"""
State Space Representation
Author: Chad Fulton
License: Simplified-BSD
"""
import numpy as np
from .tools import (
find_best_blas_type, validate_matrix_shape, validate_vector_shape
)
from .initialization import Initialization
from . import tools
class OptionWrapper(object):
def __init__(self, mask_attribute, mask_value):
# Name of the class-level bitmask attribute
self.mask_attribute = mask_attribute
# Value of this option
self.mask_value = mask_value
def __get__(self, obj, objtype):
# Return True / False based on whether the bit is set in the bitmask
return bool(getattr(obj, self.mask_attribute, 0) & self.mask_value)
def __set__(self, obj, value):
mask_attribute_value = getattr(obj, self.mask_attribute, 0)
if bool(value):
value = mask_attribute_value | self.mask_value
else:
value = mask_attribute_value & ~self.mask_value
setattr(obj, self.mask_attribute, value)
class MatrixWrapper(object):
def __init__(self, name, attribute):
self.name = name
self.attribute = attribute
self._attribute = '_' + attribute
def __get__(self, obj, objtype):
matrix = getattr(obj, self._attribute, None)
# # Remove last dimension if the array is not actually time-varying
# if matrix is not None and matrix.shape[-1] == 1:
# return np.squeeze(matrix, -1)
return matrix
def __set__(self, obj, value):
value = np.asarray(value, order="F")
shape = obj.shapes[self.attribute]
if len(shape) == 3:
value = self._set_matrix(obj, value, shape)
else:
value = self._set_vector(obj, value, shape)
setattr(obj, self._attribute, value)
obj.shapes[self.attribute] = value.shape
def _set_matrix(self, obj, value, shape):
# Expand 1-dimensional array if possible
if (value.ndim == 1 and shape[0] == 1 and
value.shape[0] == shape[1]):
value = value[None, :]
# Enforce that the matrix is appropriate size
validate_matrix_shape(
self.name, value.shape, shape[0], shape[1], obj.nobs
)
# Expand time-invariant matrix
if value.ndim == 2:
value = np.array(value[:, :, None], order="F")
return value
def _set_vector(self, obj, value, shape):
# Enforce that the vector has appropriate length
validate_vector_shape(
self.name, value.shape, shape[0], obj.nobs
)
# Expand the time-invariant vector
if value.ndim == 1:
value = np.array(value[:, None], order="F")
return value
class Representation(object):
r"""
State space representation of a time series process
Parameters
----------
k_endog : {array_like, int}
The observed time-series process :math:`y` if array like or the
number of variables in the process if an integer.
k_states : int
The dimension of the unobserved state process.
k_posdef : int, optional
The dimension of a guaranteed positive definite covariance matrix
describing the shocks in the measurement equation. Must be less than
or equal to `k_states`. Default is `k_states`.
initial_variance : float, optional
Initial variance used when approximate diffuse initialization is
specified. Default is 1e6.
initialization : Initialization object or str, optional
Initialization method for the initial state. If a string, must be one
of {'diffuse', 'approximate_diffuse', 'stationary', 'known'}.
initial_state : array_like, optional
If `initialization='known'` is used, the mean of the initial state's
distribution.
initial_state_cov : array_like, optional
If `initialization='known'` is used, the covariance matrix of the
initial state's distribution.
nobs : int, optional
If an endogenous vector is not given (i.e. `k_endog` is an integer),
the number of observations can optionally be specified. If not
specified, they will be set to zero until data is bound to the model.
dtype : np.dtype, optional
If an endogenous vector is not given (i.e. `k_endog` is an integer),
the default datatype of the state space matrices can optionally be
specified. Default is `np.float64`.
design : array_like, optional
The design matrix, :math:`Z`. Default is set to zeros.
obs_intercept : array_like, optional
The intercept for the observation equation, :math:`d`. Default is set
to zeros.
obs_cov : array_like, optional
The covariance matrix for the observation equation :math:`H`. Default
is set to zeros.
transition : array_like, optional
The transition matrix, :math:`T`. Default is set to zeros.
state_intercept : array_like, optional
The intercept for the transition equation, :math:`c`. Default is set to
zeros.
selection : array_like, optional
The selection matrix, :math:`R`. Default is set to zeros.
state_cov : array_like, optional
The covariance matrix for the state equation :math:`Q`. Default is set
to zeros.
**kwargs
Additional keyword arguments. Not used directly. It is present to
improve compatibility with subclasses, so that they can use `**kwargs`
to specify any default state space matrices (e.g. `design`) without
having to clean out any other keyword arguments they might have been
passed.
Attributes
----------
nobs : int
The number of observations.
k_endog : int
The dimension of the observation series.
k_states : int
The dimension of the unobserved state process.
k_posdef : int
The dimension of a guaranteed positive
definite covariance matrix describing
the shocks in the measurement equation.
shapes : dictionary of name:tuple
A dictionary recording the initial shapes
of each of the representation matrices as
tuples.
initialization : str
Kalman filter initialization method. Default is unset.
initial_variance : float
Initial variance for approximate diffuse
initialization. Default is 1e6.
Notes
-----
A general state space model is of the form
.. math::
y_t & = Z_t \alpha_t + d_t + \varepsilon_t \\
\alpha_t & = T_t \alpha_{t-1} + c_t + R_t \eta_t \\
where :math:`y_t` refers to the observation vector at time :math:`t`,
:math:`\alpha_t` refers to the (unobserved) state vector at time
:math:`t`, and where the irregular components are defined as
.. math::
\varepsilon_t \sim N(0, H_t) \\
\eta_t \sim N(0, Q_t) \\
The remaining variables (:math:`Z_t, d_t, H_t, T_t, c_t, R_t, Q_t`) in the
equations are matrices describing the process. Their variable names and
dimensions are as follows
Z : `design` :math:`(k\_endog \times k\_states \times nobs)`
d : `obs_intercept` :math:`(k\_endog \times nobs)`
H : `obs_cov` :math:`(k\_endog \times k\_endog \times nobs)`
T : `transition` :math:`(k\_states \times k\_states \times nobs)`
c : `state_intercept` :math:`(k\_states \times nobs)`
R : `selection` :math:`(k\_states \times k\_posdef \times nobs)`
Q : `state_cov` :math:`(k\_posdef \times k\_posdef \times nobs)`
In the case that one of the matrices is time-invariant (so that, for
example, :math:`Z_t = Z_{t+1} ~ \forall ~ t`), its last dimension may
be of size :math:`1` rather than size `nobs`.
References
----------
.. [*] Durbin, James, and Siem Jan Koopman. 2012.
Time Series Analysis by State Space Methods: Second Edition.
Oxford University Press.
"""
endog = None
r"""
(array) The observation vector, alias for `obs`.
"""
design = MatrixWrapper('design', 'design')
r"""
(array) Design matrix: :math:`Z~(k\_endog \times k\_states \times nobs)`
"""
obs_intercept = MatrixWrapper('observation intercept', 'obs_intercept')
r"""
(array) Observation intercept: :math:`d~(k\_endog \times nobs)`
"""
obs_cov = MatrixWrapper('observation covariance matrix', 'obs_cov')
r"""
(array) Observation covariance matrix:
:math:`H~(k\_endog \times k\_endog \times nobs)`
"""
transition = MatrixWrapper('transition', 'transition')
r"""
(array) Transition matrix:
:math:`T~(k\_states \times k\_states \times nobs)`
"""
state_intercept = MatrixWrapper('state intercept', 'state_intercept')
r"""
(array) State intercept: :math:`c~(k\_states \times nobs)`
"""
selection = MatrixWrapper('selection', 'selection')
r"""
(array) Selection matrix:
:math:`R~(k\_states \times k\_posdef \times nobs)`
"""
state_cov = MatrixWrapper('state covariance matrix', 'state_cov')
r"""
(array) State covariance matrix:
:math:`Q~(k\_posdef \times k\_posdef \times nobs)`
"""
def __init__(self, k_endog, k_states, k_posdef=None,
initial_variance=1e6, nobs=0, dtype=np.float64,
design=None, obs_intercept=None, obs_cov=None,
transition=None, state_intercept=None, selection=None,
state_cov=None, statespace_classes=None, **kwargs):
self.shapes = {}
# Check if k_endog is actually the endog array
endog = None
if isinstance(k_endog, np.ndarray):
endog = k_endog
# If so, assume that it is either column-ordered and in wide format
# or row-ordered and in long format
if (endog.flags['C_CONTIGUOUS'] and
(endog.shape[0] > 1 or nobs == 1)):
endog = endog.T
k_endog = endog.shape[0]
# Endogenous array, dimensions, dtype
self.k_endog = k_endog
if k_endog < 1:
raise ValueError('Number of endogenous variables in statespace'
' model must be a positive number.')
self.nobs = nobs
# Get dimensions from transition equation
if k_states < 1:
raise ValueError('Number of states in statespace model must be a'
' positive number.')
self.k_states = k_states
self.k_posdef = k_posdef if k_posdef is not None else k_states
# Make sure k_posdef <= k_states
# TODO: we could technically allow k_posdef > k_states, but the Cython
# code needs to be more thoroughly checked to avoid seg faults.
if self.k_posdef > self.k_states:
raise ValueError('Dimension of state innovation `k_posdef` cannot'
' be larger than the dimension of the state.')
# Bind endog, if it was given
if endog is not None:
self.bind(endog)
# Record the shapes of all of our matrices
# Note: these are time-invariant shapes; in practice the last dimension
# may also be `self.nobs` for any or all of these.
self.shapes = {
'obs': (self.k_endog, self.nobs),
'design': (self.k_endog, self.k_states, 1),
'obs_intercept': (self.k_endog, 1),
'obs_cov': (self.k_endog, self.k_endog, 1),
'transition': (self.k_states, self.k_states, 1),
'state_intercept': (self.k_states, 1),
'selection': (self.k_states, self.k_posdef, 1),
'state_cov': (self.k_posdef, self.k_posdef, 1),
}
# Representation matrices
# These matrices are only used in the Python object as containers,
# which will be copied to the appropriate _statespace object if a
# filter is called.
scope = locals()
for name, shape in self.shapes.items():
if name == 'obs':
continue
# Create the initial storage array for each matrix
setattr(self, '_' + name, np.zeros(shape, dtype=dtype, order="F"))
# If we were given an initial value for the matrix, set it
# (notice it is being set via the descriptor)
if scope[name] is not None:
setattr(self, name, scope[name])
# Options
self.initial_variance = initial_variance
self.prefix_statespace_map = (statespace_classes
if statespace_classes is not None
else tools.prefix_statespace_map.copy())
# State-space initialization data
self.initialization = kwargs.get('initialization', None)
basic_inits = ['diffuse', 'approximate_diffuse', 'stationary']
if self.initialization in basic_inits:
self.initialize(self.initialization)
elif self.initialization == 'known':
if 'constant' in kwargs:
constant = kwargs['constant']
elif 'initial_state' in kwargs:
# TODO deprecation warning
constant = kwargs['initial_state']
else:
raise ValueError('Initial state must be provided when "known"'
' is the specified initialization method.')
if 'stationary_cov' in kwargs:
stationary_cov = kwargs['stationary_cov']
elif 'initial_state_cov' in kwargs:
# TODO deprecation warning
stationary_cov = kwargs['initial_state_cov']
else:
raise ValueError('Initial state covariance matrix must be'
' provided when "known" is the specified'
' initialization method.')
self.initialize('known', constant=constant,
stationary_cov=stationary_cov)
elif (not isinstance(self.initialization, Initialization) and
self.initialization is not None):
raise ValueError("Invalid state space initialization method.")
# Matrix representations storage
self._representations = {}
# Setup the underlying statespace object storage
self._statespaces = {}
# Caches
self._time_invariant = None
def __getitem__(self, key):
_type = type(key)
# If only a string is given then we must be getting an entire matrix
if _type is str:
if key not in self.shapes:
raise IndexError('"%s" is an invalid state space matrix name'
% key)
matrix = getattr(self, '_' + key)
# See note on time-varying arrays, below
if matrix.shape[-1] == 1:
return matrix[(slice(None),)*(matrix.ndim-1) + (0,)]
else:
return matrix
# Otherwise if we have a tuple, we want a slice of a matrix
elif _type is tuple:
name, slice_ = key[0], key[1:]
if name not in self.shapes:
raise IndexError('"%s" is an invalid state space matrix name'
% name)
matrix = getattr(self, '_' + name)
# Since the model can support time-varying arrays, but often we
# will instead have time-invariant arrays, we want to allow setting
# a matrix slice like mod['transition',0,:] even though technically
# it should be mod['transition',0,:,0]. Thus if the array in
# question is time-invariant but the last slice was excluded,
# add it in as a zero.
if matrix.shape[-1] == 1 and len(slice_) <= matrix.ndim-1:
slice_ = slice_ + (0,)
return matrix[slice_]
# Otherwise, we have only a single slice index, but it is not a string
else:
raise IndexError('First index must the name of a valid state space'
' matrix.')
def __setitem__(self, key, value):
_type = type(key)
# If only a string is given then we must be setting an entire matrix
if _type is str:
if key not in self.shapes:
raise IndexError('"%s" is an invalid state space matrix name'
% key)
setattr(self, key, value)
# If it's a tuple (with a string as the first element) then we must be
# setting a slice of a matrix
elif _type is tuple:
name, slice_ = key[0], key[1:]
if name not in self.shapes:
raise IndexError('"%s" is an invalid state space matrix name'
% key[0])
# Change the dtype of the corresponding matrix
dtype = np.array(value).dtype
matrix = getattr(self, '_' + name)
valid_types = ['f', 'd', 'F', 'D']
if not matrix.dtype == dtype and dtype.char in valid_types:
matrix = getattr(self, '_' + name).real.astype(dtype)
# Since the model can support time-varying arrays, but often we
# will instead have time-invariant arrays, we want to allow setting
# a matrix slice like mod['transition',0,:] even though technically
# it should be mod['transition',0,:,0]. Thus if the array in
# question is time-invariant but the last slice was excluded,
# add it in as a zero.
if matrix.shape[-1] == 1 and len(slice_) == matrix.ndim-1:
slice_ = slice_ + (0,)
# Set the new value
matrix[slice_] = value
setattr(self, name, matrix)
# Otherwise we got a single non-string key, (e.g. mod[:]), which is
# invalid
else:
raise IndexError('First index must the name of a valid state space'
' matrix.')
def _clone_kwargs(self, endog, **kwargs):
"""
Construct keyword arguments for cloning a state space model
Parameters
----------
endog : array_like
An observed time-series process :math:`y`.
**kwargs
Keyword arguments to pass to the new state space representation
model constructor. Those that are not specified are copied from
the specification of the current state space model.
"""
# We always need the base dimensions, but they cannot change from
# the base model when cloning (the idea is: if these need to change,
# need to make a new instance manually, since it's not really cloning).
kwargs['nobs'] = len(endog)
kwargs['k_endog'] = self.k_endog
for key in ['k_states', 'k_posdef']:
val = getattr(self, key)
if key not in kwargs or kwargs[key] is None:
kwargs[key] = val
if kwargs[key] != val:
raise ValueError('Cannot change the dimension of %s when'
' cloning.' % key)
# Get defaults for time-invariant system matrices, if not otherwise
# provided
# Time-varying matrices must be replaced.
for name in self.shapes.keys():
if name == 'obs':
continue
if name not in kwargs:
mat = getattr(self, name)
if mat.shape[-1] != 1:
raise ValueError('The `%s` matrix is time-varying. Cloning'
' this model requires specifying an'
' updated matrix.' % name)
kwargs[name] = mat
# Default is to use the same initialization
kwargs.setdefault('initialization', self.initialization)
return kwargs
def clone(self, endog, **kwargs):
"""
Clone a state space representation while overriding some elements
Parameters
----------
endog : array_like
An observed time-series process :math:`y`.
**kwargs
Keyword arguments to pass to the new state space representation
model constructor. Those that are not specified are copied from
the specification of the current state space model.
Returns
-------
Representation
Notes
-----
If some system matrices are time-varying, then new time-varying
matrices *must* be provided.
"""
kwargs = self._clone_kwargs(endog, **kwargs)
mod = self.__class__(**kwargs)
mod.bind(endog)
return mod
def extend(self, endog, start=None, end=None, **kwargs):
"""
Extend the current state space model, or a specific (time) subset
Parameters
----------
endog : array_like
An observed time-series process :math:`y`.
start : int, optional
The first period of a time-varying state space model to include in
the new model. Has no effect if the state space model is
time-invariant. Default is the initial period.
end : int, optional
The last period of a time-varying state space model to include in
the new model. Has no effect if the state space model is
time-invariant. Default is the final period.
**kwargs
Keyword arguments to pass to the new state space representation
model constructor. Those that are not specified are copied from
the specification of the current state space model.
Returns
-------
Representation
Notes
-----
This method does not allow replacing a time-varying system matrix with
a time-invariant one (or vice-versa). If that is required, use `clone`.
"""
endog = np.atleast_1d(endog)
if endog.ndim == 1:
endog = endog[:, np.newaxis]
nobs = len(endog)
if start is None:
start = 0
if end is None:
end = self.nobs
if start < 0:
start = self.nobs + start
if end < 0:
end = self.nobs + end
if start > self.nobs:
raise ValueError('The `start` argument of the extension within the'
' base model cannot be after the end of the'
' base model.')
if end > self.nobs:
raise ValueError('The `end` argument of the extension within the'
' base model cannot be after the end of the'
' base model.')
if start > end:
raise ValueError('The `start` argument of the extension within the'
' base model cannot be after the `end` argument.')
# Note: if start == end or if end < self.nobs, then we're just cloning
# (no extension)
endog = tools.concat([self.endog[:, start:end].T, endog])
# Extend any time-varying arrays
error_ti = ('Model has time-invariant %s matrix, so cannot provide'
' an extended matrix.')
error_tv = ('Model has time-varying %s matrix, so an updated'
' time-varying matrix for the extension period'
' is required.')
for name, shape in self.shapes.items():
if name == 'obs':
continue
mat = getattr(self, name)
# If we were *not* given an extended value for this matrix...
if name not in kwargs:
# If this is a time-varying matrix in the existing model
if mat.shape[-1] > 1:
# If we have an extension period, then raise an error
# because we should have been given an extended value
if end + nobs > self.nobs:
raise ValueError(error_tv % name)
# If we do not have an extension period, then set the new
# time-varying matrix to be the portion of the existing
# time-varying matrix that corresponds to the period of
# interest
else:
kwargs[name] = mat[..., start:end + nobs]
elif nobs == 0:
raise ValueError('Extension is being performed within-sample'
' so cannot provide an extended matrix')
# If we were given an extended value for this matrix
else:
# TODO: Need to add a check for ndim, and if the matrix has
# one fewer dimensions than the existing matrix, add a new axis
# If this is a time-invariant matrix in the existing model,
# raise an error
if mat.shape[-1] == 1 and self.nobs > 1:
raise ValueError(error_ti % name)
# Otherwise, validate the shape of the given extended value
updated_mat = np.asarray(kwargs[name])
if len(shape) == 2:
validate_vector_shape(name, updated_mat.shape,
shape[0], nobs)
else:
validate_matrix_shape(name, updated_mat.shape,
shape[0], shape[1], nobs)
if updated_mat.shape[-1] != nobs:
raise ValueError(error_tv % name)
# Concatenate to get the new time-varying matrix
kwargs[name] = np.c_[mat[..., start:end], updated_mat]
return self.clone(endog, **kwargs)
@property
def prefix(self):
"""
(str) BLAS prefix of currently active representation matrices
"""
arrays = (
self._design, self._obs_intercept, self._obs_cov,
self._transition, self._state_intercept, self._selection,
self._state_cov
)
if self.endog is not None:
arrays = (self.endog,) + arrays
return find_best_blas_type(arrays)[0]
@property
def dtype(self):
"""
(dtype) Datatype of currently active representation matrices
"""
return tools.prefix_dtype_map[self.prefix]
@property
def time_invariant(self):
"""
(bool) Whether or not currently active representation matrices are
time-invariant
"""
if self._time_invariant is None:
return (
self._design.shape[2] == self._obs_intercept.shape[1] ==
self._obs_cov.shape[2] == self._transition.shape[2] ==
self._state_intercept.shape[1] == self._selection.shape[2] ==
self._state_cov.shape[2]
)
else:
return self._time_invariant
@property
def _statespace(self):
prefix = self.prefix
if prefix in self._statespaces:
return self._statespaces[prefix]
return None
@property
def obs(self):
r"""
(array) Observation vector: :math:`y~(k\_endog \times nobs)`
"""
return self.endog
def bind(self, endog):
"""
Bind data to the statespace representation
Parameters
----------
endog : ndarray
Endogenous data to bind to the model. Must be column-ordered
ndarray with shape (`k_endog`, `nobs`) or row-ordered ndarray with
shape (`nobs`, `k_endog`).
Notes
-----
The strict requirements arise because the underlying statespace and
Kalman filtering classes require Fortran-ordered arrays in the wide
format (shaped (`k_endog`, `nobs`)), and this structure is setup to
prevent copying arrays in memory.
By default, numpy arrays are row (C)-ordered and most time series are
represented in the long format (with time on the 0-th axis). In this
case, no copying or re-ordering needs to be performed, instead the
array can simply be transposed to get it in the right order and shape.
Although this class (Representation) has stringent `bind` requirements,
it is assumed that it will rarely be used directly.
"""
if not isinstance(endog, np.ndarray):
raise ValueError("Invalid endogenous array; must be an ndarray.")
# Make sure we have a 2-dimensional array
# Note: reshaping a 1-dim array into a 2-dim array by changing the
# shape tuple always results in a row (C)-ordered array, so it
# must be shaped (nobs, k_endog)
if endog.ndim == 1:
# In the case of nobs x 0 arrays
if self.k_endog == 1:
endog.shape = (endog.shape[0], 1)
# In the case of k_endog x 0 arrays
else:
endog.shape = (1, endog.shape[0])
if not endog.ndim == 2:
raise ValueError('Invalid endogenous array provided; must be'
' 2-dimensional.')
# Check for valid column-ordered arrays
if endog.flags['F_CONTIGUOUS'] and endog.shape[0] == self.k_endog:
pass
# Check for valid row-ordered arrays, and transpose them to be the
# correct column-ordered array
elif endog.flags['C_CONTIGUOUS'] and endog.shape[1] == self.k_endog:
endog = endog.T
# Invalid column-ordered arrays
elif endog.flags['F_CONTIGUOUS']:
raise ValueError('Invalid endogenous array; column-ordered'
' arrays must have first axis shape of'
' `k_endog`.')
# Invalid row-ordered arrays
elif endog.flags['C_CONTIGUOUS']:
raise ValueError('Invalid endogenous array; row-ordered'
' arrays must have last axis shape of'
' `k_endog`.')
# Non-contiguous arrays
else:
raise ValueError('Invalid endogenous array; must be ordered in'
' contiguous memory.')
# In some corner cases (e.g. np.array(1., ndmin=2) with numpy < 1.8)
# we may still have a non-fortran contiguous array, so double-check
# that now
if not endog.flags['F_CONTIGUOUS']:
endog = np.asfortranarray(endog)
# Set a flag for complex data
self._complex_endog = np.iscomplexobj(endog)
# Set the data
self.endog = endog
self.nobs = self.endog.shape[1]
# Reset shapes
if hasattr(self, 'shapes'):
self.shapes['obs'] = self.endog.shape
def initialize(self, initialization, approximate_diffuse_variance=None,
constant=None, stationary_cov=None):
"""Create an Initialization object if necessary"""
if initialization == 'known':
initialization = Initialization(self.k_states, 'known',
constant=constant,
stationary_cov=stationary_cov)
elif initialization == 'approximate_diffuse':
if approximate_diffuse_variance is None:
approximate_diffuse_variance = self.initial_variance
initialization = Initialization(
self.k_states, 'approximate_diffuse',
approximate_diffuse_variance=approximate_diffuse_variance)
elif initialization == 'stationary':
initialization = Initialization(self.k_states, 'stationary')
elif initialization == 'diffuse':
initialization = Initialization(self.k_states, 'diffuse')
# We must have an initialization object at this point
if not isinstance(initialization, Initialization):
raise ValueError("Invalid state space initialization method.")
self.initialization = initialization
def initialize_known(self, constant, stationary_cov):
"""
Initialize the statespace model with known distribution for initial
state.
These values are assumed to be known with certainty or else
filled with parameters during, for example, maximum likelihood
estimation.
Parameters
----------
constant : array_like
Known mean of the initial state vector.
stationary_cov : array_like
Known covariance matrix of the initial state vector.
"""
constant = np.asarray(constant, order="F")
stationary_cov = np.asarray(stationary_cov, order="F")
if not constant.shape == (self.k_states,):
raise ValueError('Invalid dimensions for constant state vector.'
' Requires shape (%d,), got %s' %
(self.k_states, str(constant.shape)))
if not stationary_cov.shape == (self.k_states, self.k_states):
raise ValueError('Invalid dimensions for stationary covariance'
' matrix. Requires shape (%d,%d), got %s' %
(self.k_states, self.k_states,
str(stationary_cov.shape)))
self.initialize('known', constant=constant,
stationary_cov=stationary_cov)
def initialize_approximate_diffuse(self, variance=None):
"""
Initialize the statespace model with approximate diffuse values.
Rather than following the exact diffuse treatment (which is developed
for the case that the variance becomes infinitely large), this assigns
an arbitrary large number for the variance.
Parameters
----------
variance : float, optional
The variance for approximating diffuse initial conditions. Default
is 1e6.
"""
if variance is None:
variance = self.initial_variance
self.initialize('approximate_diffuse',
approximate_diffuse_variance=variance)
def initialize_stationary(self):
"""
Initialize the statespace model as stationary.
"""
self.initialize('stationary')
def initialize_diffuse(self):
"""
Initialize the statespace model as stationary.
"""
self.initialize('diffuse')
def _initialize_representation(self, prefix=None):
if prefix is None:
prefix = self.prefix
dtype = tools.prefix_dtype_map[prefix]
# If the dtype-specific representation matrices do not exist, create
# them
if prefix not in self._representations:
# Copy the statespace representation matrices
self._representations[prefix] = {}
for matrix in self.shapes.keys():
if matrix == 'obs':
self._representations[prefix][matrix] = (
self.obs.astype(dtype)
)
else:
# Note: this always makes a copy
self._representations[prefix][matrix] = (
getattr(self, '_' + matrix).astype(dtype)
)
# If they do exist, update them
else:
for matrix in self.shapes.keys():
existing = self._representations[prefix][matrix]
if matrix == 'obs':
# existing[:] = self.obs.astype(dtype)
pass
else:
new = getattr(self, '_' + matrix).astype(dtype)
if existing.shape == new.shape:
existing[:] = new[:]
else:
self._representations[prefix][matrix] = new
# Determine if we need to (re-)create the _statespace models
# (if time-varying matrices changed)
if prefix in self._statespaces:
ss = self._statespaces[prefix]
create = (
not ss.obs.shape[1] == self.endog.shape[1] or
not ss.design.shape[2] == self.design.shape[2] or
not ss.obs_intercept.shape[1] == self.obs_intercept.shape[1] or
not ss.obs_cov.shape[2] == self.obs_cov.shape[2] or
not ss.transition.shape[2] == self.transition.shape[2] or
not (ss.state_intercept.shape[1] ==
self.state_intercept.shape[1]) or
not ss.selection.shape[2] == self.selection.shape[2] or
not ss.state_cov.shape[2] == self.state_cov.shape[2]
)
else:
create = True
# (re-)create if necessary
if create:
if prefix in self._statespaces:
del self._statespaces[prefix]
# Setup the base statespace object
cls = self.prefix_statespace_map[prefix]
self._statespaces[prefix] = cls(
self._representations[prefix]['obs'],
self._representations[prefix]['design'],
self._representations[prefix]['obs_intercept'],
self._representations[prefix]['obs_cov'],
self._representations[prefix]['transition'],
self._representations[prefix]['state_intercept'],
self._representations[prefix]['selection'],
self._representations[prefix]['state_cov']
)
return prefix, dtype, create
def _initialize_state(self, prefix=None, complex_step=False):
# TODO once the transition to using the Initialization objects is
# complete, this should be moved entirely to the _{{prefix}}Statespace
# object.
if prefix is None:
prefix = self.prefix
# (Re-)initialize the statespace model
if isinstance(self.initialization, Initialization):
if not self.initialization.initialized:
raise RuntimeError('Initialization is incomplete.')
self._statespaces[prefix].initialize(self.initialization,
complex_step=complex_step)
else:
raise RuntimeError('Statespace model not initialized.')
class FrozenRepresentation(object):
"""
Frozen Statespace Model
Takes a snapshot of a Statespace model.
Parameters
----------
model : Representation
A Statespace representation
Attributes
----------
nobs : int
Number of observations.
k_endog : int
The dimension of the observation series.
k_states : int
The dimension of the unobserved state process.
k_posdef : int
The dimension of a guaranteed positive definite
covariance matrix describing the shocks in the
measurement equation.
dtype : dtype
Datatype of representation matrices
prefix : str
BLAS prefix of representation matrices
shapes : dictionary of name:tuple
A dictionary recording the shapes of each of
the representation matrices as tuples.
endog : ndarray
The observation vector.
design : ndarray
The design matrix, :math:`Z`.
obs_intercept : ndarray
The intercept for the observation equation, :math:`d`.
obs_cov : ndarray
The covariance matrix for the observation equation :math:`H`.
transition : ndarray
The transition matrix, :math:`T`.
state_intercept : ndarray
The intercept for the transition equation, :math:`c`.
selection : ndarray
The selection matrix, :math:`R`.
state_cov : ndarray
The covariance matrix for the state equation :math:`Q`.
missing : array of bool
An array of the same size as `endog`, filled
with boolean values that are True if the
corresponding entry in `endog` is NaN and False
otherwise.
nmissing : array of int
An array of size `nobs`, where the ith entry
is the number (between 0 and `k_endog`) of NaNs in
the ith row of the `endog` array.
time_invariant : bool
Whether or not the representation matrices are time-invariant
initialization : Initialization object
Kalman filter initialization method.
initial_state : array_like
The state vector used to initialize the Kalamn filter.
initial_state_cov : array_like
The state covariance matrix used to initialize the Kalamn filter.
"""
_model_attributes = [
'model', 'prefix', 'dtype', 'nobs', 'k_endog', 'k_states',
'k_posdef', 'time_invariant', 'endog', 'design', 'obs_intercept',
'obs_cov', 'transition', 'state_intercept', 'selection',
'state_cov', 'missing', 'nmissing', 'shapes', 'initialization',
'initial_state', 'initial_state_cov', 'initial_variance'
]
_attributes = _model_attributes
def __init__(self, model):
# Initialize all attributes to None
for name in self._attributes:
setattr(self, name, None)
# Update the representation attributes
self.update_representation(model)
def update_representation(self, model):
"""Update model Representation"""
# Model
self.model = model
# Data type
self.prefix = model.prefix
self.dtype = model.dtype
# Copy the model dimensions
self.nobs = model.nobs
self.k_endog = model.k_endog
self.k_states = model.k_states
self.k_posdef = model.k_posdef
self.time_invariant = model.time_invariant
# Save the state space representation at the time
self.endog = model.endog
self.design = model._design.copy()
self.obs_intercept = model._obs_intercept.copy()
self.obs_cov = model._obs_cov.copy()
self.transition = model._transition.copy()
self.state_intercept = model._state_intercept.copy()
self.selection = model._selection.copy()
self.state_cov = model._state_cov.copy()
self.missing = np.array(model._statespaces[self.prefix].missing,
copy=True)
self.nmissing = np.array(model._statespaces[self.prefix].nmissing,
copy=True)
# Save the final shapes of the matrices
self.shapes = dict(model.shapes)
for name in self.shapes.keys():
if name == 'obs':
continue
self.shapes[name] = getattr(self, name).shape
self.shapes['obs'] = self.endog.shape
# Save the state space initialization
self.initialization = model.initialization
if model.initialization is not None:
model._initialize_state()
self.initial_state = np.array(
model._statespaces[self.prefix].initial_state, copy=True)
self.initial_state_cov = np.array(
model._statespaces[self.prefix].initial_state_cov, copy=True)
self.initial_diffuse_state_cov = np.array(
model._statespaces[self.prefix].initial_diffuse_state_cov,
copy=True)