updates = pytensor.scan(
|
|
2210
|
+
irf_step,
|
|
2211
|
+
sequences=[shock_trajectory],
|
|
2212
|
+
outputs_info=[x0],
|
|
2213
|
+
non_sequences=[c, T, R],
|
|
2214
|
+
n_steps=n_steps,
|
|
2215
|
+
strict=True,
|
|
2216
|
+
mode=self._fit_mode,
|
|
2217
|
+
)
|
|
2218
|
+
|
|
2219
|
+
pm.Deterministic("irf", irf, dims=[TIME_DIM, ALL_STATE_DIM])
|
|
2220
|
+
|
|
2221
|
+
compile_kwargs = kwargs.get("compile_kwargs", {})
|
|
2222
|
+
if "mode" not in compile_kwargs.keys():
|
|
2223
|
+
compile_kwargs = {"mode": self._fit_mode}
|
|
2224
|
+
else:
|
|
2225
|
+
mode = compile_kwargs.get("mode")
|
|
2226
|
+
if mode is not None and mode != self._fit_mode:
|
|
2227
|
+
raise ValueError(
|
|
2228
|
+
f"User provided compile mode ({mode}) does not match the compile mode used to "
|
|
2229
|
+
f"construct the model ({self._fit_mode})."
|
|
2230
|
+
)
|
|
2231
|
+
|
|
2232
|
+
compile_kwargs.update({"mode": self._fit_mode})
|
|
2233
|
+
|
|
2234
|
+
irf_idata = pm.sample_posterior_predictive(
|
|
2235
|
+
idata,
|
|
2236
|
+
var_names=["irf"],
|
|
2237
|
+
compile_kwargs=compile_kwargs,
|
|
2238
|
+
random_seed=random_seed,
|
|
2239
|
+
**kwargs,
|
|
2240
|
+
)
|
|
2241
|
+
|
|
2242
|
+
return irf_idata.posterior_predictive
|
|
2243
|
+
|
|
2244
|
+
def _sort_obs_inputs_by_time_varying(self, d, Z):
|
|
2245
|
+
seqs = []
|
|
2246
|
+
non_seqs = []
|
|
2247
|
+
|
|
2248
|
+
for matrix, name in zip([d, Z], ["d", "Z"]):
|
|
2249
|
+
if name in self.kalman_filter.seq_names:
|
|
2250
|
+
seqs.append(matrix)
|
|
2251
|
+
else:
|
|
2252
|
+
non_seqs.append(matrix)
|
|
2253
|
+
|
|
2254
|
+
return seqs, non_seqs
|
|
2255
|
+
|
|
2256
|
+
@staticmethod
|
|
2257
|
+
def _sort_obs_scan_args(args):
|
|
2258
|
+
args = list(args)
|
|
2259
|
+
|
|
2260
|
+
# If a matrix is time-varying, pytensor will put a [t] on the name
|
|
2261
|
+
arg_names = [x.name.replace("[t]", "") for x in args]
|
|
2262
|
+
ordered_args = []
|
|
2263
|
+
|
|
2264
|
+
for name in ["d", "Z"]:
|
|
2265
|
+
idx = arg_names.index(name)
|
|
2266
|
+
ordered_args.append(args[idx])
|
|
2267
|
+
|
|
2268
|
+
return ordered_args
|