peacock-data-public-datasets-idc-cronscript
/
venv
/lib
/python3.10
/site-packages
/scipy
/stats
/_multivariate.py
# | |
# Author: Joris Vankerschaver 2013 | |
# | |
import math | |
import numpy as np | |
import scipy.linalg | |
from scipy._lib import doccer | |
from scipy.special import (gammaln, psi, multigammaln, xlogy, entr, betaln, | |
ive, loggamma) | |
from scipy._lib._util import check_random_state, _lazywhere | |
from scipy.linalg.blas import drot, get_blas_funcs | |
from ._continuous_distns import norm | |
from ._discrete_distns import binom | |
from . import _mvn, _covariance, _rcont | |
from ._qmvnt import _qmvt | |
from ._morestats import directional_stats | |
from scipy.optimize import root_scalar | |
__all__ = ['multivariate_normal', | |
'matrix_normal', | |
'dirichlet', | |
'dirichlet_multinomial', | |
'wishart', | |
'invwishart', | |
'multinomial', | |
'special_ortho_group', | |
'ortho_group', | |
'random_correlation', | |
'unitary_group', | |
'multivariate_t', | |
'multivariate_hypergeom', | |
'random_table', | |
'uniform_direction', | |
'vonmises_fisher'] | |
_LOG_2PI = np.log(2 * np.pi) | |
_LOG_2 = np.log(2) | |
_LOG_PI = np.log(np.pi) | |
_doc_random_state = """\ | |
seed : {None, int, np.random.RandomState, np.random.Generator}, optional | |
Used for drawing random variates. | |
If `seed` is `None`, the `~np.random.RandomState` singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, seeded | |
with seed. | |
If `seed` is already a ``RandomState`` or ``Generator`` instance, | |
then that object is used. | |
Default is `None`. | |
""" | |
def _squeeze_output(out): | |
""" | |
Remove single-dimensional entries from array and convert to scalar, | |
if necessary. | |
""" | |
out = out.squeeze() | |
if out.ndim == 0: | |
out = out[()] | |
return out | |
def _eigvalsh_to_eps(spectrum, cond=None, rcond=None): | |
"""Determine which eigenvalues are "small" given the spectrum. | |
This is for compatibility across various linear algebra functions | |
that should agree about whether or not a Hermitian matrix is numerically | |
singular and what is its numerical matrix rank. | |
This is designed to be compatible with scipy.linalg.pinvh. | |
Parameters | |
---------- | |
spectrum : 1d ndarray | |
Array of eigenvalues of a Hermitian matrix. | |
cond, rcond : float, optional | |
Cutoff for small eigenvalues. | |
Singular values smaller than rcond * largest_eigenvalue are | |
considered zero. | |
If None or -1, suitable machine precision is used. | |
Returns | |
------- | |
eps : float | |
Magnitude cutoff for numerical negligibility. | |
""" | |
if rcond is not None: | |
cond = rcond | |
if cond in [None, -1]: | |
t = spectrum.dtype.char.lower() | |
factor = {'f': 1E3, 'd': 1E6} | |
cond = factor[t] * np.finfo(t).eps | |
eps = cond * np.max(abs(spectrum)) | |
return eps | |
def _pinv_1d(v, eps=1e-5): | |
"""A helper function for computing the pseudoinverse. | |
Parameters | |
---------- | |
v : iterable of numbers | |
This may be thought of as a vector of eigenvalues or singular values. | |
eps : float | |
Values with magnitude no greater than eps are considered negligible. | |
Returns | |
------- | |
v_pinv : 1d float ndarray | |
A vector of pseudo-inverted numbers. | |
""" | |
return np.array([0 if abs(x) <= eps else 1/x for x in v], dtype=float) | |
class _PSD: | |
""" | |
Compute coordinated functions of a symmetric positive semidefinite matrix. | |
This class addresses two issues. Firstly it allows the pseudoinverse, | |
the logarithm of the pseudo-determinant, and the rank of the matrix | |
to be computed using one call to eigh instead of three. | |
Secondly it allows these functions to be computed in a way | |
that gives mutually compatible results. | |
All of the functions are computed with a common understanding as to | |
which of the eigenvalues are to be considered negligibly small. | |
The functions are designed to coordinate with scipy.linalg.pinvh() | |
but not necessarily with np.linalg.det() or with np.linalg.matrix_rank(). | |
Parameters | |
---------- | |
M : array_like | |
Symmetric positive semidefinite matrix (2-D). | |
cond, rcond : float, optional | |
Cutoff for small eigenvalues. | |
Singular values smaller than rcond * largest_eigenvalue are | |
considered zero. | |
If None or -1, suitable machine precision is used. | |
lower : bool, optional | |
Whether the pertinent array data is taken from the lower | |
or upper triangle of M. (Default: lower) | |
check_finite : bool, optional | |
Whether to check that the input matrices contain only finite | |
numbers. Disabling may give a performance gain, but may result | |
in problems (crashes, non-termination) if the inputs do contain | |
infinities or NaNs. | |
allow_singular : bool, optional | |
Whether to allow a singular matrix. (Default: True) | |
Notes | |
----- | |
The arguments are similar to those of scipy.linalg.pinvh(). | |
""" | |
def __init__(self, M, cond=None, rcond=None, lower=True, | |
check_finite=True, allow_singular=True): | |
self._M = np.asarray(M) | |
# Compute the symmetric eigendecomposition. | |
# Note that eigh takes care of array conversion, chkfinite, | |
# and assertion that the matrix is square. | |
s, u = scipy.linalg.eigh(M, lower=lower, check_finite=check_finite) | |
eps = _eigvalsh_to_eps(s, cond, rcond) | |
if np.min(s) < -eps: | |
msg = "The input matrix must be symmetric positive semidefinite." | |
raise ValueError(msg) | |
d = s[s > eps] | |
if len(d) < len(s) and not allow_singular: | |
msg = ("When `allow_singular is False`, the input matrix must be " | |
"symmetric positive definite.") | |
raise np.linalg.LinAlgError(msg) | |
s_pinv = _pinv_1d(s, eps) | |
U = np.multiply(u, np.sqrt(s_pinv)) | |
# Save the eigenvector basis, and tolerance for testing support | |
self.eps = 1e3*eps | |
self.V = u[:, s <= eps] | |
# Initialize the eagerly precomputed attributes. | |
self.rank = len(d) | |
self.U = U | |
self.log_pdet = np.sum(np.log(d)) | |
# Initialize attributes to be lazily computed. | |
self._pinv = None | |
def _support_mask(self, x): | |
""" | |
Check whether x lies in the support of the distribution. | |
""" | |
residual = np.linalg.norm(x @ self.V, axis=-1) | |
in_support = residual < self.eps | |
return in_support | |
def pinv(self): | |
if self._pinv is None: | |
self._pinv = np.dot(self.U, self.U.T) | |
return self._pinv | |
class multi_rv_generic: | |
""" | |
Class which encapsulates common functionality between all multivariate | |
distributions. | |
""" | |
def __init__(self, seed=None): | |
super().__init__() | |
self._random_state = check_random_state(seed) | |
def random_state(self): | |
""" Get or set the Generator object for generating random variates. | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance then | |
that instance is used. | |
""" | |
return self._random_state | |
def random_state(self, seed): | |
self._random_state = check_random_state(seed) | |
def _get_random_state(self, random_state): | |
if random_state is not None: | |
return check_random_state(random_state) | |
else: | |
return self._random_state | |
class multi_rv_frozen: | |
""" | |
Class which encapsulates common functionality between all frozen | |
multivariate distributions. | |
""" | |
def random_state(self): | |
return self._dist._random_state | |
def random_state(self, seed): | |
self._dist._random_state = check_random_state(seed) | |
_mvn_doc_default_callparams = """\ | |
mean : array_like, default: ``[0]`` | |
Mean of the distribution. | |
cov : array_like or `Covariance`, default: ``[1]`` | |
Symmetric positive (semi)definite covariance matrix of the distribution. | |
allow_singular : bool, default: ``False`` | |
Whether to allow a singular covariance matrix. This is ignored if `cov` is | |
a `Covariance` object. | |
""" | |
_mvn_doc_callparams_note = """\ | |
Setting the parameter `mean` to `None` is equivalent to having `mean` | |
be the zero-vector. The parameter `cov` can be a scalar, in which case | |
the covariance matrix is the identity times that value, a vector of | |
diagonal entries for the covariance matrix, a two-dimensional array_like, | |
or a `Covariance` object. | |
""" | |
_mvn_doc_frozen_callparams = "" | |
_mvn_doc_frozen_callparams_note = """\ | |
See class definition for a detailed description of parameters.""" | |
mvn_docdict_params = { | |
'_mvn_doc_default_callparams': _mvn_doc_default_callparams, | |
'_mvn_doc_callparams_note': _mvn_doc_callparams_note, | |
'_doc_random_state': _doc_random_state | |
} | |
mvn_docdict_noparams = { | |
'_mvn_doc_default_callparams': _mvn_doc_frozen_callparams, | |
'_mvn_doc_callparams_note': _mvn_doc_frozen_callparams_note, | |
'_doc_random_state': _doc_random_state | |
} | |
class multivariate_normal_gen(multi_rv_generic): | |
r"""A multivariate normal random variable. | |
The `mean` keyword specifies the mean. The `cov` keyword specifies the | |
covariance matrix. | |
Methods | |
------- | |
pdf(x, mean=None, cov=1, allow_singular=False) | |
Probability density function. | |
logpdf(x, mean=None, cov=1, allow_singular=False) | |
Log of the probability density function. | |
cdf(x, mean=None, cov=1, allow_singular=False, maxpts=1000000*dim, abseps=1e-5, releps=1e-5, lower_limit=None) | |
Cumulative distribution function. | |
logcdf(x, mean=None, cov=1, allow_singular=False, maxpts=1000000*dim, abseps=1e-5, releps=1e-5) | |
Log of the cumulative distribution function. | |
rvs(mean=None, cov=1, size=1, random_state=None) | |
Draw random samples from a multivariate normal distribution. | |
entropy(mean=None, cov=1) | |
Compute the differential entropy of the multivariate normal. | |
fit(x, fix_mean=None, fix_cov=None) | |
Fit a multivariate normal distribution to data. | |
Parameters | |
---------- | |
%(_mvn_doc_default_callparams)s | |
%(_doc_random_state)s | |
Notes | |
----- | |
%(_mvn_doc_callparams_note)s | |
The covariance matrix `cov` may be an instance of a subclass of | |
`Covariance`, e.g. `scipy.stats.CovViaPrecision`. If so, `allow_singular` | |
is ignored. | |
Otherwise, `cov` must be a symmetric positive semidefinite | |
matrix when `allow_singular` is True; it must be (strictly) positive | |
definite when `allow_singular` is False. | |
Symmetry is not checked; only the lower triangular portion is used. | |
The determinant and inverse of `cov` are computed | |
as the pseudo-determinant and pseudo-inverse, respectively, so | |
that `cov` does not need to have full rank. | |
The probability density function for `multivariate_normal` is | |
.. math:: | |
f(x) = \frac{1}{\sqrt{(2 \pi)^k \det \Sigma}} | |
\exp\left( -\frac{1}{2} (x - \mu)^T \Sigma^{-1} (x - \mu) \right), | |
where :math:`\mu` is the mean, :math:`\Sigma` the covariance matrix, | |
:math:`k` the rank of :math:`\Sigma`. In case of singular :math:`\Sigma`, | |
SciPy extends this definition according to [1]_. | |
.. versionadded:: 0.14.0 | |
References | |
---------- | |
.. [1] Multivariate Normal Distribution - Degenerate Case, Wikipedia, | |
https://en.wikipedia.org/wiki/Multivariate_normal_distribution#Degenerate_case | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> import matplotlib.pyplot as plt | |
>>> from scipy.stats import multivariate_normal | |
>>> x = np.linspace(0, 5, 10, endpoint=False) | |
>>> y = multivariate_normal.pdf(x, mean=2.5, cov=0.5); y | |
array([ 0.00108914, 0.01033349, 0.05946514, 0.20755375, 0.43939129, | |
0.56418958, 0.43939129, 0.20755375, 0.05946514, 0.01033349]) | |
>>> fig1 = plt.figure() | |
>>> ax = fig1.add_subplot(111) | |
>>> ax.plot(x, y) | |
>>> plt.show() | |
Alternatively, the object may be called (as a function) to fix the mean | |
and covariance parameters, returning a "frozen" multivariate normal | |
random variable: | |
>>> rv = multivariate_normal(mean=None, cov=1, allow_singular=False) | |
>>> # Frozen object with the same methods but holding the given | |
>>> # mean and covariance fixed. | |
The input quantiles can be any shape of array, as long as the last | |
axis labels the components. This allows us for instance to | |
display the frozen pdf for a non-isotropic random variable in 2D as | |
follows: | |
>>> x, y = np.mgrid[-1:1:.01, -1:1:.01] | |
>>> pos = np.dstack((x, y)) | |
>>> rv = multivariate_normal([0.5, -0.2], [[2.0, 0.3], [0.3, 0.5]]) | |
>>> fig2 = plt.figure() | |
>>> ax2 = fig2.add_subplot(111) | |
>>> ax2.contourf(x, y, rv.pdf(pos)) | |
""" # noqa: E501 | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__, mvn_docdict_params) | |
def __call__(self, mean=None, cov=1, allow_singular=False, seed=None): | |
"""Create a frozen multivariate normal distribution. | |
See `multivariate_normal_frozen` for more information. | |
""" | |
return multivariate_normal_frozen(mean, cov, | |
allow_singular=allow_singular, | |
seed=seed) | |
def _process_parameters(self, mean, cov, allow_singular=True): | |
""" | |
Infer dimensionality from mean or covariance matrix, ensure that | |
mean and covariance are full vector resp. matrix. | |
""" | |
if isinstance(cov, _covariance.Covariance): | |
return self._process_parameters_Covariance(mean, cov) | |
else: | |
# Before `Covariance` classes were introduced, | |
# `multivariate_normal` accepted plain arrays as `cov` and used the | |
# following input validation. To avoid disturbing the behavior of | |
# `multivariate_normal` when plain arrays are used, we use the | |
# original input validation here. | |
dim, mean, cov = self._process_parameters_psd(None, mean, cov) | |
# After input validation, some methods then processed the arrays | |
# with a `_PSD` object and used that to perform computation. | |
# To avoid branching statements in each method depending on whether | |
# `cov` is an array or `Covariance` object, we always process the | |
# array with `_PSD`, and then use wrapper that satisfies the | |
# `Covariance` interface, `CovViaPSD`. | |
psd = _PSD(cov, allow_singular=allow_singular) | |
cov_object = _covariance.CovViaPSD(psd) | |
return dim, mean, cov_object | |
def _process_parameters_Covariance(self, mean, cov): | |
dim = cov.shape[-1] | |
mean = np.array([0.]) if mean is None else mean | |
message = (f"`cov` represents a covariance matrix in {dim} dimensions," | |
f"and so `mean` must be broadcastable to shape {(dim,)}") | |
try: | |
mean = np.broadcast_to(mean, dim) | |
except ValueError as e: | |
raise ValueError(message) from e | |
return dim, mean, cov | |
def _process_parameters_psd(self, dim, mean, cov): | |
# Try to infer dimensionality | |
if dim is None: | |
if mean is None: | |
if cov is None: | |
dim = 1 | |
else: | |
cov = np.asarray(cov, dtype=float) | |
if cov.ndim < 2: | |
dim = 1 | |
else: | |
dim = cov.shape[0] | |
else: | |
mean = np.asarray(mean, dtype=float) | |
dim = mean.size | |
else: | |
if not np.isscalar(dim): | |
raise ValueError("Dimension of random variable must be " | |
"a scalar.") | |
# Check input sizes and return full arrays for mean and cov if | |
# necessary | |
if mean is None: | |
mean = np.zeros(dim) | |
mean = np.asarray(mean, dtype=float) | |
if cov is None: | |
cov = 1.0 | |
cov = np.asarray(cov, dtype=float) | |
if dim == 1: | |
mean = mean.reshape(1) | |
cov = cov.reshape(1, 1) | |
if mean.ndim != 1 or mean.shape[0] != dim: | |
raise ValueError("Array 'mean' must be a vector of length %d." % | |
dim) | |
if cov.ndim == 0: | |
cov = cov * np.eye(dim) | |
elif cov.ndim == 1: | |
cov = np.diag(cov) | |
elif cov.ndim == 2 and cov.shape != (dim, dim): | |
rows, cols = cov.shape | |
if rows != cols: | |
msg = ("Array 'cov' must be square if it is two dimensional," | |
" but cov.shape = %s." % str(cov.shape)) | |
else: | |
msg = ("Dimension mismatch: array 'cov' is of shape %s," | |
" but 'mean' is a vector of length %d.") | |
msg = msg % (str(cov.shape), len(mean)) | |
raise ValueError(msg) | |
elif cov.ndim > 2: | |
raise ValueError("Array 'cov' must be at most two-dimensional," | |
" but cov.ndim = %d" % cov.ndim) | |
return dim, mean, cov | |
def _process_quantiles(self, x, dim): | |
""" | |
Adjust quantiles array so that last axis labels the components of | |
each data point. | |
""" | |
x = np.asarray(x, dtype=float) | |
if x.ndim == 0: | |
x = x[np.newaxis] | |
elif x.ndim == 1: | |
if dim == 1: | |
x = x[:, np.newaxis] | |
else: | |
x = x[np.newaxis, :] | |
return x | |
def _logpdf(self, x, mean, cov_object): | |
"""Log of the multivariate normal probability density function. | |
Parameters | |
---------- | |
x : ndarray | |
Points at which to evaluate the log of the probability | |
density function | |
mean : ndarray | |
Mean of the distribution | |
cov_object : Covariance | |
An object representing the Covariance matrix | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'logpdf' instead. | |
""" | |
log_det_cov, rank = cov_object.log_pdet, cov_object.rank | |
dev = x - mean | |
if dev.ndim > 1: | |
log_det_cov = log_det_cov[..., np.newaxis] | |
rank = rank[..., np.newaxis] | |
maha = np.sum(np.square(cov_object.whiten(dev)), axis=-1) | |
return -0.5 * (rank * _LOG_2PI + log_det_cov + maha) | |
def logpdf(self, x, mean=None, cov=1, allow_singular=False): | |
"""Log of the multivariate normal probability density function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
%(_mvn_doc_default_callparams)s | |
Returns | |
------- | |
pdf : ndarray or scalar | |
Log of the probability density function evaluated at `x` | |
Notes | |
----- | |
%(_mvn_doc_callparams_note)s | |
""" | |
params = self._process_parameters(mean, cov, allow_singular) | |
dim, mean, cov_object = params | |
x = self._process_quantiles(x, dim) | |
out = self._logpdf(x, mean, cov_object) | |
if np.any(cov_object.rank < dim): | |
out_of_bounds = ~cov_object._support_mask(x-mean) | |
out[out_of_bounds] = -np.inf | |
return _squeeze_output(out) | |
def pdf(self, x, mean=None, cov=1, allow_singular=False): | |
"""Multivariate normal probability density function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
%(_mvn_doc_default_callparams)s | |
Returns | |
------- | |
pdf : ndarray or scalar | |
Probability density function evaluated at `x` | |
Notes | |
----- | |
%(_mvn_doc_callparams_note)s | |
""" | |
params = self._process_parameters(mean, cov, allow_singular) | |
dim, mean, cov_object = params | |
x = self._process_quantiles(x, dim) | |
out = np.exp(self._logpdf(x, mean, cov_object)) | |
if np.any(cov_object.rank < dim): | |
out_of_bounds = ~cov_object._support_mask(x-mean) | |
out[out_of_bounds] = 0.0 | |
return _squeeze_output(out) | |
def _cdf(self, x, mean, cov, maxpts, abseps, releps, lower_limit): | |
"""Multivariate normal cumulative distribution function. | |
Parameters | |
---------- | |
x : ndarray | |
Points at which to evaluate the cumulative distribution function. | |
mean : ndarray | |
Mean of the distribution | |
cov : array_like | |
Covariance matrix of the distribution | |
maxpts : integer | |
The maximum number of points to use for integration | |
abseps : float | |
Absolute error tolerance | |
releps : float | |
Relative error tolerance | |
lower_limit : array_like, optional | |
Lower limit of integration of the cumulative distribution function. | |
Default is negative infinity. Must be broadcastable with `x`. | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'cdf' instead. | |
.. versionadded:: 1.0.0 | |
""" | |
lower = (np.full(mean.shape, -np.inf) | |
if lower_limit is None else lower_limit) | |
# In 2d, _mvn.mvnun accepts input in which `lower` bound elements | |
# are greater than `x`. Not so in other dimensions. Fix this by | |
# ensuring that lower bounds are indeed lower when passed, then | |
# set signs of resulting CDF manually. | |
b, a = np.broadcast_arrays(x, lower) | |
i_swap = b < a | |
signs = (-1)**(i_swap.sum(axis=-1)) # odd # of swaps -> negative | |
a, b = a.copy(), b.copy() | |
a[i_swap], b[i_swap] = b[i_swap], a[i_swap] | |
n = x.shape[-1] | |
limits = np.concatenate((a, b), axis=-1) | |
# mvnun expects 1-d arguments, so process points sequentially | |
def func1d(limits): | |
return _mvn.mvnun(limits[:n], limits[n:], mean, cov, | |
maxpts, abseps, releps)[0] | |
out = np.apply_along_axis(func1d, -1, limits) * signs | |
return _squeeze_output(out) | |
def logcdf(self, x, mean=None, cov=1, allow_singular=False, maxpts=None, | |
abseps=1e-5, releps=1e-5, *, lower_limit=None): | |
"""Log of the multivariate normal cumulative distribution function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
%(_mvn_doc_default_callparams)s | |
maxpts : integer, optional | |
The maximum number of points to use for integration | |
(default `1000000*dim`) | |
abseps : float, optional | |
Absolute error tolerance (default 1e-5) | |
releps : float, optional | |
Relative error tolerance (default 1e-5) | |
lower_limit : array_like, optional | |
Lower limit of integration of the cumulative distribution function. | |
Default is negative infinity. Must be broadcastable with `x`. | |
Returns | |
------- | |
cdf : ndarray or scalar | |
Log of the cumulative distribution function evaluated at `x` | |
Notes | |
----- | |
%(_mvn_doc_callparams_note)s | |
.. versionadded:: 1.0.0 | |
""" | |
params = self._process_parameters(mean, cov, allow_singular) | |
dim, mean, cov_object = params | |
cov = cov_object.covariance | |
x = self._process_quantiles(x, dim) | |
if not maxpts: | |
maxpts = 1000000 * dim | |
cdf = self._cdf(x, mean, cov, maxpts, abseps, releps, lower_limit) | |
# the log of a negative real is complex, and cdf can be negative | |
# if lower limit is greater than upper limit | |
cdf = cdf + 0j if np.any(cdf < 0) else cdf | |
out = np.log(cdf) | |
return out | |
def cdf(self, x, mean=None, cov=1, allow_singular=False, maxpts=None, | |
abseps=1e-5, releps=1e-5, *, lower_limit=None): | |
"""Multivariate normal cumulative distribution function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
%(_mvn_doc_default_callparams)s | |
maxpts : integer, optional | |
The maximum number of points to use for integration | |
(default `1000000*dim`) | |
abseps : float, optional | |
Absolute error tolerance (default 1e-5) | |
releps : float, optional | |
Relative error tolerance (default 1e-5) | |
lower_limit : array_like, optional | |
Lower limit of integration of the cumulative distribution function. | |
Default is negative infinity. Must be broadcastable with `x`. | |
Returns | |
------- | |
cdf : ndarray or scalar | |
Cumulative distribution function evaluated at `x` | |
Notes | |
----- | |
%(_mvn_doc_callparams_note)s | |
.. versionadded:: 1.0.0 | |
""" | |
params = self._process_parameters(mean, cov, allow_singular) | |
dim, mean, cov_object = params | |
cov = cov_object.covariance | |
x = self._process_quantiles(x, dim) | |
if not maxpts: | |
maxpts = 1000000 * dim | |
out = self._cdf(x, mean, cov, maxpts, abseps, releps, lower_limit) | |
return out | |
def rvs(self, mean=None, cov=1, size=1, random_state=None): | |
"""Draw random samples from a multivariate normal distribution. | |
Parameters | |
---------- | |
%(_mvn_doc_default_callparams)s | |
size : integer, optional | |
Number of samples to draw (default 1). | |
%(_doc_random_state)s | |
Returns | |
------- | |
rvs : ndarray or scalar | |
Random variates of size (`size`, `N`), where `N` is the | |
dimension of the random variable. | |
Notes | |
----- | |
%(_mvn_doc_callparams_note)s | |
""" | |
dim, mean, cov_object = self._process_parameters(mean, cov) | |
random_state = self._get_random_state(random_state) | |
if isinstance(cov_object, _covariance.CovViaPSD): | |
cov = cov_object.covariance | |
out = random_state.multivariate_normal(mean, cov, size) | |
out = _squeeze_output(out) | |
else: | |
size = size or tuple() | |
if not np.iterable(size): | |
size = (size,) | |
shape = tuple(size) + (cov_object.shape[-1],) | |
x = random_state.normal(size=shape) | |
out = mean + cov_object.colorize(x) | |
return out | |
def entropy(self, mean=None, cov=1): | |
"""Compute the differential entropy of the multivariate normal. | |
Parameters | |
---------- | |
%(_mvn_doc_default_callparams)s | |
Returns | |
------- | |
h : scalar | |
Entropy of the multivariate normal distribution | |
Notes | |
----- | |
%(_mvn_doc_callparams_note)s | |
""" | |
dim, mean, cov_object = self._process_parameters(mean, cov) | |
return 0.5 * (cov_object.rank * (_LOG_2PI + 1) + cov_object.log_pdet) | |
def fit(self, x, fix_mean=None, fix_cov=None): | |
"""Fit a multivariate normal distribution to data. | |
Parameters | |
---------- | |
x : ndarray (m, n) | |
Data the distribution is fitted to. Must have two axes. | |
The first axis of length `m` represents the number of vectors | |
the distribution is fitted to. The second axis of length `n` | |
determines the dimensionality of the fitted distribution. | |
fix_mean : ndarray(n, ) | |
Fixed mean vector. Must have length `n`. | |
fix_cov: ndarray (n, n) | |
Fixed covariance matrix. Must have shape `(n, n)`. | |
Returns | |
------- | |
mean : ndarray (n, ) | |
Maximum likelihood estimate of the mean vector | |
cov : ndarray (n, n) | |
Maximum likelihood estimate of the covariance matrix | |
""" | |
# input validation for data to be fitted | |
x = np.asarray(x) | |
if x.ndim != 2: | |
raise ValueError("`x` must be two-dimensional.") | |
n_vectors, dim = x.shape | |
# parameter estimation | |
# reference: https://home.ttic.edu/~shubhendu/Slides/Estimation.pdf | |
if fix_mean is not None: | |
# input validation for `fix_mean` | |
fix_mean = np.atleast_1d(fix_mean) | |
if fix_mean.shape != (dim, ): | |
msg = ("`fix_mean` must be a one-dimensional array the same " | |
"length as the dimensionality of the vectors `x`.") | |
raise ValueError(msg) | |
mean = fix_mean | |
else: | |
mean = x.mean(axis=0) | |
if fix_cov is not None: | |
# input validation for `fix_cov` | |
fix_cov = np.atleast_2d(fix_cov) | |
# validate shape | |
if fix_cov.shape != (dim, dim): | |
msg = ("`fix_cov` must be a two-dimensional square array " | |
"of same side length as the dimensionality of the " | |
"vectors `x`.") | |
raise ValueError(msg) | |
# validate positive semidefiniteness | |
# a trimmed down copy from _PSD | |
s, u = scipy.linalg.eigh(fix_cov, lower=True, check_finite=True) | |
eps = _eigvalsh_to_eps(s) | |
if np.min(s) < -eps: | |
msg = "`fix_cov` must be symmetric positive semidefinite." | |
raise ValueError(msg) | |
cov = fix_cov | |
else: | |
centered_data = x - mean | |
cov = centered_data.T @ centered_data / n_vectors | |
return mean, cov | |
multivariate_normal = multivariate_normal_gen() | |
class multivariate_normal_frozen(multi_rv_frozen): | |
def __init__(self, mean=None, cov=1, allow_singular=False, seed=None, | |
maxpts=None, abseps=1e-5, releps=1e-5): | |
"""Create a frozen multivariate normal distribution. | |
Parameters | |
---------- | |
mean : array_like, default: ``[0]`` | |
Mean of the distribution. | |
cov : array_like, default: ``[1]`` | |
Symmetric positive (semi)definite covariance matrix of the | |
distribution. | |
allow_singular : bool, default: ``False`` | |
Whether to allow a singular covariance matrix. | |
seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance | |
then that instance is used. | |
maxpts : integer, optional | |
The maximum number of points to use for integration of the | |
cumulative distribution function (default `1000000*dim`) | |
abseps : float, optional | |
Absolute error tolerance for the cumulative distribution function | |
(default 1e-5) | |
releps : float, optional | |
Relative error tolerance for the cumulative distribution function | |
(default 1e-5) | |
Examples | |
-------- | |
When called with the default parameters, this will create a 1D random | |
variable with mean 0 and covariance 1: | |
>>> from scipy.stats import multivariate_normal | |
>>> r = multivariate_normal() | |
>>> r.mean | |
array([ 0.]) | |
>>> r.cov | |
array([[1.]]) | |
""" # numpy/numpydoc#87 # noqa: E501 | |
self._dist = multivariate_normal_gen(seed) | |
self.dim, self.mean, self.cov_object = ( | |
self._dist._process_parameters(mean, cov, allow_singular)) | |
self.allow_singular = allow_singular or self.cov_object._allow_singular | |
if not maxpts: | |
maxpts = 1000000 * self.dim | |
self.maxpts = maxpts | |
self.abseps = abseps | |
self.releps = releps | |
def cov(self): | |
return self.cov_object.covariance | |
def logpdf(self, x): | |
x = self._dist._process_quantiles(x, self.dim) | |
out = self._dist._logpdf(x, self.mean, self.cov_object) | |
if np.any(self.cov_object.rank < self.dim): | |
out_of_bounds = ~self.cov_object._support_mask(x-self.mean) | |
out[out_of_bounds] = -np.inf | |
return _squeeze_output(out) | |
def pdf(self, x): | |
return np.exp(self.logpdf(x)) | |
def logcdf(self, x, *, lower_limit=None): | |
cdf = self.cdf(x, lower_limit=lower_limit) | |
# the log of a negative real is complex, and cdf can be negative | |
# if lower limit is greater than upper limit | |
cdf = cdf + 0j if np.any(cdf < 0) else cdf | |
out = np.log(cdf) | |
return out | |
def cdf(self, x, *, lower_limit=None): | |
x = self._dist._process_quantiles(x, self.dim) | |
out = self._dist._cdf(x, self.mean, self.cov_object.covariance, | |
self.maxpts, self.abseps, self.releps, | |
lower_limit) | |
return _squeeze_output(out) | |
def rvs(self, size=1, random_state=None): | |
return self._dist.rvs(self.mean, self.cov_object, size, random_state) | |
def entropy(self): | |
"""Computes the differential entropy of the multivariate normal. | |
Returns | |
------- | |
h : scalar | |
Entropy of the multivariate normal distribution | |
""" | |
log_pdet = self.cov_object.log_pdet | |
rank = self.cov_object.rank | |
return 0.5 * (rank * (_LOG_2PI + 1) + log_pdet) | |
# Set frozen generator docstrings from corresponding docstrings in | |
# multivariate_normal_gen and fill in default strings in class docstrings | |
for name in ['logpdf', 'pdf', 'logcdf', 'cdf', 'rvs']: | |
method = multivariate_normal_gen.__dict__[name] | |
method_frozen = multivariate_normal_frozen.__dict__[name] | |
method_frozen.__doc__ = doccer.docformat(method.__doc__, | |
mvn_docdict_noparams) | |
method.__doc__ = doccer.docformat(method.__doc__, mvn_docdict_params) | |
_matnorm_doc_default_callparams = """\ | |
mean : array_like, optional | |
Mean of the distribution (default: `None`) | |
rowcov : array_like, optional | |
Among-row covariance matrix of the distribution (default: `1`) | |
colcov : array_like, optional | |
Among-column covariance matrix of the distribution (default: `1`) | |
""" | |
_matnorm_doc_callparams_note = """\ | |
If `mean` is set to `None` then a matrix of zeros is used for the mean. | |
The dimensions of this matrix are inferred from the shape of `rowcov` and | |
`colcov`, if these are provided, or set to `1` if ambiguous. | |
`rowcov` and `colcov` can be two-dimensional array_likes specifying the | |
covariance matrices directly. Alternatively, a one-dimensional array will | |
be be interpreted as the entries of a diagonal matrix, and a scalar or | |
zero-dimensional array will be interpreted as this value times the | |
identity matrix. | |
""" | |
_matnorm_doc_frozen_callparams = "" | |
_matnorm_doc_frozen_callparams_note = """\ | |
See class definition for a detailed description of parameters.""" | |
matnorm_docdict_params = { | |
'_matnorm_doc_default_callparams': _matnorm_doc_default_callparams, | |
'_matnorm_doc_callparams_note': _matnorm_doc_callparams_note, | |
'_doc_random_state': _doc_random_state | |
} | |
matnorm_docdict_noparams = { | |
'_matnorm_doc_default_callparams': _matnorm_doc_frozen_callparams, | |
'_matnorm_doc_callparams_note': _matnorm_doc_frozen_callparams_note, | |
'_doc_random_state': _doc_random_state | |
} | |
class matrix_normal_gen(multi_rv_generic): | |
r"""A matrix normal random variable. | |
The `mean` keyword specifies the mean. The `rowcov` keyword specifies the | |
among-row covariance matrix. The 'colcov' keyword specifies the | |
among-column covariance matrix. | |
Methods | |
------- | |
pdf(X, mean=None, rowcov=1, colcov=1) | |
Probability density function. | |
logpdf(X, mean=None, rowcov=1, colcov=1) | |
Log of the probability density function. | |
rvs(mean=None, rowcov=1, colcov=1, size=1, random_state=None) | |
Draw random samples. | |
entropy(rowcol=1, colcov=1) | |
Differential entropy. | |
Parameters | |
---------- | |
%(_matnorm_doc_default_callparams)s | |
%(_doc_random_state)s | |
Notes | |
----- | |
%(_matnorm_doc_callparams_note)s | |
The covariance matrices specified by `rowcov` and `colcov` must be | |
(symmetric) positive definite. If the samples in `X` are | |
:math:`m \times n`, then `rowcov` must be :math:`m \times m` and | |
`colcov` must be :math:`n \times n`. `mean` must be the same shape as `X`. | |
The probability density function for `matrix_normal` is | |
.. math:: | |
f(X) = (2 \pi)^{-\frac{mn}{2}}|U|^{-\frac{n}{2}} |V|^{-\frac{m}{2}} | |
\exp\left( -\frac{1}{2} \mathrm{Tr}\left[ U^{-1} (X-M) V^{-1} | |
(X-M)^T \right] \right), | |
where :math:`M` is the mean, :math:`U` the among-row covariance matrix, | |
:math:`V` the among-column covariance matrix. | |
The `allow_singular` behaviour of the `multivariate_normal` | |
distribution is not currently supported. Covariance matrices must be | |
full rank. | |
The `matrix_normal` distribution is closely related to the | |
`multivariate_normal` distribution. Specifically, :math:`\mathrm{Vec}(X)` | |
(the vector formed by concatenating the columns of :math:`X`) has a | |
multivariate normal distribution with mean :math:`\mathrm{Vec}(M)` | |
and covariance :math:`V \otimes U` (where :math:`\otimes` is the Kronecker | |
product). Sampling and pdf evaluation are | |
:math:`\mathcal{O}(m^3 + n^3 + m^2 n + m n^2)` for the matrix normal, but | |
:math:`\mathcal{O}(m^3 n^3)` for the equivalent multivariate normal, | |
making this equivalent form algorithmically inefficient. | |
.. versionadded:: 0.17.0 | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.stats import matrix_normal | |
>>> M = np.arange(6).reshape(3,2); M | |
array([[0, 1], | |
[2, 3], | |
[4, 5]]) | |
>>> U = np.diag([1,2,3]); U | |
array([[1, 0, 0], | |
[0, 2, 0], | |
[0, 0, 3]]) | |
>>> V = 0.3*np.identity(2); V | |
array([[ 0.3, 0. ], | |
[ 0. , 0.3]]) | |
>>> X = M + 0.1; X | |
array([[ 0.1, 1.1], | |
[ 2.1, 3.1], | |
[ 4.1, 5.1]]) | |
>>> matrix_normal.pdf(X, mean=M, rowcov=U, colcov=V) | |
0.023410202050005054 | |
>>> # Equivalent multivariate normal | |
>>> from scipy.stats import multivariate_normal | |
>>> vectorised_X = X.T.flatten() | |
>>> equiv_mean = M.T.flatten() | |
>>> equiv_cov = np.kron(V,U) | |
>>> multivariate_normal.pdf(vectorised_X, mean=equiv_mean, cov=equiv_cov) | |
0.023410202050005054 | |
Alternatively, the object may be called (as a function) to fix the mean | |
and covariance parameters, returning a "frozen" matrix normal | |
random variable: | |
>>> rv = matrix_normal(mean=None, rowcov=1, colcov=1) | |
>>> # Frozen object with the same methods but holding the given | |
>>> # mean and covariance fixed. | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__, matnorm_docdict_params) | |
def __call__(self, mean=None, rowcov=1, colcov=1, seed=None): | |
"""Create a frozen matrix normal distribution. | |
See `matrix_normal_frozen` for more information. | |
""" | |
return matrix_normal_frozen(mean, rowcov, colcov, seed=seed) | |
def _process_parameters(self, mean, rowcov, colcov): | |
""" | |
Infer dimensionality from mean or covariance matrices. Handle | |
defaults. Ensure compatible dimensions. | |
""" | |
# Process mean | |
if mean is not None: | |
mean = np.asarray(mean, dtype=float) | |
meanshape = mean.shape | |
if len(meanshape) != 2: | |
raise ValueError("Array `mean` must be two dimensional.") | |
if np.any(meanshape == 0): | |
raise ValueError("Array `mean` has invalid shape.") | |
# Process among-row covariance | |
rowcov = np.asarray(rowcov, dtype=float) | |
if rowcov.ndim == 0: | |
if mean is not None: | |
rowcov = rowcov * np.identity(meanshape[0]) | |
else: | |
rowcov = rowcov * np.identity(1) | |
elif rowcov.ndim == 1: | |
rowcov = np.diag(rowcov) | |
rowshape = rowcov.shape | |
if len(rowshape) != 2: | |
raise ValueError("`rowcov` must be a scalar or a 2D array.") | |
if rowshape[0] != rowshape[1]: | |
raise ValueError("Array `rowcov` must be square.") | |
if rowshape[0] == 0: | |
raise ValueError("Array `rowcov` has invalid shape.") | |
numrows = rowshape[0] | |
# Process among-column covariance | |
colcov = np.asarray(colcov, dtype=float) | |
if colcov.ndim == 0: | |
if mean is not None: | |
colcov = colcov * np.identity(meanshape[1]) | |
else: | |
colcov = colcov * np.identity(1) | |
elif colcov.ndim == 1: | |
colcov = np.diag(colcov) | |
colshape = colcov.shape | |
if len(colshape) != 2: | |
raise ValueError("`colcov` must be a scalar or a 2D array.") | |
if colshape[0] != colshape[1]: | |
raise ValueError("Array `colcov` must be square.") | |
if colshape[0] == 0: | |
raise ValueError("Array `colcov` has invalid shape.") | |
numcols = colshape[0] | |
# Ensure mean and covariances compatible | |
if mean is not None: | |
if meanshape[0] != numrows: | |
raise ValueError("Arrays `mean` and `rowcov` must have the " | |
"same number of rows.") | |
if meanshape[1] != numcols: | |
raise ValueError("Arrays `mean` and `colcov` must have the " | |
"same number of columns.") | |
else: | |
mean = np.zeros((numrows, numcols)) | |
dims = (numrows, numcols) | |
return dims, mean, rowcov, colcov | |
def _process_quantiles(self, X, dims): | |
""" | |
Adjust quantiles array so that last two axes labels the components of | |
each data point. | |
""" | |
X = np.asarray(X, dtype=float) | |
if X.ndim == 2: | |
X = X[np.newaxis, :] | |
if X.shape[-2:] != dims: | |
raise ValueError("The shape of array `X` is not compatible " | |
"with the distribution parameters.") | |
return X | |
def _logpdf(self, dims, X, mean, row_prec_rt, log_det_rowcov, | |
col_prec_rt, log_det_colcov): | |
"""Log of the matrix normal probability density function. | |
Parameters | |
---------- | |
dims : tuple | |
Dimensions of the matrix variates | |
X : ndarray | |
Points at which to evaluate the log of the probability | |
density function | |
mean : ndarray | |
Mean of the distribution | |
row_prec_rt : ndarray | |
A decomposition such that np.dot(row_prec_rt, row_prec_rt.T) | |
is the inverse of the among-row covariance matrix | |
log_det_rowcov : float | |
Logarithm of the determinant of the among-row covariance matrix | |
col_prec_rt : ndarray | |
A decomposition such that np.dot(col_prec_rt, col_prec_rt.T) | |
is the inverse of the among-column covariance matrix | |
log_det_colcov : float | |
Logarithm of the determinant of the among-column covariance matrix | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'logpdf' instead. | |
""" | |
numrows, numcols = dims | |
roll_dev = np.moveaxis(X-mean, -1, 0) | |
scale_dev = np.tensordot(col_prec_rt.T, | |
np.dot(roll_dev, row_prec_rt), 1) | |
maha = np.sum(np.sum(np.square(scale_dev), axis=-1), axis=0) | |
return -0.5 * (numrows*numcols*_LOG_2PI + numcols*log_det_rowcov | |
+ numrows*log_det_colcov + maha) | |
def logpdf(self, X, mean=None, rowcov=1, colcov=1): | |
"""Log of the matrix normal probability density function. | |
Parameters | |
---------- | |
X : array_like | |
Quantiles, with the last two axes of `X` denoting the components. | |
%(_matnorm_doc_default_callparams)s | |
Returns | |
------- | |
logpdf : ndarray | |
Log of the probability density function evaluated at `X` | |
Notes | |
----- | |
%(_matnorm_doc_callparams_note)s | |
""" | |
dims, mean, rowcov, colcov = self._process_parameters(mean, rowcov, | |
colcov) | |
X = self._process_quantiles(X, dims) | |
rowpsd = _PSD(rowcov, allow_singular=False) | |
colpsd = _PSD(colcov, allow_singular=False) | |
out = self._logpdf(dims, X, mean, rowpsd.U, rowpsd.log_pdet, colpsd.U, | |
colpsd.log_pdet) | |
return _squeeze_output(out) | |
def pdf(self, X, mean=None, rowcov=1, colcov=1): | |
"""Matrix normal probability density function. | |
Parameters | |
---------- | |
X : array_like | |
Quantiles, with the last two axes of `X` denoting the components. | |
%(_matnorm_doc_default_callparams)s | |
Returns | |
------- | |
pdf : ndarray | |
Probability density function evaluated at `X` | |
Notes | |
----- | |
%(_matnorm_doc_callparams_note)s | |
""" | |
return np.exp(self.logpdf(X, mean, rowcov, colcov)) | |
def rvs(self, mean=None, rowcov=1, colcov=1, size=1, random_state=None): | |
"""Draw random samples from a matrix normal distribution. | |
Parameters | |
---------- | |
%(_matnorm_doc_default_callparams)s | |
size : integer, optional | |
Number of samples to draw (default 1). | |
%(_doc_random_state)s | |
Returns | |
------- | |
rvs : ndarray or scalar | |
Random variates of size (`size`, `dims`), where `dims` is the | |
dimension of the random matrices. | |
Notes | |
----- | |
%(_matnorm_doc_callparams_note)s | |
""" | |
size = int(size) | |
dims, mean, rowcov, colcov = self._process_parameters(mean, rowcov, | |
colcov) | |
rowchol = scipy.linalg.cholesky(rowcov, lower=True) | |
colchol = scipy.linalg.cholesky(colcov, lower=True) | |
random_state = self._get_random_state(random_state) | |
# We aren't generating standard normal variates with size=(size, | |
# dims[0], dims[1]) directly to ensure random variates remain backwards | |
# compatible. See https://github.com/scipy/scipy/pull/12312 for more | |
# details. | |
std_norm = random_state.standard_normal( | |
size=(dims[1], size, dims[0]) | |
).transpose(1, 2, 0) | |
out = mean + np.einsum('jp,ipq,kq->ijk', | |
rowchol, std_norm, colchol, | |
optimize=True) | |
if size == 1: | |
out = out.reshape(mean.shape) | |
return out | |
def entropy(self, rowcov=1, colcov=1): | |
"""Log of the matrix normal probability density function. | |
Parameters | |
---------- | |
rowcov : array_like, optional | |
Among-row covariance matrix of the distribution (default: `1`) | |
colcov : array_like, optional | |
Among-column covariance matrix of the distribution (default: `1`) | |
Returns | |
------- | |
entropy : float | |
Entropy of the distribution | |
Notes | |
----- | |
%(_matnorm_doc_callparams_note)s | |
""" | |
dummy_mean = np.zeros((rowcov.shape[0], colcov.shape[0])) | |
dims, _, rowcov, colcov = self._process_parameters(dummy_mean, | |
rowcov, | |
colcov) | |
rowpsd = _PSD(rowcov, allow_singular=False) | |
colpsd = _PSD(colcov, allow_singular=False) | |
return self._entropy(dims, rowpsd.log_pdet, colpsd.log_pdet) | |
def _entropy(self, dims, row_cov_logdet, col_cov_logdet): | |
n, p = dims | |
return (0.5 * n * p * (1 + _LOG_2PI) + 0.5 * p * row_cov_logdet + | |
0.5 * n * col_cov_logdet) | |
matrix_normal = matrix_normal_gen() | |
class matrix_normal_frozen(multi_rv_frozen): | |
""" | |
Create a frozen matrix normal distribution. | |
Parameters | |
---------- | |
%(_matnorm_doc_default_callparams)s | |
seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional | |
If `seed` is `None` the `~np.random.RandomState` singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, seeded | |
with seed. | |
If `seed` is already a ``RandomState`` or ``Generator`` instance, | |
then that object is used. | |
Default is `None`. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.stats import matrix_normal | |
>>> distn = matrix_normal(mean=np.zeros((3,3))) | |
>>> X = distn.rvs(); X | |
array([[-0.02976962, 0.93339138, -0.09663178], | |
[ 0.67405524, 0.28250467, -0.93308929], | |
[-0.31144782, 0.74535536, 1.30412916]]) | |
>>> distn.pdf(X) | |
2.5160642368346784e-05 | |
>>> distn.logpdf(X) | |
-10.590229595124615 | |
""" | |
def __init__(self, mean=None, rowcov=1, colcov=1, seed=None): | |
self._dist = matrix_normal_gen(seed) | |
self.dims, self.mean, self.rowcov, self.colcov = \ | |
self._dist._process_parameters(mean, rowcov, colcov) | |
self.rowpsd = _PSD(self.rowcov, allow_singular=False) | |
self.colpsd = _PSD(self.colcov, allow_singular=False) | |
def logpdf(self, X): | |
X = self._dist._process_quantiles(X, self.dims) | |
out = self._dist._logpdf(self.dims, X, self.mean, self.rowpsd.U, | |
self.rowpsd.log_pdet, self.colpsd.U, | |
self.colpsd.log_pdet) | |
return _squeeze_output(out) | |
def pdf(self, X): | |
return np.exp(self.logpdf(X)) | |
def rvs(self, size=1, random_state=None): | |
return self._dist.rvs(self.mean, self.rowcov, self.colcov, size, | |
random_state) | |
def entropy(self): | |
return self._dist._entropy(self.dims, self.rowpsd.log_pdet, | |
self.colpsd.log_pdet) | |
# Set frozen generator docstrings from corresponding docstrings in | |
# matrix_normal_gen and fill in default strings in class docstrings | |
for name in ['logpdf', 'pdf', 'rvs', 'entropy']: | |
method = matrix_normal_gen.__dict__[name] | |
method_frozen = matrix_normal_frozen.__dict__[name] | |
method_frozen.__doc__ = doccer.docformat(method.__doc__, | |
matnorm_docdict_noparams) | |
method.__doc__ = doccer.docformat(method.__doc__, matnorm_docdict_params) | |
_dirichlet_doc_default_callparams = """\ | |
alpha : array_like | |
The concentration parameters. The number of entries determines the | |
dimensionality of the distribution. | |
""" | |
_dirichlet_doc_frozen_callparams = "" | |
_dirichlet_doc_frozen_callparams_note = """\ | |
See class definition for a detailed description of parameters.""" | |
dirichlet_docdict_params = { | |
'_dirichlet_doc_default_callparams': _dirichlet_doc_default_callparams, | |
'_doc_random_state': _doc_random_state | |
} | |
dirichlet_docdict_noparams = { | |
'_dirichlet_doc_default_callparams': _dirichlet_doc_frozen_callparams, | |
'_doc_random_state': _doc_random_state | |
} | |
def _dirichlet_check_parameters(alpha): | |
alpha = np.asarray(alpha) | |
if np.min(alpha) <= 0: | |
raise ValueError("All parameters must be greater than 0") | |
elif alpha.ndim != 1: | |
raise ValueError("Parameter vector 'a' must be one dimensional, " | |
f"but a.shape = {alpha.shape}.") | |
return alpha | |
def _dirichlet_check_input(alpha, x): | |
x = np.asarray(x) | |
if x.shape[0] + 1 != alpha.shape[0] and x.shape[0] != alpha.shape[0]: | |
raise ValueError("Vector 'x' must have either the same number " | |
"of entries as, or one entry fewer than, " | |
f"parameter vector 'a', but alpha.shape = {alpha.shape} " | |
f"and x.shape = {x.shape}.") | |
if x.shape[0] != alpha.shape[0]: | |
xk = np.array([1 - np.sum(x, 0)]) | |
if xk.ndim == 1: | |
x = np.append(x, xk) | |
elif xk.ndim == 2: | |
x = np.vstack((x, xk)) | |
else: | |
raise ValueError("The input must be one dimensional or a two " | |
"dimensional matrix containing the entries.") | |
if np.min(x) < 0: | |
raise ValueError("Each entry in 'x' must be greater than or equal " | |
"to zero.") | |
if np.max(x) > 1: | |
raise ValueError("Each entry in 'x' must be smaller or equal one.") | |
# Check x_i > 0 or alpha_i > 1 | |
xeq0 = (x == 0) | |
alphalt1 = (alpha < 1) | |
if x.shape != alpha.shape: | |
alphalt1 = np.repeat(alphalt1, x.shape[-1], axis=-1).reshape(x.shape) | |
chk = np.logical_and(xeq0, alphalt1) | |
if np.sum(chk): | |
raise ValueError("Each entry in 'x' must be greater than zero if its " | |
"alpha is less than one.") | |
if (np.abs(np.sum(x, 0) - 1.0) > 10e-10).any(): | |
raise ValueError("The input vector 'x' must lie within the normal " | |
"simplex. but np.sum(x, 0) = %s." % np.sum(x, 0)) | |
return x | |
def _lnB(alpha): | |
r"""Internal helper function to compute the log of the useful quotient. | |
.. math:: | |
B(\alpha) = \frac{\prod_{i=1}{K}\Gamma(\alpha_i)} | |
{\Gamma\left(\sum_{i=1}^{K} \alpha_i \right)} | |
Parameters | |
---------- | |
%(_dirichlet_doc_default_callparams)s | |
Returns | |
------- | |
B : scalar | |
Helper quotient, internal use only | |
""" | |
return np.sum(gammaln(alpha)) - gammaln(np.sum(alpha)) | |
class dirichlet_gen(multi_rv_generic): | |
r"""A Dirichlet random variable. | |
The ``alpha`` keyword specifies the concentration parameters of the | |
distribution. | |
.. versionadded:: 0.15.0 | |
Methods | |
------- | |
pdf(x, alpha) | |
Probability density function. | |
logpdf(x, alpha) | |
Log of the probability density function. | |
rvs(alpha, size=1, random_state=None) | |
Draw random samples from a Dirichlet distribution. | |
mean(alpha) | |
The mean of the Dirichlet distribution | |
var(alpha) | |
The variance of the Dirichlet distribution | |
cov(alpha) | |
The covariance of the Dirichlet distribution | |
entropy(alpha) | |
Compute the differential entropy of the Dirichlet distribution. | |
Parameters | |
---------- | |
%(_dirichlet_doc_default_callparams)s | |
%(_doc_random_state)s | |
Notes | |
----- | |
Each :math:`\alpha` entry must be positive. The distribution has only | |
support on the simplex defined by | |
.. math:: | |
\sum_{i=1}^{K} x_i = 1 | |
where :math:`0 < x_i < 1`. | |
If the quantiles don't lie within the simplex, a ValueError is raised. | |
The probability density function for `dirichlet` is | |
.. math:: | |
f(x) = \frac{1}{\mathrm{B}(\boldsymbol\alpha)} \prod_{i=1}^K x_i^{\alpha_i - 1} | |
where | |
.. math:: | |
\mathrm{B}(\boldsymbol\alpha) = \frac{\prod_{i=1}^K \Gamma(\alpha_i)} | |
{\Gamma\bigl(\sum_{i=1}^K \alpha_i\bigr)} | |
and :math:`\boldsymbol\alpha=(\alpha_1,\ldots,\alpha_K)`, the | |
concentration parameters and :math:`K` is the dimension of the space | |
where :math:`x` takes values. | |
Note that the `dirichlet` interface is somewhat inconsistent. | |
The array returned by the rvs function is transposed | |
with respect to the format expected by the pdf and logpdf. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.stats import dirichlet | |
Generate a dirichlet random variable | |
>>> quantiles = np.array([0.2, 0.2, 0.6]) # specify quantiles | |
>>> alpha = np.array([0.4, 5, 15]) # specify concentration parameters | |
>>> dirichlet.pdf(quantiles, alpha) | |
0.2843831684937255 | |
The same PDF but following a log scale | |
>>> dirichlet.logpdf(quantiles, alpha) | |
-1.2574327653159187 | |
Once we specify the dirichlet distribution | |
we can then calculate quantities of interest | |
>>> dirichlet.mean(alpha) # get the mean of the distribution | |
array([0.01960784, 0.24509804, 0.73529412]) | |
>>> dirichlet.var(alpha) # get variance | |
array([0.00089829, 0.00864603, 0.00909517]) | |
>>> dirichlet.entropy(alpha) # calculate the differential entropy | |
-4.3280162474082715 | |
We can also return random samples from the distribution | |
>>> dirichlet.rvs(alpha, size=1, random_state=1) | |
array([[0.00766178, 0.24670518, 0.74563305]]) | |
>>> dirichlet.rvs(alpha, size=2, random_state=2) | |
array([[0.01639427, 0.1292273 , 0.85437844], | |
[0.00156917, 0.19033695, 0.80809388]]) | |
Alternatively, the object may be called (as a function) to fix | |
concentration parameters, returning a "frozen" Dirichlet | |
random variable: | |
>>> rv = dirichlet(alpha) | |
>>> # Frozen object with the same methods but holding the given | |
>>> # concentration parameters fixed. | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__, dirichlet_docdict_params) | |
def __call__(self, alpha, seed=None): | |
return dirichlet_frozen(alpha, seed=seed) | |
def _logpdf(self, x, alpha): | |
"""Log of the Dirichlet probability density function. | |
Parameters | |
---------- | |
x : ndarray | |
Points at which to evaluate the log of the probability | |
density function | |
%(_dirichlet_doc_default_callparams)s | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'logpdf' instead. | |
""" | |
lnB = _lnB(alpha) | |
return - lnB + np.sum((xlogy(alpha - 1, x.T)).T, 0) | |
def logpdf(self, x, alpha): | |
"""Log of the Dirichlet probability density function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
%(_dirichlet_doc_default_callparams)s | |
Returns | |
------- | |
pdf : ndarray or scalar | |
Log of the probability density function evaluated at `x`. | |
""" | |
alpha = _dirichlet_check_parameters(alpha) | |
x = _dirichlet_check_input(alpha, x) | |
out = self._logpdf(x, alpha) | |
return _squeeze_output(out) | |
def pdf(self, x, alpha): | |
"""The Dirichlet probability density function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
%(_dirichlet_doc_default_callparams)s | |
Returns | |
------- | |
pdf : ndarray or scalar | |
The probability density function evaluated at `x`. | |
""" | |
alpha = _dirichlet_check_parameters(alpha) | |
x = _dirichlet_check_input(alpha, x) | |
out = np.exp(self._logpdf(x, alpha)) | |
return _squeeze_output(out) | |
def mean(self, alpha): | |
"""Mean of the Dirichlet distribution. | |
Parameters | |
---------- | |
%(_dirichlet_doc_default_callparams)s | |
Returns | |
------- | |
mu : ndarray or scalar | |
Mean of the Dirichlet distribution. | |
""" | |
alpha = _dirichlet_check_parameters(alpha) | |
out = alpha / (np.sum(alpha)) | |
return _squeeze_output(out) | |
def var(self, alpha): | |
"""Variance of the Dirichlet distribution. | |
Parameters | |
---------- | |
%(_dirichlet_doc_default_callparams)s | |
Returns | |
------- | |
v : ndarray or scalar | |
Variance of the Dirichlet distribution. | |
""" | |
alpha = _dirichlet_check_parameters(alpha) | |
alpha0 = np.sum(alpha) | |
out = (alpha * (alpha0 - alpha)) / ((alpha0 * alpha0) * (alpha0 + 1)) | |
return _squeeze_output(out) | |
def cov(self, alpha): | |
"""Covariance matrix of the Dirichlet distribution. | |
Parameters | |
---------- | |
%(_dirichlet_doc_default_callparams)s | |
Returns | |
------- | |
cov : ndarray | |
The covariance matrix of the distribution. | |
""" | |
alpha = _dirichlet_check_parameters(alpha) | |
alpha0 = np.sum(alpha) | |
a = alpha / alpha0 | |
cov = (np.diag(a) - np.outer(a, a)) / (alpha0 + 1) | |
return _squeeze_output(cov) | |
def entropy(self, alpha): | |
""" | |
Differential entropy of the Dirichlet distribution. | |
Parameters | |
---------- | |
%(_dirichlet_doc_default_callparams)s | |
Returns | |
------- | |
h : scalar | |
Entropy of the Dirichlet distribution | |
""" | |
alpha = _dirichlet_check_parameters(alpha) | |
alpha0 = np.sum(alpha) | |
lnB = _lnB(alpha) | |
K = alpha.shape[0] | |
out = lnB + (alpha0 - K) * scipy.special.psi(alpha0) - np.sum( | |
(alpha - 1) * scipy.special.psi(alpha)) | |
return _squeeze_output(out) | |
def rvs(self, alpha, size=1, random_state=None): | |
""" | |
Draw random samples from a Dirichlet distribution. | |
Parameters | |
---------- | |
%(_dirichlet_doc_default_callparams)s | |
size : int, optional | |
Number of samples to draw (default 1). | |
%(_doc_random_state)s | |
Returns | |
------- | |
rvs : ndarray or scalar | |
Random variates of size (`size`, `N`), where `N` is the | |
dimension of the random variable. | |
""" | |
alpha = _dirichlet_check_parameters(alpha) | |
random_state = self._get_random_state(random_state) | |
return random_state.dirichlet(alpha, size=size) | |
dirichlet = dirichlet_gen() | |
class dirichlet_frozen(multi_rv_frozen): | |
def __init__(self, alpha, seed=None): | |
self.alpha = _dirichlet_check_parameters(alpha) | |
self._dist = dirichlet_gen(seed) | |
def logpdf(self, x): | |
return self._dist.logpdf(x, self.alpha) | |
def pdf(self, x): | |
return self._dist.pdf(x, self.alpha) | |
def mean(self): | |
return self._dist.mean(self.alpha) | |
def var(self): | |
return self._dist.var(self.alpha) | |
def cov(self): | |
return self._dist.cov(self.alpha) | |
def entropy(self): | |
return self._dist.entropy(self.alpha) | |
def rvs(self, size=1, random_state=None): | |
return self._dist.rvs(self.alpha, size, random_state) | |
# Set frozen generator docstrings from corresponding docstrings in | |
# multivariate_normal_gen and fill in default strings in class docstrings | |
for name in ['logpdf', 'pdf', 'rvs', 'mean', 'var', 'cov', 'entropy']: | |
method = dirichlet_gen.__dict__[name] | |
method_frozen = dirichlet_frozen.__dict__[name] | |
method_frozen.__doc__ = doccer.docformat( | |
method.__doc__, dirichlet_docdict_noparams) | |
method.__doc__ = doccer.docformat(method.__doc__, dirichlet_docdict_params) | |
_wishart_doc_default_callparams = """\ | |
df : int | |
Degrees of freedom, must be greater than or equal to dimension of the | |
scale matrix | |
scale : array_like | |
Symmetric positive definite scale matrix of the distribution | |
""" | |
_wishart_doc_callparams_note = "" | |
_wishart_doc_frozen_callparams = "" | |
_wishart_doc_frozen_callparams_note = """\ | |
See class definition for a detailed description of parameters.""" | |
wishart_docdict_params = { | |
'_doc_default_callparams': _wishart_doc_default_callparams, | |
'_doc_callparams_note': _wishart_doc_callparams_note, | |
'_doc_random_state': _doc_random_state | |
} | |
wishart_docdict_noparams = { | |
'_doc_default_callparams': _wishart_doc_frozen_callparams, | |
'_doc_callparams_note': _wishart_doc_frozen_callparams_note, | |
'_doc_random_state': _doc_random_state | |
} | |
class wishart_gen(multi_rv_generic): | |
r"""A Wishart random variable. | |
The `df` keyword specifies the degrees of freedom. The `scale` keyword | |
specifies the scale matrix, which must be symmetric and positive definite. | |
In this context, the scale matrix is often interpreted in terms of a | |
multivariate normal precision matrix (the inverse of the covariance | |
matrix). These arguments must satisfy the relationship | |
``df > scale.ndim - 1``, but see notes on using the `rvs` method with | |
``df < scale.ndim``. | |
Methods | |
------- | |
pdf(x, df, scale) | |
Probability density function. | |
logpdf(x, df, scale) | |
Log of the probability density function. | |
rvs(df, scale, size=1, random_state=None) | |
Draw random samples from a Wishart distribution. | |
entropy() | |
Compute the differential entropy of the Wishart distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
%(_doc_random_state)s | |
Raises | |
------ | |
scipy.linalg.LinAlgError | |
If the scale matrix `scale` is not positive definite. | |
See Also | |
-------- | |
invwishart, chi2 | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
The scale matrix `scale` must be a symmetric positive definite | |
matrix. Singular matrices, including the symmetric positive semi-definite | |
case, are not supported. Symmetry is not checked; only the lower triangular | |
portion is used. | |
The Wishart distribution is often denoted | |
.. math:: | |
W_p(\nu, \Sigma) | |
where :math:`\nu` is the degrees of freedom and :math:`\Sigma` is the | |
:math:`p \times p` scale matrix. | |
The probability density function for `wishart` has support over positive | |
definite matrices :math:`S`; if :math:`S \sim W_p(\nu, \Sigma)`, then | |
its PDF is given by: | |
.. math:: | |
f(S) = \frac{|S|^{\frac{\nu - p - 1}{2}}}{2^{ \frac{\nu p}{2} } | |
|\Sigma|^\frac{\nu}{2} \Gamma_p \left ( \frac{\nu}{2} \right )} | |
\exp\left( -tr(\Sigma^{-1} S) / 2 \right) | |
If :math:`S \sim W_p(\nu, \Sigma)` (Wishart) then | |
:math:`S^{-1} \sim W_p^{-1}(\nu, \Sigma^{-1})` (inverse Wishart). | |
If the scale matrix is 1-dimensional and equal to one, then the Wishart | |
distribution :math:`W_1(\nu, 1)` collapses to the :math:`\chi^2(\nu)` | |
distribution. | |
The algorithm [2]_ implemented by the `rvs` method may | |
produce numerically singular matrices with :math:`p - 1 < \nu < p`; the | |
user may wish to check for this condition and generate replacement samples | |
as necessary. | |
.. versionadded:: 0.16.0 | |
References | |
---------- | |
.. [1] M.L. Eaton, "Multivariate Statistics: A Vector Space Approach", | |
Wiley, 1983. | |
.. [2] W.B. Smith and R.R. Hocking, "Algorithm AS 53: Wishart Variate | |
Generator", Applied Statistics, vol. 21, pp. 341-345, 1972. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> import matplotlib.pyplot as plt | |
>>> from scipy.stats import wishart, chi2 | |
>>> x = np.linspace(1e-5, 8, 100) | |
>>> w = wishart.pdf(x, df=3, scale=1); w[:5] | |
array([ 0.00126156, 0.10892176, 0.14793434, 0.17400548, 0.1929669 ]) | |
>>> c = chi2.pdf(x, 3); c[:5] | |
array([ 0.00126156, 0.10892176, 0.14793434, 0.17400548, 0.1929669 ]) | |
>>> plt.plot(x, w) | |
>>> plt.show() | |
The input quantiles can be any shape of array, as long as the last | |
axis labels the components. | |
Alternatively, the object may be called (as a function) to fix the degrees | |
of freedom and scale parameters, returning a "frozen" Wishart random | |
variable: | |
>>> rv = wishart(df=1, scale=1) | |
>>> # Frozen object with the same methods but holding the given | |
>>> # degrees of freedom and scale fixed. | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__, wishart_docdict_params) | |
def __call__(self, df=None, scale=None, seed=None): | |
"""Create a frozen Wishart distribution. | |
See `wishart_frozen` for more information. | |
""" | |
return wishart_frozen(df, scale, seed) | |
def _process_parameters(self, df, scale): | |
if scale is None: | |
scale = 1.0 | |
scale = np.asarray(scale, dtype=float) | |
if scale.ndim == 0: | |
scale = scale[np.newaxis, np.newaxis] | |
elif scale.ndim == 1: | |
scale = np.diag(scale) | |
elif scale.ndim == 2 and not scale.shape[0] == scale.shape[1]: | |
raise ValueError("Array 'scale' must be square if it is two" | |
" dimensional, but scale.scale = %s." | |
% str(scale.shape)) | |
elif scale.ndim > 2: | |
raise ValueError("Array 'scale' must be at most two-dimensional," | |
" but scale.ndim = %d" % scale.ndim) | |
dim = scale.shape[0] | |
if df is None: | |
df = dim | |
elif not np.isscalar(df): | |
raise ValueError("Degrees of freedom must be a scalar.") | |
elif df <= dim - 1: | |
raise ValueError("Degrees of freedom must be greater than the " | |
"dimension of scale matrix minus 1.") | |
return dim, df, scale | |
def _process_quantiles(self, x, dim): | |
""" | |
Adjust quantiles array so that last axis labels the components of | |
each data point. | |
""" | |
x = np.asarray(x, dtype=float) | |
if x.ndim == 0: | |
x = x * np.eye(dim)[:, :, np.newaxis] | |
if x.ndim == 1: | |
if dim == 1: | |
x = x[np.newaxis, np.newaxis, :] | |
else: | |
x = np.diag(x)[:, :, np.newaxis] | |
elif x.ndim == 2: | |
if not x.shape[0] == x.shape[1]: | |
raise ValueError("Quantiles must be square if they are two" | |
" dimensional, but x.shape = %s." | |
% str(x.shape)) | |
x = x[:, :, np.newaxis] | |
elif x.ndim == 3: | |
if not x.shape[0] == x.shape[1]: | |
raise ValueError("Quantiles must be square in the first two" | |
" dimensions if they are three dimensional" | |
", but x.shape = %s." % str(x.shape)) | |
elif x.ndim > 3: | |
raise ValueError("Quantiles must be at most two-dimensional with" | |
" an additional dimension for multiple" | |
"components, but x.ndim = %d" % x.ndim) | |
# Now we have 3-dim array; should have shape [dim, dim, *] | |
if not x.shape[0:2] == (dim, dim): | |
raise ValueError('Quantiles have incompatible dimensions: should' | |
f' be {(dim, dim)}, got {x.shape[0:2]}.') | |
return x | |
def _process_size(self, size): | |
size = np.asarray(size) | |
if size.ndim == 0: | |
size = size[np.newaxis] | |
elif size.ndim > 1: | |
raise ValueError('Size must be an integer or tuple of integers;' | |
' thus must have dimension <= 1.' | |
' Got size.ndim = %s' % str(tuple(size))) | |
n = size.prod() | |
shape = tuple(size) | |
return n, shape | |
def _logpdf(self, x, dim, df, scale, log_det_scale, C): | |
"""Log of the Wishart probability density function. | |
Parameters | |
---------- | |
x : ndarray | |
Points at which to evaluate the log of the probability | |
density function | |
dim : int | |
Dimension of the scale matrix | |
df : int | |
Degrees of freedom | |
scale : ndarray | |
Scale matrix | |
log_det_scale : float | |
Logarithm of the determinant of the scale matrix | |
C : ndarray | |
Cholesky factorization of the scale matrix, lower triagular. | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'logpdf' instead. | |
""" | |
# log determinant of x | |
# Note: x has components along the last axis, so that x.T has | |
# components alone the 0-th axis. Then since det(A) = det(A'), this | |
# gives us a 1-dim vector of determinants | |
# Retrieve tr(scale^{-1} x) | |
log_det_x = np.empty(x.shape[-1]) | |
scale_inv_x = np.empty(x.shape) | |
tr_scale_inv_x = np.empty(x.shape[-1]) | |
for i in range(x.shape[-1]): | |
_, log_det_x[i] = self._cholesky_logdet(x[:, :, i]) | |
scale_inv_x[:, :, i] = scipy.linalg.cho_solve((C, True), x[:, :, i]) | |
tr_scale_inv_x[i] = scale_inv_x[:, :, i].trace() | |
# Log PDF | |
out = ((0.5 * (df - dim - 1) * log_det_x - 0.5 * tr_scale_inv_x) - | |
(0.5 * df * dim * _LOG_2 + 0.5 * df * log_det_scale + | |
multigammaln(0.5*df, dim))) | |
return out | |
def logpdf(self, x, df, scale): | |
"""Log of the Wishart probability density function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
Each quantile must be a symmetric positive definite matrix. | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
pdf : ndarray | |
Log of the probability density function evaluated at `x` | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
dim, df, scale = self._process_parameters(df, scale) | |
x = self._process_quantiles(x, dim) | |
# Cholesky decomposition of scale, get log(det(scale)) | |
C, log_det_scale = self._cholesky_logdet(scale) | |
out = self._logpdf(x, dim, df, scale, log_det_scale, C) | |
return _squeeze_output(out) | |
def pdf(self, x, df, scale): | |
"""Wishart probability density function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
Each quantile must be a symmetric positive definite matrix. | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
pdf : ndarray | |
Probability density function evaluated at `x` | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
return np.exp(self.logpdf(x, df, scale)) | |
def _mean(self, dim, df, scale): | |
"""Mean of the Wishart distribution. | |
Parameters | |
---------- | |
dim : int | |
Dimension of the scale matrix | |
%(_doc_default_callparams)s | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'mean' instead. | |
""" | |
return df * scale | |
def mean(self, df, scale): | |
"""Mean of the Wishart distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
mean : float | |
The mean of the distribution | |
""" | |
dim, df, scale = self._process_parameters(df, scale) | |
out = self._mean(dim, df, scale) | |
return _squeeze_output(out) | |
def _mode(self, dim, df, scale): | |
"""Mode of the Wishart distribution. | |
Parameters | |
---------- | |
dim : int | |
Dimension of the scale matrix | |
%(_doc_default_callparams)s | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'mode' instead. | |
""" | |
if df >= dim + 1: | |
out = (df-dim-1) * scale | |
else: | |
out = None | |
return out | |
def mode(self, df, scale): | |
"""Mode of the Wishart distribution | |
Only valid if the degrees of freedom are greater than the dimension of | |
the scale matrix. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
mode : float or None | |
The Mode of the distribution | |
""" | |
dim, df, scale = self._process_parameters(df, scale) | |
out = self._mode(dim, df, scale) | |
return _squeeze_output(out) if out is not None else out | |
def _var(self, dim, df, scale): | |
"""Variance of the Wishart distribution. | |
Parameters | |
---------- | |
dim : int | |
Dimension of the scale matrix | |
%(_doc_default_callparams)s | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'var' instead. | |
""" | |
var = scale**2 | |
diag = scale.diagonal() # 1 x dim array | |
var += np.outer(diag, diag) | |
var *= df | |
return var | |
def var(self, df, scale): | |
"""Variance of the Wishart distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
var : float | |
The variance of the distribution | |
""" | |
dim, df, scale = self._process_parameters(df, scale) | |
out = self._var(dim, df, scale) | |
return _squeeze_output(out) | |
def _standard_rvs(self, n, shape, dim, df, random_state): | |
""" | |
Parameters | |
---------- | |
n : integer | |
Number of variates to generate | |
shape : iterable | |
Shape of the variates to generate | |
dim : int | |
Dimension of the scale matrix | |
df : int | |
Degrees of freedom | |
random_state : {None, int, `numpy.random.Generator`, | |
`numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance | |
then that instance is used. | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'rvs' instead. | |
""" | |
# Random normal variates for off-diagonal elements | |
n_tril = dim * (dim-1) // 2 | |
covariances = random_state.normal( | |
size=n*n_tril).reshape(shape+(n_tril,)) | |
# Random chi-square variates for diagonal elements | |
variances = (np.r_[[random_state.chisquare(df-(i+1)+1, size=n)**0.5 | |
for i in range(dim)]].reshape((dim,) + | |
shape[::-1]).T) | |
# Create the A matri(ces) - lower triangular | |
A = np.zeros(shape + (dim, dim)) | |
# Input the covariances | |
size_idx = tuple([slice(None, None, None)]*len(shape)) | |
tril_idx = np.tril_indices(dim, k=-1) | |
A[size_idx + tril_idx] = covariances | |
# Input the variances | |
diag_idx = np.diag_indices(dim) | |
A[size_idx + diag_idx] = variances | |
return A | |
def _rvs(self, n, shape, dim, df, C, random_state): | |
"""Draw random samples from a Wishart distribution. | |
Parameters | |
---------- | |
n : integer | |
Number of variates to generate | |
shape : iterable | |
Shape of the variates to generate | |
dim : int | |
Dimension of the scale matrix | |
df : int | |
Degrees of freedom | |
C : ndarray | |
Cholesky factorization of the scale matrix, lower triangular. | |
%(_doc_random_state)s | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'rvs' instead. | |
""" | |
random_state = self._get_random_state(random_state) | |
# Calculate the matrices A, which are actually lower triangular | |
# Cholesky factorizations of a matrix B such that B ~ W(df, I) | |
A = self._standard_rvs(n, shape, dim, df, random_state) | |
# Calculate SA = C A A' C', where SA ~ W(df, scale) | |
# Note: this is the product of a (lower) (lower) (lower)' (lower)' | |
# or, denoting B = AA', it is C B C' where C is the lower | |
# triangular Cholesky factorization of the scale matrix. | |
# this appears to conflict with the instructions in [1]_, which | |
# suggest that it should be D' B D where D is the lower | |
# triangular factorization of the scale matrix. However, it is | |
# meant to refer to the Bartlett (1933) representation of a | |
# Wishart random variate as L A A' L' where L is lower triangular | |
# so it appears that understanding D' to be upper triangular | |
# is either a typo in or misreading of [1]_. | |
for index in np.ndindex(shape): | |
CA = np.dot(C, A[index]) | |
A[index] = np.dot(CA, CA.T) | |
return A | |
def rvs(self, df, scale, size=1, random_state=None): | |
"""Draw random samples from a Wishart distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
size : integer or iterable of integers, optional | |
Number of samples to draw (default 1). | |
%(_doc_random_state)s | |
Returns | |
------- | |
rvs : ndarray | |
Random variates of shape (`size`) + (``dim``, ``dim``), where | |
``dim`` is the dimension of the scale matrix. | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
n, shape = self._process_size(size) | |
dim, df, scale = self._process_parameters(df, scale) | |
# Cholesky decomposition of scale | |
C = scipy.linalg.cholesky(scale, lower=True) | |
out = self._rvs(n, shape, dim, df, C, random_state) | |
return _squeeze_output(out) | |
def _entropy(self, dim, df, log_det_scale): | |
"""Compute the differential entropy of the Wishart. | |
Parameters | |
---------- | |
dim : int | |
Dimension of the scale matrix | |
df : int | |
Degrees of freedom | |
log_det_scale : float | |
Logarithm of the determinant of the scale matrix | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'entropy' instead. | |
""" | |
return ( | |
0.5 * (dim+1) * log_det_scale + | |
0.5 * dim * (dim+1) * _LOG_2 + | |
multigammaln(0.5*df, dim) - | |
0.5 * (df - dim - 1) * np.sum( | |
[psi(0.5*(df + 1 - (i+1))) for i in range(dim)] | |
) + | |
0.5 * df * dim | |
) | |
def entropy(self, df, scale): | |
"""Compute the differential entropy of the Wishart. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
h : scalar | |
Entropy of the Wishart distribution | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
dim, df, scale = self._process_parameters(df, scale) | |
_, log_det_scale = self._cholesky_logdet(scale) | |
return self._entropy(dim, df, log_det_scale) | |
def _cholesky_logdet(self, scale): | |
"""Compute Cholesky decomposition and determine (log(det(scale)). | |
Parameters | |
---------- | |
scale : ndarray | |
Scale matrix. | |
Returns | |
------- | |
c_decomp : ndarray | |
The Cholesky decomposition of `scale`. | |
logdet : scalar | |
The log of the determinant of `scale`. | |
Notes | |
----- | |
This computation of ``logdet`` is equivalent to | |
``np.linalg.slogdet(scale)``. It is ~2x faster though. | |
""" | |
c_decomp = scipy.linalg.cholesky(scale, lower=True) | |
logdet = 2 * np.sum(np.log(c_decomp.diagonal())) | |
return c_decomp, logdet | |
wishart = wishart_gen() | |
class wishart_frozen(multi_rv_frozen): | |
"""Create a frozen Wishart distribution. | |
Parameters | |
---------- | |
df : array_like | |
Degrees of freedom of the distribution | |
scale : array_like | |
Scale matrix of the distribution | |
seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance then | |
that instance is used. | |
""" | |
def __init__(self, df, scale, seed=None): | |
self._dist = wishart_gen(seed) | |
self.dim, self.df, self.scale = self._dist._process_parameters( | |
df, scale) | |
self.C, self.log_det_scale = self._dist._cholesky_logdet(self.scale) | |
def logpdf(self, x): | |
x = self._dist._process_quantiles(x, self.dim) | |
out = self._dist._logpdf(x, self.dim, self.df, self.scale, | |
self.log_det_scale, self.C) | |
return _squeeze_output(out) | |
def pdf(self, x): | |
return np.exp(self.logpdf(x)) | |
def mean(self): | |
out = self._dist._mean(self.dim, self.df, self.scale) | |
return _squeeze_output(out) | |
def mode(self): | |
out = self._dist._mode(self.dim, self.df, self.scale) | |
return _squeeze_output(out) if out is not None else out | |
def var(self): | |
out = self._dist._var(self.dim, self.df, self.scale) | |
return _squeeze_output(out) | |
def rvs(self, size=1, random_state=None): | |
n, shape = self._dist._process_size(size) | |
out = self._dist._rvs(n, shape, self.dim, self.df, | |
self.C, random_state) | |
return _squeeze_output(out) | |
def entropy(self): | |
return self._dist._entropy(self.dim, self.df, self.log_det_scale) | |
# Set frozen generator docstrings from corresponding docstrings in | |
# Wishart and fill in default strings in class docstrings | |
for name in ['logpdf', 'pdf', 'mean', 'mode', 'var', 'rvs', 'entropy']: | |
method = wishart_gen.__dict__[name] | |
method_frozen = wishart_frozen.__dict__[name] | |
method_frozen.__doc__ = doccer.docformat( | |
method.__doc__, wishart_docdict_noparams) | |
method.__doc__ = doccer.docformat(method.__doc__, wishart_docdict_params) | |
class invwishart_gen(wishart_gen): | |
r"""An inverse Wishart random variable. | |
The `df` keyword specifies the degrees of freedom. The `scale` keyword | |
specifies the scale matrix, which must be symmetric and positive definite. | |
In this context, the scale matrix is often interpreted in terms of a | |
multivariate normal covariance matrix. | |
Methods | |
------- | |
pdf(x, df, scale) | |
Probability density function. | |
logpdf(x, df, scale) | |
Log of the probability density function. | |
rvs(df, scale, size=1, random_state=None) | |
Draw random samples from an inverse Wishart distribution. | |
entropy(df, scale) | |
Differential entropy of the distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
%(_doc_random_state)s | |
Raises | |
------ | |
scipy.linalg.LinAlgError | |
If the scale matrix `scale` is not positive definite. | |
See Also | |
-------- | |
wishart | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
The scale matrix `scale` must be a symmetric positive definite | |
matrix. Singular matrices, including the symmetric positive semi-definite | |
case, are not supported. Symmetry is not checked; only the lower triangular | |
portion is used. | |
The inverse Wishart distribution is often denoted | |
.. math:: | |
W_p^{-1}(\nu, \Psi) | |
where :math:`\nu` is the degrees of freedom and :math:`\Psi` is the | |
:math:`p \times p` scale matrix. | |
The probability density function for `invwishart` has support over positive | |
definite matrices :math:`S`; if :math:`S \sim W^{-1}_p(\nu, \Sigma)`, | |
then its PDF is given by: | |
.. math:: | |
f(S) = \frac{|\Sigma|^\frac{\nu}{2}}{2^{ \frac{\nu p}{2} } | |
|S|^{\frac{\nu + p + 1}{2}} \Gamma_p \left(\frac{\nu}{2} \right)} | |
\exp\left( -tr(\Sigma S^{-1}) / 2 \right) | |
If :math:`S \sim W_p^{-1}(\nu, \Psi)` (inverse Wishart) then | |
:math:`S^{-1} \sim W_p(\nu, \Psi^{-1})` (Wishart). | |
If the scale matrix is 1-dimensional and equal to one, then the inverse | |
Wishart distribution :math:`W_1(\nu, 1)` collapses to the | |
inverse Gamma distribution with parameters shape = :math:`\frac{\nu}{2}` | |
and scale = :math:`\frac{1}{2}`. | |
Instead of inverting a randomly generated Wishart matrix as described in [2], | |
here the algorithm in [4] is used to directly generate a random inverse-Wishart | |
matrix without inversion. | |
.. versionadded:: 0.16.0 | |
References | |
---------- | |
.. [1] M.L. Eaton, "Multivariate Statistics: A Vector Space Approach", | |
Wiley, 1983. | |
.. [2] M.C. Jones, "Generating Inverse Wishart Matrices", Communications | |
in Statistics - Simulation and Computation, vol. 14.2, pp.511-514, | |
1985. | |
.. [3] Gupta, M. and Srivastava, S. "Parametric Bayesian Estimation of | |
Differential Entropy and Relative Entropy". Entropy 12, 818 - 843. | |
2010. | |
.. [4] S.D. Axen, "Efficiently generating inverse-Wishart matrices and | |
their Cholesky factors", :arXiv:`2310.15884v1`. 2023. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> import matplotlib.pyplot as plt | |
>>> from scipy.stats import invwishart, invgamma | |
>>> x = np.linspace(0.01, 1, 100) | |
>>> iw = invwishart.pdf(x, df=6, scale=1) | |
>>> iw[:3] | |
array([ 1.20546865e-15, 5.42497807e-06, 4.45813929e-03]) | |
>>> ig = invgamma.pdf(x, 6/2., scale=1./2) | |
>>> ig[:3] | |
array([ 1.20546865e-15, 5.42497807e-06, 4.45813929e-03]) | |
>>> plt.plot(x, iw) | |
>>> plt.show() | |
The input quantiles can be any shape of array, as long as the last | |
axis labels the components. | |
Alternatively, the object may be called (as a function) to fix the degrees | |
of freedom and scale parameters, returning a "frozen" inverse Wishart | |
random variable: | |
>>> rv = invwishart(df=1, scale=1) | |
>>> # Frozen object with the same methods but holding the given | |
>>> # degrees of freedom and scale fixed. | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__, wishart_docdict_params) | |
def __call__(self, df=None, scale=None, seed=None): | |
"""Create a frozen inverse Wishart distribution. | |
See `invwishart_frozen` for more information. | |
""" | |
return invwishart_frozen(df, scale, seed) | |
def _logpdf(self, x, dim, df, log_det_scale, C): | |
"""Log of the inverse Wishart probability density function. | |
Parameters | |
---------- | |
x : ndarray | |
Points at which to evaluate the log of the probability | |
density function. | |
dim : int | |
Dimension of the scale matrix | |
df : int | |
Degrees of freedom | |
log_det_scale : float | |
Logarithm of the determinant of the scale matrix | |
C : ndarray | |
Cholesky factorization of the scale matrix, lower triagular. | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'logpdf' instead. | |
""" | |
# Retrieve tr(scale x^{-1}) | |
log_det_x = np.empty(x.shape[-1]) | |
tr_scale_x_inv = np.empty(x.shape[-1]) | |
trsm = get_blas_funcs(('trsm'), (x,)) | |
if dim > 1: | |
for i in range(x.shape[-1]): | |
Cx, log_det_x[i] = self._cholesky_logdet(x[:, :, i]) | |
A = trsm(1., Cx, C, side=0, lower=True) | |
tr_scale_x_inv[i] = np.linalg.norm(A)**2 | |
else: | |
log_det_x[:] = np.log(x[0, 0]) | |
tr_scale_x_inv[:] = C[0, 0]**2 / x[0, 0] | |
# Log PDF | |
out = ((0.5 * df * log_det_scale - 0.5 * tr_scale_x_inv) - | |
(0.5 * df * dim * _LOG_2 + 0.5 * (df + dim + 1) * log_det_x) - | |
multigammaln(0.5*df, dim)) | |
return out | |
def logpdf(self, x, df, scale): | |
"""Log of the inverse Wishart probability density function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
Each quantile must be a symmetric positive definite matrix. | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
pdf : ndarray | |
Log of the probability density function evaluated at `x` | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
dim, df, scale = self._process_parameters(df, scale) | |
x = self._process_quantiles(x, dim) | |
C, log_det_scale = self._cholesky_logdet(scale) | |
out = self._logpdf(x, dim, df, log_det_scale, C) | |
return _squeeze_output(out) | |
def pdf(self, x, df, scale): | |
"""Inverse Wishart probability density function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
Each quantile must be a symmetric positive definite matrix. | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
pdf : ndarray | |
Probability density function evaluated at `x` | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
return np.exp(self.logpdf(x, df, scale)) | |
def _mean(self, dim, df, scale): | |
"""Mean of the inverse Wishart distribution. | |
Parameters | |
---------- | |
dim : int | |
Dimension of the scale matrix | |
%(_doc_default_callparams)s | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'mean' instead. | |
""" | |
if df > dim + 1: | |
out = scale / (df - dim - 1) | |
else: | |
out = None | |
return out | |
def mean(self, df, scale): | |
"""Mean of the inverse Wishart distribution. | |
Only valid if the degrees of freedom are greater than the dimension of | |
the scale matrix plus one. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
mean : float or None | |
The mean of the distribution | |
""" | |
dim, df, scale = self._process_parameters(df, scale) | |
out = self._mean(dim, df, scale) | |
return _squeeze_output(out) if out is not None else out | |
def _mode(self, dim, df, scale): | |
"""Mode of the inverse Wishart distribution. | |
Parameters | |
---------- | |
dim : int | |
Dimension of the scale matrix | |
%(_doc_default_callparams)s | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'mode' instead. | |
""" | |
return scale / (df + dim + 1) | |
def mode(self, df, scale): | |
"""Mode of the inverse Wishart distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
mode : float | |
The Mode of the distribution | |
""" | |
dim, df, scale = self._process_parameters(df, scale) | |
out = self._mode(dim, df, scale) | |
return _squeeze_output(out) | |
def _var(self, dim, df, scale): | |
"""Variance of the inverse Wishart distribution. | |
Parameters | |
---------- | |
dim : int | |
Dimension of the scale matrix | |
%(_doc_default_callparams)s | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'var' instead. | |
""" | |
if df > dim + 3: | |
var = (df - dim + 1) * scale**2 | |
diag = scale.diagonal() # 1 x dim array | |
var += (df - dim - 1) * np.outer(diag, diag) | |
var /= (df - dim) * (df - dim - 1)**2 * (df - dim - 3) | |
else: | |
var = None | |
return var | |
def var(self, df, scale): | |
"""Variance of the inverse Wishart distribution. | |
Only valid if the degrees of freedom are greater than the dimension of | |
the scale matrix plus three. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
var : float | |
The variance of the distribution | |
""" | |
dim, df, scale = self._process_parameters(df, scale) | |
out = self._var(dim, df, scale) | |
return _squeeze_output(out) if out is not None else out | |
def _inv_standard_rvs(self, n, shape, dim, df, random_state): | |
""" | |
Parameters | |
---------- | |
n : integer | |
Number of variates to generate | |
shape : iterable | |
Shape of the variates to generate | |
dim : int | |
Dimension of the scale matrix | |
df : int | |
Degrees of freedom | |
random_state : {None, int, `numpy.random.Generator`, | |
`numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance | |
then that instance is used. | |
Returns | |
------- | |
A : ndarray | |
Random variates of shape (`shape`) + (``dim``, ``dim``). | |
Each slice `A[..., :, :]` is lower-triangular, and its | |
inverse is the lower Cholesky factor of a draw from | |
`invwishart(df, np.eye(dim))`. | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'rvs' instead. | |
""" | |
A = np.zeros(shape + (dim, dim)) | |
# Random normal variates for off-diagonal elements | |
tri_rows, tri_cols = np.tril_indices(dim, k=-1) | |
n_tril = dim * (dim-1) // 2 | |
A[..., tri_rows, tri_cols] = random_state.normal( | |
size=(*shape, n_tril), | |
) | |
# Random chi variates for diagonal elements | |
rows = np.arange(dim) | |
chi_dfs = (df - dim + 1) + rows | |
A[..., rows, rows] = random_state.chisquare( | |
df=chi_dfs, size=(*shape, dim), | |
)**0.5 | |
return A | |
def _rvs(self, n, shape, dim, df, C, random_state): | |
"""Draw random samples from an inverse Wishart distribution. | |
Parameters | |
---------- | |
n : integer | |
Number of variates to generate | |
shape : iterable | |
Shape of the variates to generate | |
dim : int | |
Dimension of the scale matrix | |
df : int | |
Degrees of freedom | |
C : ndarray | |
Cholesky factorization of the scale matrix, lower triagular. | |
%(_doc_random_state)s | |
Notes | |
----- | |
As this function does no argument checking, it should not be | |
called directly; use 'rvs' instead. | |
""" | |
random_state = self._get_random_state(random_state) | |
# Get random draws A such that inv(A) ~ iW(df, I) | |
A = self._inv_standard_rvs(n, shape, dim, df, random_state) | |
# Calculate SA = (CA)'^{-1} (CA)^{-1} ~ iW(df, scale) | |
trsm = get_blas_funcs(('trsm'), (A,)) | |
trmm = get_blas_funcs(('trmm'), (A,)) | |
for index in np.ndindex(A.shape[:-2]): | |
if dim > 1: | |
# Calculate CA | |
# Get CA = C A^{-1} via triangular solver | |
CA = trsm(1., A[index], C, side=1, lower=True) | |
# get SA | |
A[index] = trmm(1., CA, CA, side=1, lower=True, trans_a=True) | |
else: | |
A[index][0, 0] = (C[0, 0] / A[index][0, 0])**2 | |
return A | |
def rvs(self, df, scale, size=1, random_state=None): | |
"""Draw random samples from an inverse Wishart distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
size : integer or iterable of integers, optional | |
Number of samples to draw (default 1). | |
%(_doc_random_state)s | |
Returns | |
------- | |
rvs : ndarray | |
Random variates of shape (`size`) + (``dim``, ``dim``), where | |
``dim`` is the dimension of the scale matrix. | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
n, shape = self._process_size(size) | |
dim, df, scale = self._process_parameters(df, scale) | |
# Cholesky decomposition of scale | |
C = scipy.linalg.cholesky(scale, lower=True) | |
out = self._rvs(n, shape, dim, df, C, random_state) | |
return _squeeze_output(out) | |
def _entropy(self, dim, df, log_det_scale): | |
# reference: eq. (17) from ref. 3 | |
psi_eval_points = [0.5 * (df - dim + i) for i in range(1, dim + 1)] | |
psi_eval_points = np.asarray(psi_eval_points) | |
return multigammaln(0.5 * df, dim) + 0.5 * dim * df + \ | |
0.5 * (dim + 1) * (log_det_scale - _LOG_2) - \ | |
0.5 * (df + dim + 1) * \ | |
psi(psi_eval_points, out=psi_eval_points).sum() | |
def entropy(self, df, scale): | |
dim, df, scale = self._process_parameters(df, scale) | |
_, log_det_scale = self._cholesky_logdet(scale) | |
return self._entropy(dim, df, log_det_scale) | |
invwishart = invwishart_gen() | |
class invwishart_frozen(multi_rv_frozen): | |
def __init__(self, df, scale, seed=None): | |
"""Create a frozen inverse Wishart distribution. | |
Parameters | |
---------- | |
df : array_like | |
Degrees of freedom of the distribution | |
scale : array_like | |
Scale matrix of the distribution | |
seed : {None, int, `numpy.random.Generator`}, optional | |
If `seed` is None the `numpy.random.Generator` singleton is used. | |
If `seed` is an int, a new ``Generator`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` instance then that instance is | |
used. | |
""" | |
self._dist = invwishart_gen(seed) | |
self.dim, self.df, self.scale = self._dist._process_parameters( | |
df, scale | |
) | |
# Get the determinant via Cholesky factorization | |
self.C = scipy.linalg.cholesky(self.scale, lower=True) | |
self.log_det_scale = 2 * np.sum(np.log(self.C.diagonal())) | |
def logpdf(self, x): | |
x = self._dist._process_quantiles(x, self.dim) | |
out = self._dist._logpdf(x, self.dim, self.df, | |
self.log_det_scale, self.C) | |
return _squeeze_output(out) | |
def pdf(self, x): | |
return np.exp(self.logpdf(x)) | |
def mean(self): | |
out = self._dist._mean(self.dim, self.df, self.scale) | |
return _squeeze_output(out) if out is not None else out | |
def mode(self): | |
out = self._dist._mode(self.dim, self.df, self.scale) | |
return _squeeze_output(out) | |
def var(self): | |
out = self._dist._var(self.dim, self.df, self.scale) | |
return _squeeze_output(out) if out is not None else out | |
def rvs(self, size=1, random_state=None): | |
n, shape = self._dist._process_size(size) | |
out = self._dist._rvs(n, shape, self.dim, self.df, | |
self.C, random_state) | |
return _squeeze_output(out) | |
def entropy(self): | |
return self._dist._entropy(self.dim, self.df, self.log_det_scale) | |
# Set frozen generator docstrings from corresponding docstrings in | |
# inverse Wishart and fill in default strings in class docstrings | |
for name in ['logpdf', 'pdf', 'mean', 'mode', 'var', 'rvs']: | |
method = invwishart_gen.__dict__[name] | |
method_frozen = wishart_frozen.__dict__[name] | |
method_frozen.__doc__ = doccer.docformat( | |
method.__doc__, wishart_docdict_noparams) | |
method.__doc__ = doccer.docformat(method.__doc__, wishart_docdict_params) | |
_multinomial_doc_default_callparams = """\ | |
n : int | |
Number of trials | |
p : array_like | |
Probability of a trial falling into each category; should sum to 1 | |
""" | |
_multinomial_doc_callparams_note = """\ | |
`n` should be a nonnegative integer. Each element of `p` should be in the | |
interval :math:`[0,1]` and the elements should sum to 1. If they do not sum to | |
1, the last element of the `p` array is not used and is replaced with the | |
remaining probability left over from the earlier elements. | |
""" | |
_multinomial_doc_frozen_callparams = "" | |
_multinomial_doc_frozen_callparams_note = """\ | |
See class definition for a detailed description of parameters.""" | |
multinomial_docdict_params = { | |
'_doc_default_callparams': _multinomial_doc_default_callparams, | |
'_doc_callparams_note': _multinomial_doc_callparams_note, | |
'_doc_random_state': _doc_random_state | |
} | |
multinomial_docdict_noparams = { | |
'_doc_default_callparams': _multinomial_doc_frozen_callparams, | |
'_doc_callparams_note': _multinomial_doc_frozen_callparams_note, | |
'_doc_random_state': _doc_random_state | |
} | |
class multinomial_gen(multi_rv_generic): | |
r"""A multinomial random variable. | |
Methods | |
------- | |
pmf(x, n, p) | |
Probability mass function. | |
logpmf(x, n, p) | |
Log of the probability mass function. | |
rvs(n, p, size=1, random_state=None) | |
Draw random samples from a multinomial distribution. | |
entropy(n, p) | |
Compute the entropy of the multinomial distribution. | |
cov(n, p) | |
Compute the covariance matrix of the multinomial distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
%(_doc_random_state)s | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
The probability mass function for `multinomial` is | |
.. math:: | |
f(x) = \frac{n!}{x_1! \cdots x_k!} p_1^{x_1} \cdots p_k^{x_k}, | |
supported on :math:`x=(x_1, \ldots, x_k)` where each :math:`x_i` is a | |
nonnegative integer and their sum is :math:`n`. | |
.. versionadded:: 0.19.0 | |
Examples | |
-------- | |
>>> from scipy.stats import multinomial | |
>>> rv = multinomial(8, [0.3, 0.2, 0.5]) | |
>>> rv.pmf([1, 3, 4]) | |
0.042000000000000072 | |
The multinomial distribution for :math:`k=2` is identical to the | |
corresponding binomial distribution (tiny numerical differences | |
notwithstanding): | |
>>> from scipy.stats import binom | |
>>> multinomial.pmf([3, 4], n=7, p=[0.4, 0.6]) | |
0.29030399999999973 | |
>>> binom.pmf(3, 7, 0.4) | |
0.29030400000000012 | |
The functions ``pmf``, ``logpmf``, ``entropy``, and ``cov`` support | |
broadcasting, under the convention that the vector parameters (``x`` and | |
``p``) are interpreted as if each row along the last axis is a single | |
object. For instance: | |
>>> multinomial.pmf([[3, 4], [3, 5]], n=[7, 8], p=[.3, .7]) | |
array([0.2268945, 0.25412184]) | |
Here, ``x.shape == (2, 2)``, ``n.shape == (2,)``, and ``p.shape == (2,)``, | |
but following the rules mentioned above they behave as if the rows | |
``[3, 4]`` and ``[3, 5]`` in ``x`` and ``[.3, .7]`` in ``p`` were a single | |
object, and as if we had ``x.shape = (2,)``, ``n.shape = (2,)``, and | |
``p.shape = ()``. To obtain the individual elements without broadcasting, | |
we would do this: | |
>>> multinomial.pmf([3, 4], n=7, p=[.3, .7]) | |
0.2268945 | |
>>> multinomial.pmf([3, 5], 8, p=[.3, .7]) | |
0.25412184 | |
This broadcasting also works for ``cov``, where the output objects are | |
square matrices of size ``p.shape[-1]``. For example: | |
>>> multinomial.cov([4, 5], [[.3, .7], [.4, .6]]) | |
array([[[ 0.84, -0.84], | |
[-0.84, 0.84]], | |
[[ 1.2 , -1.2 ], | |
[-1.2 , 1.2 ]]]) | |
In this example, ``n.shape == (2,)`` and ``p.shape == (2, 2)``, and | |
following the rules above, these broadcast as if ``p.shape == (2,)``. | |
Thus the result should also be of shape ``(2,)``, but since each output is | |
a :math:`2 \times 2` matrix, the result in fact has shape ``(2, 2, 2)``, | |
where ``result[0]`` is equal to ``multinomial.cov(n=4, p=[.3, .7])`` and | |
``result[1]`` is equal to ``multinomial.cov(n=5, p=[.4, .6])``. | |
Alternatively, the object may be called (as a function) to fix the `n` and | |
`p` parameters, returning a "frozen" multinomial random variable: | |
>>> rv = multinomial(n=7, p=[.3, .7]) | |
>>> # Frozen object with the same methods but holding the given | |
>>> # degrees of freedom and scale fixed. | |
See also | |
-------- | |
scipy.stats.binom : The binomial distribution. | |
numpy.random.Generator.multinomial : Sampling from the multinomial distribution. | |
scipy.stats.multivariate_hypergeom : | |
The multivariate hypergeometric distribution. | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = \ | |
doccer.docformat(self.__doc__, multinomial_docdict_params) | |
def __call__(self, n, p, seed=None): | |
"""Create a frozen multinomial distribution. | |
See `multinomial_frozen` for more information. | |
""" | |
return multinomial_frozen(n, p, seed) | |
def _process_parameters(self, n, p, eps=1e-15): | |
"""Returns: n_, p_, npcond. | |
n_ and p_ are arrays of the correct shape; npcond is a boolean array | |
flagging values out of the domain. | |
""" | |
p = np.array(p, dtype=np.float64, copy=True) | |
p_adjusted = 1. - p[..., :-1].sum(axis=-1) | |
i_adjusted = np.abs(p_adjusted) > eps | |
p[i_adjusted, -1] = p_adjusted[i_adjusted] | |
# true for bad p | |
pcond = np.any(p < 0, axis=-1) | |
pcond |= np.any(p > 1, axis=-1) | |
n = np.array(n, dtype=int, copy=True) | |
# true for bad n | |
ncond = n < 0 | |
return n, p, ncond | pcond | |
def _process_quantiles(self, x, n, p): | |
"""Returns: x_, xcond. | |
x_ is an int array; xcond is a boolean array flagging values out of the | |
domain. | |
""" | |
xx = np.asarray(x, dtype=int) | |
if xx.ndim == 0: | |
raise ValueError("x must be an array.") | |
if xx.size != 0 and not xx.shape[-1] == p.shape[-1]: | |
raise ValueError("Size of each quantile should be size of p: " | |
"received %d, but expected %d." % | |
(xx.shape[-1], p.shape[-1])) | |
# true for x out of the domain | |
cond = np.any(xx != x, axis=-1) | |
cond |= np.any(xx < 0, axis=-1) | |
cond = cond | (np.sum(xx, axis=-1) != n) | |
return xx, cond | |
def _checkresult(self, result, cond, bad_value): | |
result = np.asarray(result) | |
if cond.ndim != 0: | |
result[cond] = bad_value | |
elif cond: | |
if result.ndim == 0: | |
return bad_value | |
result[...] = bad_value | |
return result | |
def _logpmf(self, x, n, p): | |
return gammaln(n+1) + np.sum(xlogy(x, p) - gammaln(x+1), axis=-1) | |
def logpmf(self, x, n, p): | |
"""Log of the Multinomial probability mass function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
logpmf : ndarray or scalar | |
Log of the probability mass function evaluated at `x` | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
n, p, npcond = self._process_parameters(n, p) | |
x, xcond = self._process_quantiles(x, n, p) | |
result = self._logpmf(x, n, p) | |
# replace values for which x was out of the domain; broadcast | |
# xcond to the right shape | |
xcond_ = xcond | np.zeros(npcond.shape, dtype=np.bool_) | |
result = self._checkresult(result, xcond_, -np.inf) | |
# replace values bad for n or p; broadcast npcond to the right shape | |
npcond_ = npcond | np.zeros(xcond.shape, dtype=np.bool_) | |
return self._checkresult(result, npcond_, np.nan) | |
def pmf(self, x, n, p): | |
"""Multinomial probability mass function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
pmf : ndarray or scalar | |
Probability density function evaluated at `x` | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
return np.exp(self.logpmf(x, n, p)) | |
def mean(self, n, p): | |
"""Mean of the Multinomial distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
mean : float | |
The mean of the distribution | |
""" | |
n, p, npcond = self._process_parameters(n, p) | |
result = n[..., np.newaxis]*p | |
return self._checkresult(result, npcond, np.nan) | |
def cov(self, n, p): | |
"""Covariance matrix of the multinomial distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
cov : ndarray | |
The covariance matrix of the distribution | |
""" | |
n, p, npcond = self._process_parameters(n, p) | |
nn = n[..., np.newaxis, np.newaxis] | |
result = nn * np.einsum('...j,...k->...jk', -p, p) | |
# change the diagonal | |
for i in range(p.shape[-1]): | |
result[..., i, i] += n*p[..., i] | |
return self._checkresult(result, npcond, np.nan) | |
def entropy(self, n, p): | |
r"""Compute the entropy of the multinomial distribution. | |
The entropy is computed using this expression: | |
.. math:: | |
f(x) = - \log n! - n\sum_{i=1}^k p_i \log p_i + | |
\sum_{i=1}^k \sum_{x=0}^n \binom n x p_i^x(1-p_i)^{n-x} \log x! | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
h : scalar | |
Entropy of the Multinomial distribution | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
n, p, npcond = self._process_parameters(n, p) | |
x = np.r_[1:np.max(n)+1] | |
term1 = n*np.sum(entr(p), axis=-1) | |
term1 -= gammaln(n+1) | |
n = n[..., np.newaxis] | |
new_axes_needed = max(p.ndim, n.ndim) - x.ndim + 1 | |
x.shape += (1,)*new_axes_needed | |
term2 = np.sum(binom.pmf(x, n, p)*gammaln(x+1), | |
axis=(-1, -1-new_axes_needed)) | |
return self._checkresult(term1 + term2, npcond, np.nan) | |
def rvs(self, n, p, size=None, random_state=None): | |
"""Draw random samples from a Multinomial distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
size : integer or iterable of integers, optional | |
Number of samples to draw (default 1). | |
%(_doc_random_state)s | |
Returns | |
------- | |
rvs : ndarray or scalar | |
Random variates of shape (`size`, `len(p)`) | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
n, p, npcond = self._process_parameters(n, p) | |
random_state = self._get_random_state(random_state) | |
return random_state.multinomial(n, p, size) | |
multinomial = multinomial_gen() | |
class multinomial_frozen(multi_rv_frozen): | |
r"""Create a frozen Multinomial distribution. | |
Parameters | |
---------- | |
n : int | |
number of trials | |
p: array_like | |
probability of a trial falling into each category; should sum to 1 | |
seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance then | |
that instance is used. | |
""" | |
def __init__(self, n, p, seed=None): | |
self._dist = multinomial_gen(seed) | |
self.n, self.p, self.npcond = self._dist._process_parameters(n, p) | |
# monkey patch self._dist | |
def _process_parameters(n, p): | |
return self.n, self.p, self.npcond | |
self._dist._process_parameters = _process_parameters | |
def logpmf(self, x): | |
return self._dist.logpmf(x, self.n, self.p) | |
def pmf(self, x): | |
return self._dist.pmf(x, self.n, self.p) | |
def mean(self): | |
return self._dist.mean(self.n, self.p) | |
def cov(self): | |
return self._dist.cov(self.n, self.p) | |
def entropy(self): | |
return self._dist.entropy(self.n, self.p) | |
def rvs(self, size=1, random_state=None): | |
return self._dist.rvs(self.n, self.p, size, random_state) | |
# Set frozen generator docstrings from corresponding docstrings in | |
# multinomial and fill in default strings in class docstrings | |
for name in ['logpmf', 'pmf', 'mean', 'cov', 'rvs']: | |
method = multinomial_gen.__dict__[name] | |
method_frozen = multinomial_frozen.__dict__[name] | |
method_frozen.__doc__ = doccer.docformat( | |
method.__doc__, multinomial_docdict_noparams) | |
method.__doc__ = doccer.docformat(method.__doc__, | |
multinomial_docdict_params) | |
class special_ortho_group_gen(multi_rv_generic): | |
r"""A Special Orthogonal matrix (SO(N)) random variable. | |
Return a random rotation matrix, drawn from the Haar distribution | |
(the only uniform distribution on SO(N)) with a determinant of +1. | |
The `dim` keyword specifies the dimension N. | |
Methods | |
------- | |
rvs(dim=None, size=1, random_state=None) | |
Draw random samples from SO(N). | |
Parameters | |
---------- | |
dim : scalar | |
Dimension of matrices | |
seed : {None, int, np.random.RandomState, np.random.Generator}, optional | |
Used for drawing random variates. | |
If `seed` is `None`, the `~np.random.RandomState` singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, seeded | |
with seed. | |
If `seed` is already a ``RandomState`` or ``Generator`` instance, | |
then that object is used. | |
Default is `None`. | |
Notes | |
----- | |
This class is wrapping the random_rot code from the MDP Toolkit, | |
https://github.com/mdp-toolkit/mdp-toolkit | |
Return a random rotation matrix, drawn from the Haar distribution | |
(the only uniform distribution on SO(N)). | |
The algorithm is described in the paper | |
Stewart, G.W., "The efficient generation of random orthogonal | |
matrices with an application to condition estimators", SIAM Journal | |
on Numerical Analysis, 17(3), pp. 403-409, 1980. | |
For more information see | |
https://en.wikipedia.org/wiki/Orthogonal_matrix#Randomization | |
See also the similar `ortho_group`. For a random rotation in three | |
dimensions, see `scipy.spatial.transform.Rotation.random`. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.stats import special_ortho_group | |
>>> x = special_ortho_group.rvs(3) | |
>>> np.dot(x, x.T) | |
array([[ 1.00000000e+00, 1.13231364e-17, -2.86852790e-16], | |
[ 1.13231364e-17, 1.00000000e+00, -1.46845020e-16], | |
[ -2.86852790e-16, -1.46845020e-16, 1.00000000e+00]]) | |
>>> import scipy.linalg | |
>>> scipy.linalg.det(x) | |
1.0 | |
This generates one random matrix from SO(3). It is orthogonal and | |
has a determinant of 1. | |
Alternatively, the object may be called (as a function) to fix the `dim` | |
parameter, returning a "frozen" special_ortho_group random variable: | |
>>> rv = special_ortho_group(5) | |
>>> # Frozen object with the same methods but holding the | |
>>> # dimension parameter fixed. | |
See Also | |
-------- | |
ortho_group, scipy.spatial.transform.Rotation.random | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__) | |
def __call__(self, dim=None, seed=None): | |
"""Create a frozen SO(N) distribution. | |
See `special_ortho_group_frozen` for more information. | |
""" | |
return special_ortho_group_frozen(dim, seed=seed) | |
def _process_parameters(self, dim): | |
"""Dimension N must be specified; it cannot be inferred.""" | |
if dim is None or not np.isscalar(dim) or dim <= 1 or dim != int(dim): | |
raise ValueError("""Dimension of rotation must be specified, | |
and must be a scalar greater than 1.""") | |
return dim | |
def rvs(self, dim, size=1, random_state=None): | |
"""Draw random samples from SO(N). | |
Parameters | |
---------- | |
dim : integer | |
Dimension of rotation space (N). | |
size : integer, optional | |
Number of samples to draw (default 1). | |
Returns | |
------- | |
rvs : ndarray or scalar | |
Random size N-dimensional matrices, dimension (size, dim, dim) | |
""" | |
random_state = self._get_random_state(random_state) | |
size = int(size) | |
size = (size,) if size > 1 else () | |
dim = self._process_parameters(dim) | |
# H represents a (dim, dim) matrix, while D represents the diagonal of | |
# a (dim, dim) diagonal matrix. The algorithm that follows is | |
# broadcasted on the leading shape in `size` to vectorize along | |
# samples. | |
H = np.empty(size + (dim, dim)) | |
H[..., :, :] = np.eye(dim) | |
D = np.empty(size + (dim,)) | |
for n in range(dim-1): | |
# x is a vector with length dim-n, xrow and xcol are views of it as | |
# a row vector and column vector respectively. It's important they | |
# are views and not copies because we are going to modify x | |
# in-place. | |
x = random_state.normal(size=size + (dim-n,)) | |
xrow = x[..., None, :] | |
xcol = x[..., :, None] | |
# This is the squared norm of x, without vectorization it would be | |
# dot(x, x), to have proper broadcasting we use matmul and squeeze | |
# out (convert to scalar) the resulting 1x1 matrix | |
norm2 = np.matmul(xrow, xcol).squeeze((-2, -1)) | |
x0 = x[..., 0].copy() | |
D[..., n] = np.where(x0 != 0, np.sign(x0), 1) | |
x[..., 0] += D[..., n]*np.sqrt(norm2) | |
# In renormalizing x we have to append an additional axis with | |
# [..., None] to broadcast the scalar against the vector x | |
x /= np.sqrt((norm2 - x0**2 + x[..., 0]**2) / 2.)[..., None] | |
# Householder transformation, without vectorization the RHS can be | |
# written as outer(H @ x, x) (apart from the slicing) | |
H[..., :, n:] -= np.matmul(H[..., :, n:], xcol) * xrow | |
D[..., -1] = (-1)**(dim-1)*D[..., :-1].prod(axis=-1) | |
# Without vectorization this could be written as H = diag(D) @ H, | |
# left-multiplication by a diagonal matrix amounts to multiplying each | |
# row of H by an element of the diagonal, so we add a dummy axis for | |
# the column index | |
H *= D[..., :, None] | |
return H | |
special_ortho_group = special_ortho_group_gen() | |
class special_ortho_group_frozen(multi_rv_frozen): | |
def __init__(self, dim=None, seed=None): | |
"""Create a frozen SO(N) distribution. | |
Parameters | |
---------- | |
dim : scalar | |
Dimension of matrices | |
seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance | |
then that instance is used. | |
Examples | |
-------- | |
>>> from scipy.stats import special_ortho_group | |
>>> g = special_ortho_group(5) | |
>>> x = g.rvs() | |
""" # numpy/numpydoc#87 # noqa: E501 | |
self._dist = special_ortho_group_gen(seed) | |
self.dim = self._dist._process_parameters(dim) | |
def rvs(self, size=1, random_state=None): | |
return self._dist.rvs(self.dim, size, random_state) | |
class ortho_group_gen(multi_rv_generic): | |
r"""An Orthogonal matrix (O(N)) random variable. | |
Return a random orthogonal matrix, drawn from the O(N) Haar | |
distribution (the only uniform distribution on O(N)). | |
The `dim` keyword specifies the dimension N. | |
Methods | |
------- | |
rvs(dim=None, size=1, random_state=None) | |
Draw random samples from O(N). | |
Parameters | |
---------- | |
dim : scalar | |
Dimension of matrices | |
seed : {None, int, np.random.RandomState, np.random.Generator}, optional | |
Used for drawing random variates. | |
If `seed` is `None`, the `~np.random.RandomState` singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, seeded | |
with seed. | |
If `seed` is already a ``RandomState`` or ``Generator`` instance, | |
then that object is used. | |
Default is `None`. | |
Notes | |
----- | |
This class is closely related to `special_ortho_group`. | |
Some care is taken to avoid numerical error, as per the paper by Mezzadri. | |
References | |
---------- | |
.. [1] F. Mezzadri, "How to generate random matrices from the classical | |
compact groups", :arXiv:`math-ph/0609050v2`. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.stats import ortho_group | |
>>> x = ortho_group.rvs(3) | |
>>> np.dot(x, x.T) | |
array([[ 1.00000000e+00, 1.13231364e-17, -2.86852790e-16], | |
[ 1.13231364e-17, 1.00000000e+00, -1.46845020e-16], | |
[ -2.86852790e-16, -1.46845020e-16, 1.00000000e+00]]) | |
>>> import scipy.linalg | |
>>> np.fabs(scipy.linalg.det(x)) | |
1.0 | |
This generates one random matrix from O(3). It is orthogonal and | |
has a determinant of +1 or -1. | |
Alternatively, the object may be called (as a function) to fix the `dim` | |
parameter, returning a "frozen" ortho_group random variable: | |
>>> rv = ortho_group(5) | |
>>> # Frozen object with the same methods but holding the | |
>>> # dimension parameter fixed. | |
See Also | |
-------- | |
special_ortho_group | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__) | |
def __call__(self, dim=None, seed=None): | |
"""Create a frozen O(N) distribution. | |
See `ortho_group_frozen` for more information. | |
""" | |
return ortho_group_frozen(dim, seed=seed) | |
def _process_parameters(self, dim): | |
"""Dimension N must be specified; it cannot be inferred.""" | |
if dim is None or not np.isscalar(dim) or dim <= 1 or dim != int(dim): | |
raise ValueError("Dimension of rotation must be specified," | |
"and must be a scalar greater than 1.") | |
return dim | |
def rvs(self, dim, size=1, random_state=None): | |
"""Draw random samples from O(N). | |
Parameters | |
---------- | |
dim : integer | |
Dimension of rotation space (N). | |
size : integer, optional | |
Number of samples to draw (default 1). | |
Returns | |
------- | |
rvs : ndarray or scalar | |
Random size N-dimensional matrices, dimension (size, dim, dim) | |
""" | |
random_state = self._get_random_state(random_state) | |
size = int(size) | |
dim = self._process_parameters(dim) | |
size = (size,) if size > 1 else () | |
z = random_state.normal(size=size + (dim, dim)) | |
q, r = np.linalg.qr(z) | |
# The last two dimensions are the rows and columns of R matrices. | |
# Extract the diagonals. Note that this eliminates a dimension. | |
d = r.diagonal(offset=0, axis1=-2, axis2=-1) | |
# Add back a dimension for proper broadcasting: we're dividing | |
# each row of each R matrix by the diagonal of the R matrix. | |
q *= (d/abs(d))[..., np.newaxis, :] # to broadcast properly | |
return q | |
ortho_group = ortho_group_gen() | |
class ortho_group_frozen(multi_rv_frozen): | |
def __init__(self, dim=None, seed=None): | |
"""Create a frozen O(N) distribution. | |
Parameters | |
---------- | |
dim : scalar | |
Dimension of matrices | |
seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance | |
then that instance is used. | |
Examples | |
-------- | |
>>> from scipy.stats import ortho_group | |
>>> g = ortho_group(5) | |
>>> x = g.rvs() | |
""" # numpy/numpydoc#87 # noqa: E501 | |
self._dist = ortho_group_gen(seed) | |
self.dim = self._dist._process_parameters(dim) | |
def rvs(self, size=1, random_state=None): | |
return self._dist.rvs(self.dim, size, random_state) | |
class random_correlation_gen(multi_rv_generic): | |
r"""A random correlation matrix. | |
Return a random correlation matrix, given a vector of eigenvalues. | |
The `eigs` keyword specifies the eigenvalues of the correlation matrix, | |
and implies the dimension. | |
Methods | |
------- | |
rvs(eigs=None, random_state=None) | |
Draw random correlation matrices, all with eigenvalues eigs. | |
Parameters | |
---------- | |
eigs : 1d ndarray | |
Eigenvalues of correlation matrix | |
seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance | |
then that instance is used. | |
tol : float, optional | |
Tolerance for input parameter checks | |
diag_tol : float, optional | |
Tolerance for deviation of the diagonal of the resulting | |
matrix. Default: 1e-7 | |
Raises | |
------ | |
RuntimeError | |
Floating point error prevented generating a valid correlation | |
matrix. | |
Returns | |
------- | |
rvs : ndarray or scalar | |
Random size N-dimensional matrices, dimension (size, dim, dim), | |
each having eigenvalues eigs. | |
Notes | |
----- | |
Generates a random correlation matrix following a numerically stable | |
algorithm spelled out by Davies & Higham. This algorithm uses a single O(N) | |
similarity transformation to construct a symmetric positive semi-definite | |
matrix, and applies a series of Givens rotations to scale it to have ones | |
on the diagonal. | |
References | |
---------- | |
.. [1] Davies, Philip I; Higham, Nicholas J; "Numerically stable generation | |
of correlation matrices and their factors", BIT 2000, Vol. 40, | |
No. 4, pp. 640 651 | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.stats import random_correlation | |
>>> rng = np.random.default_rng() | |
>>> x = random_correlation.rvs((.5, .8, 1.2, 1.5), random_state=rng) | |
>>> x | |
array([[ 1. , -0.02423399, 0.03130519, 0.4946965 ], | |
[-0.02423399, 1. , 0.20334736, 0.04039817], | |
[ 0.03130519, 0.20334736, 1. , 0.02694275], | |
[ 0.4946965 , 0.04039817, 0.02694275, 1. ]]) | |
>>> import scipy.linalg | |
>>> e, v = scipy.linalg.eigh(x) | |
>>> e | |
array([ 0.5, 0.8, 1.2, 1.5]) | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__) | |
def __call__(self, eigs, seed=None, tol=1e-13, diag_tol=1e-7): | |
"""Create a frozen random correlation matrix. | |
See `random_correlation_frozen` for more information. | |
""" | |
return random_correlation_frozen(eigs, seed=seed, tol=tol, | |
diag_tol=diag_tol) | |
def _process_parameters(self, eigs, tol): | |
eigs = np.asarray(eigs, dtype=float) | |
dim = eigs.size | |
if eigs.ndim != 1 or eigs.shape[0] != dim or dim <= 1: | |
raise ValueError("Array 'eigs' must be a vector of length " | |
"greater than 1.") | |
if np.fabs(np.sum(eigs) - dim) > tol: | |
raise ValueError("Sum of eigenvalues must equal dimensionality.") | |
for x in eigs: | |
if x < -tol: | |
raise ValueError("All eigenvalues must be non-negative.") | |
return dim, eigs | |
def _givens_to_1(self, aii, ajj, aij): | |
"""Computes a 2x2 Givens matrix to put 1's on the diagonal. | |
The input matrix is a 2x2 symmetric matrix M = [ aii aij ; aij ajj ]. | |
The output matrix g is a 2x2 anti-symmetric matrix of the form | |
[ c s ; -s c ]; the elements c and s are returned. | |
Applying the output matrix to the input matrix (as b=g.T M g) | |
results in a matrix with bii=1, provided tr(M) - det(M) >= 1 | |
and floating point issues do not occur. Otherwise, some other | |
valid rotation is returned. When tr(M)==2, also bjj=1. | |
""" | |
aiid = aii - 1. | |
ajjd = ajj - 1. | |
if ajjd == 0: | |
# ajj==1, so swap aii and ajj to avoid division by zero | |
return 0., 1. | |
dd = math.sqrt(max(aij**2 - aiid*ajjd, 0)) | |
# The choice of t should be chosen to avoid cancellation [1] | |
t = (aij + math.copysign(dd, aij)) / ajjd | |
c = 1. / math.sqrt(1. + t*t) | |
if c == 0: | |
# Underflow | |
s = 1.0 | |
else: | |
s = c*t | |
return c, s | |
def _to_corr(self, m): | |
""" | |
Given a psd matrix m, rotate to put one's on the diagonal, turning it | |
into a correlation matrix. This also requires the trace equal the | |
dimensionality. Note: modifies input matrix | |
""" | |
# Check requirements for in-place Givens | |
if not (m.flags.c_contiguous and m.dtype == np.float64 and | |
m.shape[0] == m.shape[1]): | |
raise ValueError() | |
d = m.shape[0] | |
for i in range(d-1): | |
if m[i, i] == 1: | |
continue | |
elif m[i, i] > 1: | |
for j in range(i+1, d): | |
if m[j, j] < 1: | |
break | |
else: | |
for j in range(i+1, d): | |
if m[j, j] > 1: | |
break | |
c, s = self._givens_to_1(m[i, i], m[j, j], m[i, j]) | |
# Use BLAS to apply Givens rotations in-place. Equivalent to: | |
# g = np.eye(d) | |
# g[i, i] = g[j,j] = c | |
# g[j, i] = -s; g[i, j] = s | |
# m = np.dot(g.T, np.dot(m, g)) | |
mv = m.ravel() | |
drot(mv, mv, c, -s, n=d, | |
offx=i*d, incx=1, offy=j*d, incy=1, | |
overwrite_x=True, overwrite_y=True) | |
drot(mv, mv, c, -s, n=d, | |
offx=i, incx=d, offy=j, incy=d, | |
overwrite_x=True, overwrite_y=True) | |
return m | |
def rvs(self, eigs, random_state=None, tol=1e-13, diag_tol=1e-7): | |
"""Draw random correlation matrices. | |
Parameters | |
---------- | |
eigs : 1d ndarray | |
Eigenvalues of correlation matrix | |
tol : float, optional | |
Tolerance for input parameter checks | |
diag_tol : float, optional | |
Tolerance for deviation of the diagonal of the resulting | |
matrix. Default: 1e-7 | |
Raises | |
------ | |
RuntimeError | |
Floating point error prevented generating a valid correlation | |
matrix. | |
Returns | |
------- | |
rvs : ndarray or scalar | |
Random size N-dimensional matrices, dimension (size, dim, dim), | |
each having eigenvalues eigs. | |
""" | |
dim, eigs = self._process_parameters(eigs, tol=tol) | |
random_state = self._get_random_state(random_state) | |
m = ortho_group.rvs(dim, random_state=random_state) | |
m = np.dot(np.dot(m, np.diag(eigs)), m.T) # Set the trace of m | |
m = self._to_corr(m) # Carefully rotate to unit diagonal | |
# Check diagonal | |
if abs(m.diagonal() - 1).max() > diag_tol: | |
raise RuntimeError("Failed to generate a valid correlation matrix") | |
return m | |
random_correlation = random_correlation_gen() | |
class random_correlation_frozen(multi_rv_frozen): | |
def __init__(self, eigs, seed=None, tol=1e-13, diag_tol=1e-7): | |
"""Create a frozen random correlation matrix distribution. | |
Parameters | |
---------- | |
eigs : 1d ndarray | |
Eigenvalues of correlation matrix | |
seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance | |
then that instance is used. | |
tol : float, optional | |
Tolerance for input parameter checks | |
diag_tol : float, optional | |
Tolerance for deviation of the diagonal of the resulting | |
matrix. Default: 1e-7 | |
Raises | |
------ | |
RuntimeError | |
Floating point error prevented generating a valid correlation | |
matrix. | |
Returns | |
------- | |
rvs : ndarray or scalar | |
Random size N-dimensional matrices, dimension (size, dim, dim), | |
each having eigenvalues eigs. | |
""" # numpy/numpydoc#87 # noqa: E501 | |
self._dist = random_correlation_gen(seed) | |
self.tol = tol | |
self.diag_tol = diag_tol | |
_, self.eigs = self._dist._process_parameters(eigs, tol=self.tol) | |
def rvs(self, random_state=None): | |
return self._dist.rvs(self.eigs, random_state=random_state, | |
tol=self.tol, diag_tol=self.diag_tol) | |
class unitary_group_gen(multi_rv_generic): | |
r"""A matrix-valued U(N) random variable. | |
Return a random unitary matrix. | |
The `dim` keyword specifies the dimension N. | |
Methods | |
------- | |
rvs(dim=None, size=1, random_state=None) | |
Draw random samples from U(N). | |
Parameters | |
---------- | |
dim : scalar | |
Dimension of matrices, must be greater than 1. | |
seed : {None, int, np.random.RandomState, np.random.Generator}, optional | |
Used for drawing random variates. | |
If `seed` is `None`, the `~np.random.RandomState` singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, seeded | |
with seed. | |
If `seed` is already a ``RandomState`` or ``Generator`` instance, | |
then that object is used. | |
Default is `None`. | |
Notes | |
----- | |
This class is similar to `ortho_group`. | |
References | |
---------- | |
.. [1] F. Mezzadri, "How to generate random matrices from the classical | |
compact groups", :arXiv:`math-ph/0609050v2`. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.stats import unitary_group | |
>>> x = unitary_group.rvs(3) | |
>>> np.dot(x, x.conj().T) | |
array([[ 1.00000000e+00, 1.13231364e-17, -2.86852790e-16], | |
[ 1.13231364e-17, 1.00000000e+00, -1.46845020e-16], | |
[ -2.86852790e-16, -1.46845020e-16, 1.00000000e+00]]) | |
This generates one random matrix from U(3). The dot product confirms that | |
it is unitary up to machine precision. | |
Alternatively, the object may be called (as a function) to fix the `dim` | |
parameter, return a "frozen" unitary_group random variable: | |
>>> rv = unitary_group(5) | |
See Also | |
-------- | |
ortho_group | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__) | |
def __call__(self, dim=None, seed=None): | |
"""Create a frozen (U(N)) n-dimensional unitary matrix distribution. | |
See `unitary_group_frozen` for more information. | |
""" | |
return unitary_group_frozen(dim, seed=seed) | |
def _process_parameters(self, dim): | |
"""Dimension N must be specified; it cannot be inferred.""" | |
if dim is None or not np.isscalar(dim) or dim <= 1 or dim != int(dim): | |
raise ValueError("Dimension of rotation must be specified," | |
"and must be a scalar greater than 1.") | |
return dim | |
def rvs(self, dim, size=1, random_state=None): | |
"""Draw random samples from U(N). | |
Parameters | |
---------- | |
dim : integer | |
Dimension of space (N). | |
size : integer, optional | |
Number of samples to draw (default 1). | |
Returns | |
------- | |
rvs : ndarray or scalar | |
Random size N-dimensional matrices, dimension (size, dim, dim) | |
""" | |
random_state = self._get_random_state(random_state) | |
size = int(size) | |
dim = self._process_parameters(dim) | |
size = (size,) if size > 1 else () | |
z = 1/math.sqrt(2)*(random_state.normal(size=size + (dim, dim)) + | |
1j*random_state.normal(size=size + (dim, dim))) | |
q, r = np.linalg.qr(z) | |
# The last two dimensions are the rows and columns of R matrices. | |
# Extract the diagonals. Note that this eliminates a dimension. | |
d = r.diagonal(offset=0, axis1=-2, axis2=-1) | |
# Add back a dimension for proper broadcasting: we're dividing | |
# each row of each R matrix by the diagonal of the R matrix. | |
q *= (d/abs(d))[..., np.newaxis, :] # to broadcast properly | |
return q | |
unitary_group = unitary_group_gen() | |
class unitary_group_frozen(multi_rv_frozen): | |
def __init__(self, dim=None, seed=None): | |
"""Create a frozen (U(N)) n-dimensional unitary matrix distribution. | |
Parameters | |
---------- | |
dim : scalar | |
Dimension of matrices | |
seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance | |
then that instance is used. | |
Examples | |
-------- | |
>>> from scipy.stats import unitary_group | |
>>> x = unitary_group(3) | |
>>> x.rvs() | |
""" # numpy/numpydoc#87 # noqa: E501 | |
self._dist = unitary_group_gen(seed) | |
self.dim = self._dist._process_parameters(dim) | |
def rvs(self, size=1, random_state=None): | |
return self._dist.rvs(self.dim, size, random_state) | |
_mvt_doc_default_callparams = """\ | |
loc : array_like, optional | |
Location of the distribution. (default ``0``) | |
shape : array_like, optional | |
Positive semidefinite matrix of the distribution. (default ``1``) | |
df : float, optional | |
Degrees of freedom of the distribution; must be greater than zero. | |
If ``np.inf`` then results are multivariate normal. The default is ``1``. | |
allow_singular : bool, optional | |
Whether to allow a singular matrix. (default ``False``) | |
""" | |
_mvt_doc_callparams_note = """\ | |
Setting the parameter `loc` to ``None`` is equivalent to having `loc` | |
be the zero-vector. The parameter `shape` can be a scalar, in which case | |
the shape matrix is the identity times that value, a vector of | |
diagonal entries for the shape matrix, or a two-dimensional array_like. | |
""" | |
_mvt_doc_frozen_callparams_note = """\ | |
See class definition for a detailed description of parameters.""" | |
mvt_docdict_params = { | |
'_mvt_doc_default_callparams': _mvt_doc_default_callparams, | |
'_mvt_doc_callparams_note': _mvt_doc_callparams_note, | |
'_doc_random_state': _doc_random_state | |
} | |
mvt_docdict_noparams = { | |
'_mvt_doc_default_callparams': "", | |
'_mvt_doc_callparams_note': _mvt_doc_frozen_callparams_note, | |
'_doc_random_state': _doc_random_state | |
} | |
class multivariate_t_gen(multi_rv_generic): | |
r"""A multivariate t-distributed random variable. | |
The `loc` parameter specifies the location. The `shape` parameter specifies | |
the positive semidefinite shape matrix. The `df` parameter specifies the | |
degrees of freedom. | |
In addition to calling the methods below, the object itself may be called | |
as a function to fix the location, shape matrix, and degrees of freedom | |
parameters, returning a "frozen" multivariate t-distribution random. | |
Methods | |
------- | |
pdf(x, loc=None, shape=1, df=1, allow_singular=False) | |
Probability density function. | |
logpdf(x, loc=None, shape=1, df=1, allow_singular=False) | |
Log of the probability density function. | |
cdf(x, loc=None, shape=1, df=1, allow_singular=False, *, | |
maxpts=None, lower_limit=None, random_state=None) | |
Cumulative distribution function. | |
rvs(loc=None, shape=1, df=1, size=1, random_state=None) | |
Draw random samples from a multivariate t-distribution. | |
entropy(loc=None, shape=1, df=1) | |
Differential entropy of a multivariate t-distribution. | |
Parameters | |
---------- | |
%(_mvt_doc_default_callparams)s | |
%(_doc_random_state)s | |
Notes | |
----- | |
%(_mvt_doc_callparams_note)s | |
The matrix `shape` must be a (symmetric) positive semidefinite matrix. The | |
determinant and inverse of `shape` are computed as the pseudo-determinant | |
and pseudo-inverse, respectively, so that `shape` does not need to have | |
full rank. | |
The probability density function for `multivariate_t` is | |
.. math:: | |
f(x) = \frac{\Gamma((\nu + p)/2)}{\Gamma(\nu/2)\nu^{p/2}\pi^{p/2}|\Sigma|^{1/2}} | |
\left[1 + \frac{1}{\nu} (\mathbf{x} - \boldsymbol{\mu})^{\top} | |
\boldsymbol{\Sigma}^{-1} | |
(\mathbf{x} - \boldsymbol{\mu}) \right]^{-(\nu + p)/2}, | |
where :math:`p` is the dimension of :math:`\mathbf{x}`, | |
:math:`\boldsymbol{\mu}` is the :math:`p`-dimensional location, | |
:math:`\boldsymbol{\Sigma}` the :math:`p \times p`-dimensional shape | |
matrix, and :math:`\nu` is the degrees of freedom. | |
.. versionadded:: 1.6.0 | |
References | |
---------- | |
.. [1] Arellano-Valle et al. "Shannon Entropy and Mutual Information for | |
Multivariate Skew-Elliptical Distributions". Scandinavian Journal | |
of Statistics. Vol. 40, issue 1. | |
Examples | |
-------- | |
The object may be called (as a function) to fix the `loc`, `shape`, | |
`df`, and `allow_singular` parameters, returning a "frozen" | |
multivariate_t random variable: | |
>>> import numpy as np | |
>>> from scipy.stats import multivariate_t | |
>>> rv = multivariate_t([1.0, -0.5], [[2.1, 0.3], [0.3, 1.5]], df=2) | |
>>> # Frozen object with the same methods but holding the given location, | |
>>> # scale, and degrees of freedom fixed. | |
Create a contour plot of the PDF. | |
>>> import matplotlib.pyplot as plt | |
>>> x, y = np.mgrid[-1:3:.01, -2:1.5:.01] | |
>>> pos = np.dstack((x, y)) | |
>>> fig, ax = plt.subplots(1, 1) | |
>>> ax.set_aspect('equal') | |
>>> plt.contourf(x, y, rv.pdf(pos)) | |
""" | |
def __init__(self, seed=None): | |
"""Initialize a multivariate t-distributed random variable. | |
Parameters | |
---------- | |
seed : Random state. | |
""" | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__, mvt_docdict_params) | |
self._random_state = check_random_state(seed) | |
def __call__(self, loc=None, shape=1, df=1, allow_singular=False, | |
seed=None): | |
"""Create a frozen multivariate t-distribution. | |
See `multivariate_t_frozen` for parameters. | |
""" | |
if df == np.inf: | |
return multivariate_normal_frozen(mean=loc, cov=shape, | |
allow_singular=allow_singular, | |
seed=seed) | |
return multivariate_t_frozen(loc=loc, shape=shape, df=df, | |
allow_singular=allow_singular, seed=seed) | |
def pdf(self, x, loc=None, shape=1, df=1, allow_singular=False): | |
"""Multivariate t-distribution probability density function. | |
Parameters | |
---------- | |
x : array_like | |
Points at which to evaluate the probability density function. | |
%(_mvt_doc_default_callparams)s | |
Returns | |
------- | |
pdf : Probability density function evaluated at `x`. | |
Examples | |
-------- | |
>>> from scipy.stats import multivariate_t | |
>>> x = [0.4, 5] | |
>>> loc = [0, 1] | |
>>> shape = [[1, 0.1], [0.1, 1]] | |
>>> df = 7 | |
>>> multivariate_t.pdf(x, loc, shape, df) | |
0.00075713 | |
""" | |
dim, loc, shape, df = self._process_parameters(loc, shape, df) | |
x = self._process_quantiles(x, dim) | |
shape_info = _PSD(shape, allow_singular=allow_singular) | |
logpdf = self._logpdf(x, loc, shape_info.U, shape_info.log_pdet, df, | |
dim, shape_info.rank) | |
return np.exp(logpdf) | |
def logpdf(self, x, loc=None, shape=1, df=1): | |
"""Log of the multivariate t-distribution probability density function. | |
Parameters | |
---------- | |
x : array_like | |
Points at which to evaluate the log of the probability density | |
function. | |
%(_mvt_doc_default_callparams)s | |
Returns | |
------- | |
logpdf : Log of the probability density function evaluated at `x`. | |
Examples | |
-------- | |
>>> from scipy.stats import multivariate_t | |
>>> x = [0.4, 5] | |
>>> loc = [0, 1] | |
>>> shape = [[1, 0.1], [0.1, 1]] | |
>>> df = 7 | |
>>> multivariate_t.logpdf(x, loc, shape, df) | |
-7.1859802 | |
See Also | |
-------- | |
pdf : Probability density function. | |
""" | |
dim, loc, shape, df = self._process_parameters(loc, shape, df) | |
x = self._process_quantiles(x, dim) | |
shape_info = _PSD(shape) | |
return self._logpdf(x, loc, shape_info.U, shape_info.log_pdet, df, dim, | |
shape_info.rank) | |
def _logpdf(self, x, loc, prec_U, log_pdet, df, dim, rank): | |
"""Utility method `pdf`, `logpdf` for parameters. | |
Parameters | |
---------- | |
x : ndarray | |
Points at which to evaluate the log of the probability density | |
function. | |
loc : ndarray | |
Location of the distribution. | |
prec_U : ndarray | |
A decomposition such that `np.dot(prec_U, prec_U.T)` is the inverse | |
of the shape matrix. | |
log_pdet : float | |
Logarithm of the determinant of the shape matrix. | |
df : float | |
Degrees of freedom of the distribution. | |
dim : int | |
Dimension of the quantiles x. | |
rank : int | |
Rank of the shape matrix. | |
Notes | |
----- | |
As this function does no argument checking, it should not be called | |
directly; use 'logpdf' instead. | |
""" | |
if df == np.inf: | |
return multivariate_normal._logpdf(x, loc, prec_U, log_pdet, rank) | |
dev = x - loc | |
maha = np.square(np.dot(dev, prec_U)).sum(axis=-1) | |
t = 0.5 * (df + dim) | |
A = gammaln(t) | |
B = gammaln(0.5 * df) | |
C = dim/2. * np.log(df * np.pi) | |
D = 0.5 * log_pdet | |
E = -t * np.log(1 + (1./df) * maha) | |
return _squeeze_output(A - B - C - D + E) | |
def _cdf(self, x, loc, shape, df, dim, maxpts=None, lower_limit=None, | |
random_state=None): | |
# All of this - random state validation, maxpts, apply_along_axis, | |
# etc. needs to go in this private method unless we want | |
# frozen distribution's `cdf` method to duplicate it or call `cdf`, | |
# which would require re-processing parameters | |
if random_state is not None: | |
rng = check_random_state(random_state) | |
else: | |
rng = self._random_state | |
if not maxpts: | |
maxpts = 1000 * dim | |
x = self._process_quantiles(x, dim) | |
lower_limit = (np.full(loc.shape, -np.inf) | |
if lower_limit is None else lower_limit) | |
# remove the mean | |
x, lower_limit = x - loc, lower_limit - loc | |
b, a = np.broadcast_arrays(x, lower_limit) | |
i_swap = b < a | |
signs = (-1)**(i_swap.sum(axis=-1)) # odd # of swaps -> negative | |
a, b = a.copy(), b.copy() | |
a[i_swap], b[i_swap] = b[i_swap], a[i_swap] | |
n = x.shape[-1] | |
limits = np.concatenate((a, b), axis=-1) | |
def func1d(limits): | |
a, b = limits[:n], limits[n:] | |
return _qmvt(maxpts, df, shape, a, b, rng)[0] | |
res = np.apply_along_axis(func1d, -1, limits) * signs | |
# Fixing the output shape for existing distributions is a separate | |
# issue. For now, let's keep this consistent with pdf. | |
return _squeeze_output(res) | |
def cdf(self, x, loc=None, shape=1, df=1, allow_singular=False, *, | |
maxpts=None, lower_limit=None, random_state=None): | |
"""Multivariate t-distribution cumulative distribution function. | |
Parameters | |
---------- | |
x : array_like | |
Points at which to evaluate the cumulative distribution function. | |
%(_mvt_doc_default_callparams)s | |
maxpts : int, optional | |
Maximum number of points to use for integration. The default is | |
1000 times the number of dimensions. | |
lower_limit : array_like, optional | |
Lower limit of integration of the cumulative distribution function. | |
Default is negative infinity. Must be broadcastable with `x`. | |
%(_doc_random_state)s | |
Returns | |
------- | |
cdf : ndarray or scalar | |
Cumulative distribution function evaluated at `x`. | |
Examples | |
-------- | |
>>> from scipy.stats import multivariate_t | |
>>> x = [0.4, 5] | |
>>> loc = [0, 1] | |
>>> shape = [[1, 0.1], [0.1, 1]] | |
>>> df = 7 | |
>>> multivariate_t.cdf(x, loc, shape, df) | |
0.64798491 | |
""" | |
dim, loc, shape, df = self._process_parameters(loc, shape, df) | |
shape = _PSD(shape, allow_singular=allow_singular)._M | |
return self._cdf(x, loc, shape, df, dim, maxpts, | |
lower_limit, random_state) | |
def _entropy(self, dim, df=1, shape=1): | |
if df == np.inf: | |
return multivariate_normal(None, cov=shape).entropy() | |
shape_info = _PSD(shape) | |
shape_term = 0.5 * shape_info.log_pdet | |
def regular(dim, df): | |
halfsum = 0.5 * (dim + df) | |
half_df = 0.5 * df | |
return ( | |
-gammaln(halfsum) + gammaln(half_df) | |
+ 0.5 * dim * np.log(df * np.pi) + halfsum | |
* (psi(halfsum) - psi(half_df)) | |
+ shape_term | |
) | |
def asymptotic(dim, df): | |
# Formula from Wolfram Alpha: | |
# "asymptotic expansion -gammaln((m+d)/2) + gammaln(d/2) + (m*log(d*pi))/2 | |
# + ((m+d)/2) * (digamma((m+d)/2) - digamma(d/2))" | |
return ( | |
dim * norm._entropy() + dim / df | |
- dim * (dim - 2) * df**-2.0 / 4 | |
+ dim**2 * (dim - 2) * df**-3.0 / 6 | |
+ dim * (-3 * dim**3 + 8 * dim**2 - 8) * df**-4.0 / 24 | |
+ dim**2 * (3 * dim**3 - 10 * dim**2 + 16) * df**-5.0 / 30 | |
+ shape_term | |
)[()] | |
# preserves ~12 digits accuracy up to at least `dim=1e5`. See gh-18465. | |
threshold = dim * 100 * 4 / (np.log(dim) + 1) | |
return _lazywhere(df >= threshold, (dim, df), f=asymptotic, f2=regular) | |
def entropy(self, loc=None, shape=1, df=1): | |
"""Calculate the differential entropy of a multivariate | |
t-distribution. | |
Parameters | |
---------- | |
%(_mvt_doc_default_callparams)s | |
Returns | |
------- | |
h : float | |
Differential entropy | |
""" | |
dim, loc, shape, df = self._process_parameters(None, shape, df) | |
return self._entropy(dim, df, shape) | |
def rvs(self, loc=None, shape=1, df=1, size=1, random_state=None): | |
"""Draw random samples from a multivariate t-distribution. | |
Parameters | |
---------- | |
%(_mvt_doc_default_callparams)s | |
size : integer, optional | |
Number of samples to draw (default 1). | |
%(_doc_random_state)s | |
Returns | |
------- | |
rvs : ndarray or scalar | |
Random variates of size (`size`, `P`), where `P` is the | |
dimension of the random variable. | |
Examples | |
-------- | |
>>> from scipy.stats import multivariate_t | |
>>> x = [0.4, 5] | |
>>> loc = [0, 1] | |
>>> shape = [[1, 0.1], [0.1, 1]] | |
>>> df = 7 | |
>>> multivariate_t.rvs(loc, shape, df) | |
array([[0.93477495, 3.00408716]]) | |
""" | |
# For implementation details, see equation (3): | |
# | |
# Hofert, "On Sampling from the Multivariatet Distribution", 2013 | |
# http://rjournal.github.io/archive/2013-2/hofert.pdf | |
# | |
dim, loc, shape, df = self._process_parameters(loc, shape, df) | |
if random_state is not None: | |
rng = check_random_state(random_state) | |
else: | |
rng = self._random_state | |
if np.isinf(df): | |
x = np.ones(size) | |
else: | |
x = rng.chisquare(df, size=size) / df | |
z = rng.multivariate_normal(np.zeros(dim), shape, size=size) | |
samples = loc + z / np.sqrt(x)[..., None] | |
return _squeeze_output(samples) | |
def _process_quantiles(self, x, dim): | |
""" | |
Adjust quantiles array so that last axis labels the components of | |
each data point. | |
""" | |
x = np.asarray(x, dtype=float) | |
if x.ndim == 0: | |
x = x[np.newaxis] | |
elif x.ndim == 1: | |
if dim == 1: | |
x = x[:, np.newaxis] | |
else: | |
x = x[np.newaxis, :] | |
return x | |
def _process_parameters(self, loc, shape, df): | |
""" | |
Infer dimensionality from location array and shape matrix, handle | |
defaults, and ensure compatible dimensions. | |
""" | |
if loc is None and shape is None: | |
loc = np.asarray(0, dtype=float) | |
shape = np.asarray(1, dtype=float) | |
dim = 1 | |
elif loc is None: | |
shape = np.asarray(shape, dtype=float) | |
if shape.ndim < 2: | |
dim = 1 | |
else: | |
dim = shape.shape[0] | |
loc = np.zeros(dim) | |
elif shape is None: | |
loc = np.asarray(loc, dtype=float) | |
dim = loc.size | |
shape = np.eye(dim) | |
else: | |
shape = np.asarray(shape, dtype=float) | |
loc = np.asarray(loc, dtype=float) | |
dim = loc.size | |
if dim == 1: | |
loc = loc.reshape(1) | |
shape = shape.reshape(1, 1) | |
if loc.ndim != 1 or loc.shape[0] != dim: | |
raise ValueError("Array 'loc' must be a vector of length %d." % | |
dim) | |
if shape.ndim == 0: | |
shape = shape * np.eye(dim) | |
elif shape.ndim == 1: | |
shape = np.diag(shape) | |
elif shape.ndim == 2 and shape.shape != (dim, dim): | |
rows, cols = shape.shape | |
if rows != cols: | |
msg = ("Array 'cov' must be square if it is two dimensional," | |
" but cov.shape = %s." % str(shape.shape)) | |
else: | |
msg = ("Dimension mismatch: array 'cov' is of shape %s," | |
" but 'loc' is a vector of length %d.") | |
msg = msg % (str(shape.shape), len(loc)) | |
raise ValueError(msg) | |
elif shape.ndim > 2: | |
raise ValueError("Array 'cov' must be at most two-dimensional," | |
" but cov.ndim = %d" % shape.ndim) | |
# Process degrees of freedom. | |
if df is None: | |
df = 1 | |
elif df <= 0: | |
raise ValueError("'df' must be greater than zero.") | |
elif np.isnan(df): | |
raise ValueError("'df' is 'nan' but must be greater than zero or 'np.inf'.") | |
return dim, loc, shape, df | |
class multivariate_t_frozen(multi_rv_frozen): | |
def __init__(self, loc=None, shape=1, df=1, allow_singular=False, | |
seed=None): | |
"""Create a frozen multivariate t distribution. | |
Parameters | |
---------- | |
%(_mvt_doc_default_callparams)s | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.stats import multivariate_t | |
>>> loc = np.zeros(3) | |
>>> shape = np.eye(3) | |
>>> df = 10 | |
>>> dist = multivariate_t(loc, shape, df) | |
>>> dist.rvs() | |
array([[ 0.81412036, -1.53612361, 0.42199647]]) | |
>>> dist.pdf([1, 1, 1]) | |
array([0.01237803]) | |
""" | |
self._dist = multivariate_t_gen(seed) | |
dim, loc, shape, df = self._dist._process_parameters(loc, shape, df) | |
self.dim, self.loc, self.shape, self.df = dim, loc, shape, df | |
self.shape_info = _PSD(shape, allow_singular=allow_singular) | |
def logpdf(self, x): | |
x = self._dist._process_quantiles(x, self.dim) | |
U = self.shape_info.U | |
log_pdet = self.shape_info.log_pdet | |
return self._dist._logpdf(x, self.loc, U, log_pdet, self.df, self.dim, | |
self.shape_info.rank) | |
def cdf(self, x, *, maxpts=None, lower_limit=None, random_state=None): | |
x = self._dist._process_quantiles(x, self.dim) | |
return self._dist._cdf(x, self.loc, self.shape, self.df, self.dim, | |
maxpts, lower_limit, random_state) | |
def pdf(self, x): | |
return np.exp(self.logpdf(x)) | |
def rvs(self, size=1, random_state=None): | |
return self._dist.rvs(loc=self.loc, | |
shape=self.shape, | |
df=self.df, | |
size=size, | |
random_state=random_state) | |
def entropy(self): | |
return self._dist._entropy(self.dim, self.df, self.shape) | |
multivariate_t = multivariate_t_gen() | |
# Set frozen generator docstrings from corresponding docstrings in | |
# multivariate_t_gen and fill in default strings in class docstrings | |
for name in ['logpdf', 'pdf', 'rvs', 'cdf', 'entropy']: | |
method = multivariate_t_gen.__dict__[name] | |
method_frozen = multivariate_t_frozen.__dict__[name] | |
method_frozen.__doc__ = doccer.docformat(method.__doc__, | |
mvt_docdict_noparams) | |
method.__doc__ = doccer.docformat(method.__doc__, mvt_docdict_params) | |
_mhg_doc_default_callparams = """\ | |
m : array_like | |
The number of each type of object in the population. | |
That is, :math:`m[i]` is the number of objects of | |
type :math:`i`. | |
n : array_like | |
The number of samples taken from the population. | |
""" | |
_mhg_doc_callparams_note = """\ | |
`m` must be an array of positive integers. If the quantile | |
:math:`i` contains values out of the range :math:`[0, m_i]` | |
where :math:`m_i` is the number of objects of type :math:`i` | |
in the population or if the parameters are inconsistent with one | |
another (e.g. ``x.sum() != n``), methods return the appropriate | |
value (e.g. ``0`` for ``pmf``). If `m` or `n` contain negative | |
values, the result will contain ``nan`` there. | |
""" | |
_mhg_doc_frozen_callparams = "" | |
_mhg_doc_frozen_callparams_note = """\ | |
See class definition for a detailed description of parameters.""" | |
mhg_docdict_params = { | |
'_doc_default_callparams': _mhg_doc_default_callparams, | |
'_doc_callparams_note': _mhg_doc_callparams_note, | |
'_doc_random_state': _doc_random_state | |
} | |
mhg_docdict_noparams = { | |
'_doc_default_callparams': _mhg_doc_frozen_callparams, | |
'_doc_callparams_note': _mhg_doc_frozen_callparams_note, | |
'_doc_random_state': _doc_random_state | |
} | |
class multivariate_hypergeom_gen(multi_rv_generic): | |
r"""A multivariate hypergeometric random variable. | |
Methods | |
------- | |
pmf(x, m, n) | |
Probability mass function. | |
logpmf(x, m, n) | |
Log of the probability mass function. | |
rvs(m, n, size=1, random_state=None) | |
Draw random samples from a multivariate hypergeometric | |
distribution. | |
mean(m, n) | |
Mean of the multivariate hypergeometric distribution. | |
var(m, n) | |
Variance of the multivariate hypergeometric distribution. | |
cov(m, n) | |
Compute the covariance matrix of the multivariate | |
hypergeometric distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
%(_doc_random_state)s | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
The probability mass function for `multivariate_hypergeom` is | |
.. math:: | |
P(X_1 = x_1, X_2 = x_2, \ldots, X_k = x_k) = \frac{\binom{m_1}{x_1} | |
\binom{m_2}{x_2} \cdots \binom{m_k}{x_k}}{\binom{M}{n}}, \\ \quad | |
(x_1, x_2, \ldots, x_k) \in \mathbb{N}^k \text{ with } | |
\sum_{i=1}^k x_i = n | |
where :math:`m_i` are the number of objects of type :math:`i`, :math:`M` | |
is the total number of objects in the population (sum of all the | |
:math:`m_i`), and :math:`n` is the size of the sample to be taken | |
from the population. | |
.. versionadded:: 1.6.0 | |
Examples | |
-------- | |
To evaluate the probability mass function of the multivariate | |
hypergeometric distribution, with a dichotomous population of size | |
:math:`10` and :math:`20`, at a sample of size :math:`12` with | |
:math:`8` objects of the first type and :math:`4` objects of the | |
second type, use: | |
>>> from scipy.stats import multivariate_hypergeom | |
>>> multivariate_hypergeom.pmf(x=[8, 4], m=[10, 20], n=12) | |
0.0025207176631464523 | |
The `multivariate_hypergeom` distribution is identical to the | |
corresponding `hypergeom` distribution (tiny numerical differences | |
notwithstanding) when only two types (good and bad) of objects | |
are present in the population as in the example above. Consider | |
another example for a comparison with the hypergeometric distribution: | |
>>> from scipy.stats import hypergeom | |
>>> multivariate_hypergeom.pmf(x=[3, 1], m=[10, 5], n=4) | |
0.4395604395604395 | |
>>> hypergeom.pmf(k=3, M=15, n=4, N=10) | |
0.43956043956044005 | |
The functions ``pmf``, ``logpmf``, ``mean``, ``var``, ``cov``, and ``rvs`` | |
support broadcasting, under the convention that the vector parameters | |
(``x``, ``m``, and ``n``) are interpreted as if each row along the last | |
axis is a single object. For instance, we can combine the previous two | |
calls to `multivariate_hypergeom` as | |
>>> multivariate_hypergeom.pmf(x=[[8, 4], [3, 1]], m=[[10, 20], [10, 5]], | |
... n=[12, 4]) | |
array([0.00252072, 0.43956044]) | |
This broadcasting also works for ``cov``, where the output objects are | |
square matrices of size ``m.shape[-1]``. For example: | |
>>> multivariate_hypergeom.cov(m=[[7, 9], [10, 15]], n=[8, 12]) | |
array([[[ 1.05, -1.05], | |
[-1.05, 1.05]], | |
[[ 1.56, -1.56], | |
[-1.56, 1.56]]]) | |
That is, ``result[0]`` is equal to | |
``multivariate_hypergeom.cov(m=[7, 9], n=8)`` and ``result[1]`` is equal | |
to ``multivariate_hypergeom.cov(m=[10, 15], n=12)``. | |
Alternatively, the object may be called (as a function) to fix the `m` | |
and `n` parameters, returning a "frozen" multivariate hypergeometric | |
random variable. | |
>>> rv = multivariate_hypergeom(m=[10, 20], n=12) | |
>>> rv.pmf(x=[8, 4]) | |
0.0025207176631464523 | |
See Also | |
-------- | |
scipy.stats.hypergeom : The hypergeometric distribution. | |
scipy.stats.multinomial : The multinomial distribution. | |
References | |
---------- | |
.. [1] The Multivariate Hypergeometric Distribution, | |
http://www.randomservices.org/random/urn/MultiHypergeometric.html | |
.. [2] Thomas J. Sargent and John Stachurski, 2020, | |
Multivariate Hypergeometric Distribution | |
https://python.quantecon.org/multi_hyper.html | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__, mhg_docdict_params) | |
def __call__(self, m, n, seed=None): | |
"""Create a frozen multivariate_hypergeom distribution. | |
See `multivariate_hypergeom_frozen` for more information. | |
""" | |
return multivariate_hypergeom_frozen(m, n, seed=seed) | |
def _process_parameters(self, m, n): | |
m = np.asarray(m) | |
n = np.asarray(n) | |
if m.size == 0: | |
m = m.astype(int) | |
if n.size == 0: | |
n = n.astype(int) | |
if not np.issubdtype(m.dtype, np.integer): | |
raise TypeError("'m' must an array of integers.") | |
if not np.issubdtype(n.dtype, np.integer): | |
raise TypeError("'n' must an array of integers.") | |
if m.ndim == 0: | |
raise ValueError("'m' must be an array with" | |
" at least one dimension.") | |
# check for empty arrays | |
if m.size != 0: | |
n = n[..., np.newaxis] | |
m, n = np.broadcast_arrays(m, n) | |
# check for empty arrays | |
if m.size != 0: | |
n = n[..., 0] | |
mcond = m < 0 | |
M = m.sum(axis=-1) | |
ncond = (n < 0) | (n > M) | |
return M, m, n, mcond, ncond, np.any(mcond, axis=-1) | ncond | |
def _process_quantiles(self, x, M, m, n): | |
x = np.asarray(x) | |
if not np.issubdtype(x.dtype, np.integer): | |
raise TypeError("'x' must an array of integers.") | |
if x.ndim == 0: | |
raise ValueError("'x' must be an array with" | |
" at least one dimension.") | |
if not x.shape[-1] == m.shape[-1]: | |
raise ValueError(f"Size of each quantile must be size of 'm': " | |
f"received {x.shape[-1]}, " | |
f"but expected {m.shape[-1]}.") | |
# check for empty arrays | |
if m.size != 0: | |
n = n[..., np.newaxis] | |
M = M[..., np.newaxis] | |
x, m, n, M = np.broadcast_arrays(x, m, n, M) | |
# check for empty arrays | |
if m.size != 0: | |
n, M = n[..., 0], M[..., 0] | |
xcond = (x < 0) | (x > m) | |
return (x, M, m, n, xcond, | |
np.any(xcond, axis=-1) | (x.sum(axis=-1) != n)) | |
def _checkresult(self, result, cond, bad_value): | |
result = np.asarray(result) | |
if cond.ndim != 0: | |
result[cond] = bad_value | |
elif cond: | |
return bad_value | |
if result.ndim == 0: | |
return result[()] | |
return result | |
def _logpmf(self, x, M, m, n, mxcond, ncond): | |
# This equation of the pmf comes from the relation, | |
# n combine r = beta(n+1, 1) / beta(r+1, n-r+1) | |
num = np.zeros_like(m, dtype=np.float64) | |
den = np.zeros_like(n, dtype=np.float64) | |
m, x = m[~mxcond], x[~mxcond] | |
M, n = M[~ncond], n[~ncond] | |
num[~mxcond] = (betaln(m+1, 1) - betaln(x+1, m-x+1)) | |
den[~ncond] = (betaln(M+1, 1) - betaln(n+1, M-n+1)) | |
num[mxcond] = np.nan | |
den[ncond] = np.nan | |
num = num.sum(axis=-1) | |
return num - den | |
def logpmf(self, x, m, n): | |
"""Log of the multivariate hypergeometric probability mass function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
logpmf : ndarray or scalar | |
Log of the probability mass function evaluated at `x` | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
M, m, n, mcond, ncond, mncond = self._process_parameters(m, n) | |
(x, M, m, n, xcond, | |
xcond_reduced) = self._process_quantiles(x, M, m, n) | |
mxcond = mcond | xcond | |
ncond = ncond | np.zeros(n.shape, dtype=np.bool_) | |
result = self._logpmf(x, M, m, n, mxcond, ncond) | |
# replace values for which x was out of the domain; broadcast | |
# xcond to the right shape | |
xcond_ = xcond_reduced | np.zeros(mncond.shape, dtype=np.bool_) | |
result = self._checkresult(result, xcond_, -np.inf) | |
# replace values bad for n or m; broadcast | |
# mncond to the right shape | |
mncond_ = mncond | np.zeros(xcond_reduced.shape, dtype=np.bool_) | |
return self._checkresult(result, mncond_, np.nan) | |
def pmf(self, x, m, n): | |
"""Multivariate hypergeometric probability mass function. | |
Parameters | |
---------- | |
x : array_like | |
Quantiles, with the last axis of `x` denoting the components. | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
pmf : ndarray or scalar | |
Probability density function evaluated at `x` | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
""" | |
out = np.exp(self.logpmf(x, m, n)) | |
return out | |
def mean(self, m, n): | |
"""Mean of the multivariate hypergeometric distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
mean : array_like or scalar | |
The mean of the distribution | |
""" | |
M, m, n, _, _, mncond = self._process_parameters(m, n) | |
# check for empty arrays | |
if m.size != 0: | |
M, n = M[..., np.newaxis], n[..., np.newaxis] | |
cond = (M == 0) | |
M = np.ma.masked_array(M, mask=cond) | |
mu = n*(m/M) | |
if m.size != 0: | |
mncond = (mncond[..., np.newaxis] | | |
np.zeros(mu.shape, dtype=np.bool_)) | |
return self._checkresult(mu, mncond, np.nan) | |
def var(self, m, n): | |
"""Variance of the multivariate hypergeometric distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
array_like | |
The variances of the components of the distribution. This is | |
the diagonal of the covariance matrix of the distribution | |
""" | |
M, m, n, _, _, mncond = self._process_parameters(m, n) | |
# check for empty arrays | |
if m.size != 0: | |
M, n = M[..., np.newaxis], n[..., np.newaxis] | |
cond = (M == 0) & (M-1 == 0) | |
M = np.ma.masked_array(M, mask=cond) | |
output = n * m/M * (M-m)/M * (M-n)/(M-1) | |
if m.size != 0: | |
mncond = (mncond[..., np.newaxis] | | |
np.zeros(output.shape, dtype=np.bool_)) | |
return self._checkresult(output, mncond, np.nan) | |
def cov(self, m, n): | |
"""Covariance matrix of the multivariate hypergeometric distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
Returns | |
------- | |
cov : array_like | |
The covariance matrix of the distribution | |
""" | |
# see [1]_ for the formula and [2]_ for implementation | |
# cov( x_i,x_j ) = -n * (M-n)/(M-1) * (K_i*K_j) / (M**2) | |
M, m, n, _, _, mncond = self._process_parameters(m, n) | |
# check for empty arrays | |
if m.size != 0: | |
M = M[..., np.newaxis, np.newaxis] | |
n = n[..., np.newaxis, np.newaxis] | |
cond = (M == 0) & (M-1 == 0) | |
M = np.ma.masked_array(M, mask=cond) | |
output = (-n * (M-n)/(M-1) * | |
np.einsum("...i,...j->...ij", m, m) / (M**2)) | |
# check for empty arrays | |
if m.size != 0: | |
M, n = M[..., 0, 0], n[..., 0, 0] | |
cond = cond[..., 0, 0] | |
dim = m.shape[-1] | |
# diagonal entries need to be computed differently | |
for i in range(dim): | |
output[..., i, i] = (n * (M-n) * m[..., i]*(M-m[..., i])) | |
output[..., i, i] = output[..., i, i] / (M-1) | |
output[..., i, i] = output[..., i, i] / (M**2) | |
if m.size != 0: | |
mncond = (mncond[..., np.newaxis, np.newaxis] | | |
np.zeros(output.shape, dtype=np.bool_)) | |
return self._checkresult(output, mncond, np.nan) | |
def rvs(self, m, n, size=None, random_state=None): | |
"""Draw random samples from a multivariate hypergeometric distribution. | |
Parameters | |
---------- | |
%(_doc_default_callparams)s | |
size : integer or iterable of integers, optional | |
Number of samples to draw. Default is ``None``, in which case a | |
single variate is returned as an array with shape ``m.shape``. | |
%(_doc_random_state)s | |
Returns | |
------- | |
rvs : array_like | |
Random variates of shape ``size`` or ``m.shape`` | |
(if ``size=None``). | |
Notes | |
----- | |
%(_doc_callparams_note)s | |
Also note that NumPy's `multivariate_hypergeometric` sampler is not | |
used as it doesn't support broadcasting. | |
""" | |
M, m, n, _, _, _ = self._process_parameters(m, n) | |
random_state = self._get_random_state(random_state) | |
if size is not None and isinstance(size, int): | |
size = (size, ) | |
if size is None: | |
rvs = np.empty(m.shape, dtype=m.dtype) | |
else: | |
rvs = np.empty(size + (m.shape[-1], ), dtype=m.dtype) | |
rem = M | |
# This sampler has been taken from numpy gh-13794 | |
# https://github.com/numpy/numpy/pull/13794 | |
for c in range(m.shape[-1] - 1): | |
rem = rem - m[..., c] | |
n0mask = n == 0 | |
rvs[..., c] = (~n0mask * | |
random_state.hypergeometric(m[..., c], | |
rem + n0mask, | |
n + n0mask, | |
size=size)) | |
n = n - rvs[..., c] | |
rvs[..., m.shape[-1] - 1] = n | |
return rvs | |
multivariate_hypergeom = multivariate_hypergeom_gen() | |
class multivariate_hypergeom_frozen(multi_rv_frozen): | |
def __init__(self, m, n, seed=None): | |
self._dist = multivariate_hypergeom_gen(seed) | |
(self.M, self.m, self.n, | |
self.mcond, self.ncond, | |
self.mncond) = self._dist._process_parameters(m, n) | |
# monkey patch self._dist | |
def _process_parameters(m, n): | |
return (self.M, self.m, self.n, | |
self.mcond, self.ncond, | |
self.mncond) | |
self._dist._process_parameters = _process_parameters | |
def logpmf(self, x): | |
return self._dist.logpmf(x, self.m, self.n) | |
def pmf(self, x): | |
return self._dist.pmf(x, self.m, self.n) | |
def mean(self): | |
return self._dist.mean(self.m, self.n) | |
def var(self): | |
return self._dist.var(self.m, self.n) | |
def cov(self): | |
return self._dist.cov(self.m, self.n) | |
def rvs(self, size=1, random_state=None): | |
return self._dist.rvs(self.m, self.n, | |
size=size, | |
random_state=random_state) | |
# Set frozen generator docstrings from corresponding docstrings in | |
# multivariate_hypergeom and fill in default strings in class docstrings | |
for name in ['logpmf', 'pmf', 'mean', 'var', 'cov', 'rvs']: | |
method = multivariate_hypergeom_gen.__dict__[name] | |
method_frozen = multivariate_hypergeom_frozen.__dict__[name] | |
method_frozen.__doc__ = doccer.docformat( | |
method.__doc__, mhg_docdict_noparams) | |
method.__doc__ = doccer.docformat(method.__doc__, | |
mhg_docdict_params) | |
class random_table_gen(multi_rv_generic): | |
r"""Contingency tables from independent samples with fixed marginal sums. | |
This is the distribution of random tables with given row and column vector | |
sums. This distribution represents the set of random tables under the null | |
hypothesis that rows and columns are independent. It is used in hypothesis | |
tests of independence. | |
Because of assumed independence, the expected frequency of each table | |
element can be computed from the row and column sums, so that the | |
distribution is completely determined by these two vectors. | |
Methods | |
------- | |
logpmf(x) | |
Log-probability of table `x` to occur in the distribution. | |
pmf(x) | |
Probability of table `x` to occur in the distribution. | |
mean(row, col) | |
Mean table. | |
rvs(row, col, size=None, method=None, random_state=None) | |
Draw random tables with given row and column vector sums. | |
Parameters | |
---------- | |
%(_doc_row_col)s | |
%(_doc_random_state)s | |
Notes | |
----- | |
%(_doc_row_col_note)s | |
Random elements from the distribution are generated either with Boyett's | |
[1]_ or Patefield's algorithm [2]_. Boyett's algorithm has | |
O(N) time and space complexity, where N is the total sum of entries in the | |
table. Patefield's algorithm has O(K x log(N)) time complexity, where K is | |
the number of cells in the table and requires only a small constant work | |
space. By default, the `rvs` method selects the fastest algorithm based on | |
the input, but you can specify the algorithm with the keyword `method`. | |
Allowed values are "boyett" and "patefield". | |
.. versionadded:: 1.10.0 | |
Examples | |
-------- | |
>>> from scipy.stats import random_table | |
>>> row = [1, 5] | |
>>> col = [2, 3, 1] | |
>>> random_table.mean(row, col) | |
array([[0.33333333, 0.5 , 0.16666667], | |
[1.66666667, 2.5 , 0.83333333]]) | |
Alternatively, the object may be called (as a function) to fix the row | |
and column vector sums, returning a "frozen" distribution. | |
>>> dist = random_table(row, col) | |
>>> dist.rvs(random_state=123) | |
array([[1., 0., 0.], | |
[1., 3., 1.]]) | |
References | |
---------- | |
.. [1] J. Boyett, AS 144 Appl. Statist. 28 (1979) 329-332 | |
.. [2] W.M. Patefield, AS 159 Appl. Statist. 30 (1981) 91-97 | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
def __call__(self, row, col, *, seed=None): | |
"""Create a frozen distribution of tables with given marginals. | |
See `random_table_frozen` for more information. | |
""" | |
return random_table_frozen(row, col, seed=seed) | |
def logpmf(self, x, row, col): | |
"""Log-probability of table to occur in the distribution. | |
Parameters | |
---------- | |
%(_doc_x)s | |
%(_doc_row_col)s | |
Returns | |
------- | |
logpmf : ndarray or scalar | |
Log of the probability mass function evaluated at `x`. | |
Notes | |
----- | |
%(_doc_row_col_note)s | |
If row and column marginals of `x` do not match `row` and `col`, | |
negative infinity is returned. | |
Examples | |
-------- | |
>>> from scipy.stats import random_table | |
>>> import numpy as np | |
>>> x = [[1, 5, 1], [2, 3, 1]] | |
>>> row = np.sum(x, axis=1) | |
>>> col = np.sum(x, axis=0) | |
>>> random_table.logpmf(x, row, col) | |
-1.6306401200847027 | |
Alternatively, the object may be called (as a function) to fix the row | |
and column vector sums, returning a "frozen" distribution. | |
>>> d = random_table(row, col) | |
>>> d.logpmf(x) | |
-1.6306401200847027 | |
""" | |
r, c, n = self._process_parameters(row, col) | |
x = np.asarray(x) | |
if x.ndim < 2: | |
raise ValueError("`x` must be at least two-dimensional") | |
dtype_is_int = np.issubdtype(x.dtype, np.integer) | |
with np.errstate(invalid='ignore'): | |
if not dtype_is_int and not np.all(x.astype(int) == x): | |
raise ValueError("`x` must contain only integral values") | |
# x does not contain NaN if we arrive here | |
if np.any(x < 0): | |
raise ValueError("`x` must contain only non-negative values") | |
r2 = np.sum(x, axis=-1) | |
c2 = np.sum(x, axis=-2) | |
if r2.shape[-1] != len(r): | |
raise ValueError("shape of `x` must agree with `row`") | |
if c2.shape[-1] != len(c): | |
raise ValueError("shape of `x` must agree with `col`") | |
res = np.empty(x.shape[:-2]) | |
mask = np.all(r2 == r, axis=-1) & np.all(c2 == c, axis=-1) | |
def lnfac(x): | |
return gammaln(x + 1) | |
res[mask] = (np.sum(lnfac(r), axis=-1) + np.sum(lnfac(c), axis=-1) | |
- lnfac(n) - np.sum(lnfac(x[mask]), axis=(-1, -2))) | |
res[~mask] = -np.inf | |
return res[()] | |
def pmf(self, x, row, col): | |
"""Probability of table to occur in the distribution. | |
Parameters | |
---------- | |
%(_doc_x)s | |
%(_doc_row_col)s | |
Returns | |
------- | |
pmf : ndarray or scalar | |
Probability mass function evaluated at `x`. | |
Notes | |
----- | |
%(_doc_row_col_note)s | |
If row and column marginals of `x` do not match `row` and `col`, | |
zero is returned. | |
Examples | |
-------- | |
>>> from scipy.stats import random_table | |
>>> import numpy as np | |
>>> x = [[1, 5, 1], [2, 3, 1]] | |
>>> row = np.sum(x, axis=1) | |
>>> col = np.sum(x, axis=0) | |
>>> random_table.pmf(x, row, col) | |
0.19580419580419592 | |
Alternatively, the object may be called (as a function) to fix the row | |
and column vector sums, returning a "frozen" distribution. | |
>>> d = random_table(row, col) | |
>>> d.pmf(x) | |
0.19580419580419592 | |
""" | |
return np.exp(self.logpmf(x, row, col)) | |
def mean(self, row, col): | |
"""Mean of distribution of conditional tables. | |
%(_doc_mean_params)s | |
Returns | |
------- | |
mean: ndarray | |
Mean of the distribution. | |
Notes | |
----- | |
%(_doc_row_col_note)s | |
Examples | |
-------- | |
>>> from scipy.stats import random_table | |
>>> row = [1, 5] | |
>>> col = [2, 3, 1] | |
>>> random_table.mean(row, col) | |
array([[0.33333333, 0.5 , 0.16666667], | |
[1.66666667, 2.5 , 0.83333333]]) | |
Alternatively, the object may be called (as a function) to fix the row | |
and column vector sums, returning a "frozen" distribution. | |
>>> d = random_table(row, col) | |
>>> d.mean() | |
array([[0.33333333, 0.5 , 0.16666667], | |
[1.66666667, 2.5 , 0.83333333]]) | |
""" | |
r, c, n = self._process_parameters(row, col) | |
return np.outer(r, c) / n | |
def rvs(self, row, col, *, size=None, method=None, random_state=None): | |
"""Draw random tables with fixed column and row marginals. | |
Parameters | |
---------- | |
%(_doc_row_col)s | |
size : integer, optional | |
Number of samples to draw (default 1). | |
method : str, optional | |
Which method to use, "boyett" or "patefield". If None (default), | |
selects the fastest method for this input. | |
%(_doc_random_state)s | |
Returns | |
------- | |
rvs : ndarray | |
Random 2D tables of shape (`size`, `len(row)`, `len(col)`). | |
Notes | |
----- | |
%(_doc_row_col_note)s | |
Examples | |
-------- | |
>>> from scipy.stats import random_table | |
>>> row = [1, 5] | |
>>> col = [2, 3, 1] | |
>>> random_table.rvs(row, col, random_state=123) | |
array([[1., 0., 0.], | |
[1., 3., 1.]]) | |
Alternatively, the object may be called (as a function) to fix the row | |
and column vector sums, returning a "frozen" distribution. | |
>>> d = random_table(row, col) | |
>>> d.rvs(random_state=123) | |
array([[1., 0., 0.], | |
[1., 3., 1.]]) | |
""" | |
r, c, n = self._process_parameters(row, col) | |
size, shape = self._process_size_shape(size, r, c) | |
random_state = self._get_random_state(random_state) | |
meth = self._process_rvs_method(method, r, c, n) | |
return meth(r, c, n, size, random_state).reshape(shape) | |
def _process_parameters(row, col): | |
""" | |
Check that row and column vectors are one-dimensional, that they do | |
not contain negative or non-integer entries, and that the sums over | |
both vectors are equal. | |
""" | |
r = np.array(row, dtype=np.int64, copy=True) | |
c = np.array(col, dtype=np.int64, copy=True) | |
if np.ndim(r) != 1: | |
raise ValueError("`row` must be one-dimensional") | |
if np.ndim(c) != 1: | |
raise ValueError("`col` must be one-dimensional") | |
if np.any(r < 0): | |
raise ValueError("each element of `row` must be non-negative") | |
if np.any(c < 0): | |
raise ValueError("each element of `col` must be non-negative") | |
n = np.sum(r) | |
if n != np.sum(c): | |
raise ValueError("sums over `row` and `col` must be equal") | |
if not np.all(r == np.asarray(row)): | |
raise ValueError("each element of `row` must be an integer") | |
if not np.all(c == np.asarray(col)): | |
raise ValueError("each element of `col` must be an integer") | |
return r, c, n | |
def _process_size_shape(size, r, c): | |
""" | |
Compute the number of samples to be drawn and the shape of the output | |
""" | |
shape = (len(r), len(c)) | |
if size is None: | |
return 1, shape | |
size = np.atleast_1d(size) | |
if not np.issubdtype(size.dtype, np.integer) or np.any(size < 0): | |
raise ValueError("`size` must be a non-negative integer or `None`") | |
return np.prod(size), tuple(size) + shape | |
def _process_rvs_method(cls, method, r, c, n): | |
known_methods = { | |
None: cls._rvs_select(r, c, n), | |
"boyett": cls._rvs_boyett, | |
"patefield": cls._rvs_patefield, | |
} | |
try: | |
return known_methods[method] | |
except KeyError: | |
raise ValueError(f"'{method}' not recognized, " | |
f"must be one of {set(known_methods)}") | |
def _rvs_select(cls, r, c, n): | |
fac = 1.0 # benchmarks show that this value is about 1 | |
k = len(r) * len(c) # number of cells | |
# n + 1 guards against failure if n == 0 | |
if n > fac * np.log(n + 1) * k: | |
return cls._rvs_patefield | |
return cls._rvs_boyett | |
def _rvs_boyett(row, col, ntot, size, random_state): | |
return _rcont.rvs_rcont1(row, col, ntot, size, random_state) | |
def _rvs_patefield(row, col, ntot, size, random_state): | |
return _rcont.rvs_rcont2(row, col, ntot, size, random_state) | |
random_table = random_table_gen() | |
class random_table_frozen(multi_rv_frozen): | |
def __init__(self, row, col, *, seed=None): | |
self._dist = random_table_gen(seed) | |
self._params = self._dist._process_parameters(row, col) | |
# monkey patch self._dist | |
def _process_parameters(r, c): | |
return self._params | |
self._dist._process_parameters = _process_parameters | |
def logpmf(self, x): | |
return self._dist.logpmf(x, None, None) | |
def pmf(self, x): | |
return self._dist.pmf(x, None, None) | |
def mean(self): | |
return self._dist.mean(None, None) | |
def rvs(self, size=None, method=None, random_state=None): | |
# optimisations are possible here | |
return self._dist.rvs(None, None, size=size, method=method, | |
random_state=random_state) | |
_ctab_doc_row_col = """\ | |
row : array_like | |
Sum of table entries in each row. | |
col : array_like | |
Sum of table entries in each column.""" | |
_ctab_doc_x = """\ | |
x : array-like | |
Two-dimensional table of non-negative integers, or a | |
multi-dimensional array with the last two dimensions | |
corresponding with the tables.""" | |
_ctab_doc_row_col_note = """\ | |
The row and column vectors must be one-dimensional, not empty, | |
and each sum up to the same value. They cannot contain negative | |
or noninteger entries.""" | |
_ctab_doc_mean_params = f""" | |
Parameters | |
---------- | |
{_ctab_doc_row_col}""" | |
_ctab_doc_row_col_note_frozen = """\ | |
See class definition for a detailed description of parameters.""" | |
_ctab_docdict = { | |
"_doc_random_state": _doc_random_state, | |
"_doc_row_col": _ctab_doc_row_col, | |
"_doc_x": _ctab_doc_x, | |
"_doc_mean_params": _ctab_doc_mean_params, | |
"_doc_row_col_note": _ctab_doc_row_col_note, | |
} | |
_ctab_docdict_frozen = _ctab_docdict.copy() | |
_ctab_docdict_frozen.update({ | |
"_doc_row_col": "", | |
"_doc_mean_params": "", | |
"_doc_row_col_note": _ctab_doc_row_col_note_frozen, | |
}) | |
def _docfill(obj, docdict, template=None): | |
obj.__doc__ = doccer.docformat(template or obj.__doc__, docdict) | |
# Set frozen generator docstrings from corresponding docstrings in | |
# random_table and fill in default strings in class docstrings | |
_docfill(random_table_gen, _ctab_docdict) | |
for name in ['logpmf', 'pmf', 'mean', 'rvs']: | |
method = random_table_gen.__dict__[name] | |
method_frozen = random_table_frozen.__dict__[name] | |
_docfill(method_frozen, _ctab_docdict_frozen, method.__doc__) | |
_docfill(method, _ctab_docdict) | |
class uniform_direction_gen(multi_rv_generic): | |
r"""A vector-valued uniform direction. | |
Return a random direction (unit vector). The `dim` keyword specifies | |
the dimensionality of the space. | |
Methods | |
------- | |
rvs(dim=None, size=1, random_state=None) | |
Draw random directions. | |
Parameters | |
---------- | |
dim : scalar | |
Dimension of directions. | |
seed : {None, int, `numpy.random.Generator`, | |
`numpy.random.RandomState`}, optional | |
Used for drawing random variates. | |
If `seed` is `None`, the `~np.random.RandomState` singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, seeded | |
with seed. | |
If `seed` is already a ``RandomState`` or ``Generator`` instance, | |
then that object is used. | |
Default is `None`. | |
Notes | |
----- | |
This distribution generates unit vectors uniformly distributed on | |
the surface of a hypersphere. These can be interpreted as random | |
directions. | |
For example, if `dim` is 3, 3D vectors from the surface of :math:`S^2` | |
will be sampled. | |
References | |
---------- | |
.. [1] Marsaglia, G. (1972). "Choosing a Point from the Surface of a | |
Sphere". Annals of Mathematical Statistics. 43 (2): 645-646. | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from scipy.stats import uniform_direction | |
>>> x = uniform_direction.rvs(3) | |
>>> np.linalg.norm(x) | |
1. | |
This generates one random direction, a vector on the surface of | |
:math:`S^2`. | |
Alternatively, the object may be called (as a function) to return a frozen | |
distribution with fixed `dim` parameter. Here, | |
we create a `uniform_direction` with ``dim=3`` and draw 5 observations. | |
The samples are then arranged in an array of shape 5x3. | |
>>> rng = np.random.default_rng() | |
>>> uniform_sphere_dist = uniform_direction(3) | |
>>> unit_vectors = uniform_sphere_dist.rvs(5, random_state=rng) | |
>>> unit_vectors | |
array([[ 0.56688642, -0.1332634 , -0.81294566], | |
[-0.427126 , -0.74779278, 0.50830044], | |
[ 0.3793989 , 0.92346629, 0.05715323], | |
[ 0.36428383, -0.92449076, -0.11231259], | |
[-0.27733285, 0.94410968, -0.17816678]]) | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__) | |
def __call__(self, dim=None, seed=None): | |
"""Create a frozen n-dimensional uniform direction distribution. | |
See `uniform_direction` for more information. | |
""" | |
return uniform_direction_frozen(dim, seed=seed) | |
def _process_parameters(self, dim): | |
"""Dimension N must be specified; it cannot be inferred.""" | |
if dim is None or not np.isscalar(dim) or dim < 1 or dim != int(dim): | |
raise ValueError("Dimension of vector must be specified, " | |
"and must be an integer greater than 0.") | |
return int(dim) | |
def rvs(self, dim, size=None, random_state=None): | |
"""Draw random samples from S(N-1). | |
Parameters | |
---------- | |
dim : integer | |
Dimension of space (N). | |
size : int or tuple of ints, optional | |
Given a shape of, for example, (m,n,k), m*n*k samples are | |
generated, and packed in an m-by-n-by-k arrangement. | |
Because each sample is N-dimensional, the output shape | |
is (m,n,k,N). If no shape is specified, a single (N-D) | |
sample is returned. | |
random_state : {None, int, `numpy.random.Generator`, | |
`numpy.random.RandomState`}, optional | |
Pseudorandom number generator state used to generate resamples. | |
If `random_state` is ``None`` (or `np.random`), the | |
`numpy.random.RandomState` singleton is used. | |
If `random_state` is an int, a new ``RandomState`` instance is | |
used, seeded with `random_state`. | |
If `random_state` is already a ``Generator`` or ``RandomState`` | |
instance then that instance is used. | |
Returns | |
------- | |
rvs : ndarray | |
Random direction vectors | |
""" | |
random_state = self._get_random_state(random_state) | |
if size is None: | |
size = np.array([], dtype=int) | |
size = np.atleast_1d(size) | |
dim = self._process_parameters(dim) | |
samples = _sample_uniform_direction(dim, size, random_state) | |
return samples | |
uniform_direction = uniform_direction_gen() | |
class uniform_direction_frozen(multi_rv_frozen): | |
def __init__(self, dim=None, seed=None): | |
"""Create a frozen n-dimensional uniform direction distribution. | |
Parameters | |
---------- | |
dim : int | |
Dimension of matrices | |
seed : {None, int, `numpy.random.Generator`, | |
`numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance | |
then that instance is used. | |
Examples | |
-------- | |
>>> from scipy.stats import uniform_direction | |
>>> x = uniform_direction(3) | |
>>> x.rvs() | |
""" | |
self._dist = uniform_direction_gen(seed) | |
self.dim = self._dist._process_parameters(dim) | |
def rvs(self, size=None, random_state=None): | |
return self._dist.rvs(self.dim, size, random_state) | |
def _sample_uniform_direction(dim, size, random_state): | |
""" | |
Private method to generate uniform directions | |
Reference: Marsaglia, G. (1972). "Choosing a Point from the Surface of a | |
Sphere". Annals of Mathematical Statistics. 43 (2): 645-646. | |
""" | |
samples_shape = np.append(size, dim) | |
samples = random_state.standard_normal(samples_shape) | |
samples /= np.linalg.norm(samples, axis=-1, keepdims=True) | |
return samples | |
_dirichlet_mn_doc_default_callparams = """\ | |
alpha : array_like | |
The concentration parameters. The number of entries along the last axis | |
determines the dimensionality of the distribution. Each entry must be | |
strictly positive. | |
n : int or array_like | |
The number of trials. Each element must be a strictly positive integer. | |
""" | |
_dirichlet_mn_doc_frozen_callparams = "" | |
_dirichlet_mn_doc_frozen_callparams_note = """\ | |
See class definition for a detailed description of parameters.""" | |
dirichlet_mn_docdict_params = { | |
'_dirichlet_mn_doc_default_callparams': _dirichlet_mn_doc_default_callparams, | |
'_doc_random_state': _doc_random_state | |
} | |
dirichlet_mn_docdict_noparams = { | |
'_dirichlet_mn_doc_default_callparams': _dirichlet_mn_doc_frozen_callparams, | |
'_doc_random_state': _doc_random_state | |
} | |
def _dirichlet_multinomial_check_parameters(alpha, n, x=None): | |
alpha = np.asarray(alpha) | |
n = np.asarray(n) | |
if x is not None: | |
# Ensure that `x` and `alpha` are arrays. If the shapes are | |
# incompatible, NumPy will raise an appropriate error. | |
try: | |
x, alpha = np.broadcast_arrays(x, alpha) | |
except ValueError as e: | |
msg = "`x` and `alpha` must be broadcastable." | |
raise ValueError(msg) from e | |
x_int = np.floor(x) | |
if np.any(x < 0) or np.any(x != x_int): | |
raise ValueError("`x` must contain only non-negative integers.") | |
x = x_int | |
if np.any(alpha <= 0): | |
raise ValueError("`alpha` must contain only positive values.") | |
n_int = np.floor(n) | |
if np.any(n <= 0) or np.any(n != n_int): | |
raise ValueError("`n` must be a positive integer.") | |
n = n_int | |
sum_alpha = np.sum(alpha, axis=-1) | |
sum_alpha, n = np.broadcast_arrays(sum_alpha, n) | |
return (alpha, sum_alpha, n) if x is None else (alpha, sum_alpha, n, x) | |
class dirichlet_multinomial_gen(multi_rv_generic): | |
r"""A Dirichlet multinomial random variable. | |
The Dirichlet multinomial distribution is a compound probability | |
distribution: it is the multinomial distribution with number of trials | |
`n` and class probabilities ``p`` randomly sampled from a Dirichlet | |
distribution with concentration parameters ``alpha``. | |
Methods | |
------- | |
logpmf(x, alpha, n): | |
Log of the probability mass function. | |
pmf(x, alpha, n): | |
Probability mass function. | |
mean(alpha, n): | |
Mean of the Dirichlet multinomial distribution. | |
var(alpha, n): | |
Variance of the Dirichlet multinomial distribution. | |
cov(alpha, n): | |
The covariance of the Dirichlet multinomial distribution. | |
Parameters | |
---------- | |
%(_dirichlet_mn_doc_default_callparams)s | |
%(_doc_random_state)s | |
See Also | |
-------- | |
scipy.stats.dirichlet : The dirichlet distribution. | |
scipy.stats.multinomial : The multinomial distribution. | |
References | |
---------- | |
.. [1] Dirichlet-multinomial distribution, Wikipedia, | |
https://www.wikipedia.org/wiki/Dirichlet-multinomial_distribution | |
Examples | |
-------- | |
>>> from scipy.stats import dirichlet_multinomial | |
Get the PMF | |
>>> n = 6 # number of trials | |
>>> alpha = [3, 4, 5] # concentration parameters | |
>>> x = [1, 2, 3] # counts | |
>>> dirichlet_multinomial.pmf(x, alpha, n) | |
0.08484162895927604 | |
If the sum of category counts does not equal the number of trials, | |
the probability mass is zero. | |
>>> dirichlet_multinomial.pmf(x, alpha, n=7) | |
0.0 | |
Get the log of the PMF | |
>>> dirichlet_multinomial.logpmf(x, alpha, n) | |
-2.4669689491013327 | |
Get the mean | |
>>> dirichlet_multinomial.mean(alpha, n) | |
array([1.5, 2. , 2.5]) | |
Get the variance | |
>>> dirichlet_multinomial.var(alpha, n) | |
array([1.55769231, 1.84615385, 2.01923077]) | |
Get the covariance | |
>>> dirichlet_multinomial.cov(alpha, n) | |
array([[ 1.55769231, -0.69230769, -0.86538462], | |
[-0.69230769, 1.84615385, -1.15384615], | |
[-0.86538462, -1.15384615, 2.01923077]]) | |
Alternatively, the object may be called (as a function) to fix the | |
`alpha` and `n` parameters, returning a "frozen" Dirichlet multinomial | |
random variable. | |
>>> dm = dirichlet_multinomial(alpha, n) | |
>>> dm.pmf(x) | |
0.08484162895927579 | |
All methods are fully vectorized. Each element of `x` and `alpha` is | |
a vector (along the last axis), each element of `n` is an | |
integer (scalar), and the result is computed element-wise. | |
>>> x = [[1, 2, 3], [4, 5, 6]] | |
>>> alpha = [[1, 2, 3], [4, 5, 6]] | |
>>> n = [6, 15] | |
>>> dirichlet_multinomial.pmf(x, alpha, n) | |
array([0.06493506, 0.02626937]) | |
>>> dirichlet_multinomial.cov(alpha, n).shape # both covariance matrices | |
(2, 3, 3) | |
Broadcasting according to standard NumPy conventions is supported. Here, | |
we have four sets of concentration parameters (each a two element vector) | |
for each of three numbers of trials (each a scalar). | |
>>> alpha = [[3, 4], [4, 5], [5, 6], [6, 7]] | |
>>> n = [[6], [7], [8]] | |
>>> dirichlet_multinomial.mean(alpha, n).shape | |
(3, 4, 2) | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
self.__doc__ = doccer.docformat(self.__doc__, | |
dirichlet_mn_docdict_params) | |
def __call__(self, alpha, n, seed=None): | |
return dirichlet_multinomial_frozen(alpha, n, seed=seed) | |
def logpmf(self, x, alpha, n): | |
"""The log of the probability mass function. | |
Parameters | |
---------- | |
x: ndarray | |
Category counts (non-negative integers). Must be broadcastable | |
with shape parameter ``alpha``. If multidimensional, the last axis | |
must correspond with the categories. | |
%(_dirichlet_mn_doc_default_callparams)s | |
Returns | |
------- | |
out: ndarray or scalar | |
Log of the probability mass function. | |
""" | |
a, Sa, n, x = _dirichlet_multinomial_check_parameters(alpha, n, x) | |
out = np.asarray(loggamma(Sa) + loggamma(n + 1) - loggamma(n + Sa)) | |
out += (loggamma(x + a) - (loggamma(a) + loggamma(x + 1))).sum(axis=-1) | |
np.place(out, n != x.sum(axis=-1), -np.inf) | |
return out[()] | |
def pmf(self, x, alpha, n): | |
"""Probability mass function for a Dirichlet multinomial distribution. | |
Parameters | |
---------- | |
x: ndarray | |
Category counts (non-negative integers). Must be broadcastable | |
with shape parameter ``alpha``. If multidimensional, the last axis | |
must correspond with the categories. | |
%(_dirichlet_mn_doc_default_callparams)s | |
Returns | |
------- | |
out: ndarray or scalar | |
Probability mass function. | |
""" | |
return np.exp(self.logpmf(x, alpha, n)) | |
def mean(self, alpha, n): | |
"""Mean of a Dirichlet multinomial distribution. | |
Parameters | |
---------- | |
%(_dirichlet_mn_doc_default_callparams)s | |
Returns | |
------- | |
out: ndarray | |
Mean of a Dirichlet multinomial distribution. | |
""" | |
a, Sa, n = _dirichlet_multinomial_check_parameters(alpha, n) | |
n, Sa = n[..., np.newaxis], Sa[..., np.newaxis] | |
return n * a / Sa | |
def var(self, alpha, n): | |
"""The variance of the Dirichlet multinomial distribution. | |
Parameters | |
---------- | |
%(_dirichlet_mn_doc_default_callparams)s | |
Returns | |
------- | |
out: array_like | |
The variances of the components of the distribution. This is | |
the diagonal of the covariance matrix of the distribution. | |
""" | |
a, Sa, n = _dirichlet_multinomial_check_parameters(alpha, n) | |
n, Sa = n[..., np.newaxis], Sa[..., np.newaxis] | |
return n * a / Sa * (1 - a/Sa) * (n + Sa) / (1 + Sa) | |
def cov(self, alpha, n): | |
"""Covariance matrix of a Dirichlet multinomial distribution. | |
Parameters | |
---------- | |
%(_dirichlet_mn_doc_default_callparams)s | |
Returns | |
------- | |
out : array_like | |
The covariance matrix of the distribution. | |
""" | |
a, Sa, n = _dirichlet_multinomial_check_parameters(alpha, n) | |
var = dirichlet_multinomial.var(a, n) | |
n, Sa = n[..., np.newaxis, np.newaxis], Sa[..., np.newaxis, np.newaxis] | |
aiaj = a[..., :, np.newaxis] * a[..., np.newaxis, :] | |
cov = -n * aiaj / Sa ** 2 * (n + Sa) / (1 + Sa) | |
ii = np.arange(cov.shape[-1]) | |
cov[..., ii, ii] = var | |
return cov | |
dirichlet_multinomial = dirichlet_multinomial_gen() | |
class dirichlet_multinomial_frozen(multi_rv_frozen): | |
def __init__(self, alpha, n, seed=None): | |
alpha, Sa, n = _dirichlet_multinomial_check_parameters(alpha, n) | |
self.alpha = alpha | |
self.n = n | |
self._dist = dirichlet_multinomial_gen(seed) | |
def logpmf(self, x): | |
return self._dist.logpmf(x, self.alpha, self.n) | |
def pmf(self, x): | |
return self._dist.pmf(x, self.alpha, self.n) | |
def mean(self): | |
return self._dist.mean(self.alpha, self.n) | |
def var(self): | |
return self._dist.var(self.alpha, self.n) | |
def cov(self): | |
return self._dist.cov(self.alpha, self.n) | |
# Set frozen generator docstrings from corresponding docstrings in | |
# dirichlet_multinomial and fill in default strings in class docstrings. | |
for name in ['logpmf', 'pmf', 'mean', 'var', 'cov']: | |
method = dirichlet_multinomial_gen.__dict__[name] | |
method_frozen = dirichlet_multinomial_frozen.__dict__[name] | |
method_frozen.__doc__ = doccer.docformat( | |
method.__doc__, dirichlet_mn_docdict_noparams) | |
method.__doc__ = doccer.docformat(method.__doc__, | |
dirichlet_mn_docdict_params) | |
class vonmises_fisher_gen(multi_rv_generic): | |
r"""A von Mises-Fisher variable. | |
The `mu` keyword specifies the mean direction vector. The `kappa` keyword | |
specifies the concentration parameter. | |
Methods | |
------- | |
pdf(x, mu=None, kappa=1) | |
Probability density function. | |
logpdf(x, mu=None, kappa=1) | |
Log of the probability density function. | |
rvs(mu=None, kappa=1, size=1, random_state=None) | |
Draw random samples from a von Mises-Fisher distribution. | |
entropy(mu=None, kappa=1) | |
Compute the differential entropy of the von Mises-Fisher distribution. | |
fit(data) | |
Fit a von Mises-Fisher distribution to data. | |
Parameters | |
---------- | |
mu : array_like | |
Mean direction of the distribution. Must be a one-dimensional unit | |
vector of norm 1. | |
kappa : float | |
Concentration parameter. Must be positive. | |
seed : {None, int, np.random.RandomState, np.random.Generator}, optional | |
Used for drawing random variates. | |
If `seed` is `None`, the `~np.random.RandomState` singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, seeded | |
with seed. | |
If `seed` is already a ``RandomState`` or ``Generator`` instance, | |
then that object is used. | |
Default is `None`. | |
See Also | |
-------- | |
scipy.stats.vonmises : Von-Mises Fisher distribution in 2D on a circle | |
uniform_direction : uniform distribution on the surface of a hypersphere | |
Notes | |
----- | |
The von Mises-Fisher distribution is a directional distribution on the | |
surface of the unit hypersphere. The probability density | |
function of a unit vector :math:`\mathbf{x}` is | |
.. math:: | |
f(\mathbf{x}) = \frac{\kappa^{d/2-1}}{(2\pi)^{d/2}I_{d/2-1}(\kappa)} | |
\exp\left(\kappa \mathbf{\mu}^T\mathbf{x}\right), | |
where :math:`\mathbf{\mu}` is the mean direction, :math:`\kappa` the | |
concentration parameter, :math:`d` the dimension and :math:`I` the | |
modified Bessel function of the first kind. As :math:`\mu` represents | |
a direction, it must be a unit vector or in other words, a point | |
on the hypersphere: :math:`\mathbf{\mu}\in S^{d-1}`. :math:`\kappa` is a | |
concentration parameter, which means that it must be positive | |
(:math:`\kappa>0`) and that the distribution becomes more narrow with | |
increasing :math:`\kappa`. In that sense, the reciprocal value | |
:math:`1/\kappa` resembles the variance parameter of the normal | |
distribution. | |
The von Mises-Fisher distribution often serves as an analogue of the | |
normal distribution on the sphere. Intuitively, for unit vectors, a | |
useful distance measure is given by the angle :math:`\alpha` between | |
them. This is exactly what the scalar product | |
:math:`\mathbf{\mu}^T\mathbf{x}=\cos(\alpha)` in the | |
von Mises-Fisher probability density function describes: the angle | |
between the mean direction :math:`\mathbf{\mu}` and the vector | |
:math:`\mathbf{x}`. The larger the angle between them, the smaller the | |
probability to observe :math:`\mathbf{x}` for this particular mean | |
direction :math:`\mathbf{\mu}`. | |
In dimensions 2 and 3, specialized algorithms are used for fast sampling | |
[2]_, [3]_. For dimensions of 4 or higher the rejection sampling algorithm | |
described in [4]_ is utilized. This implementation is partially based on | |
the geomstats package [5]_, [6]_. | |
.. versionadded:: 1.11 | |
References | |
---------- | |
.. [1] Von Mises-Fisher distribution, Wikipedia, | |
https://en.wikipedia.org/wiki/Von_Mises%E2%80%93Fisher_distribution | |
.. [2] Mardia, K., and Jupp, P. Directional statistics. Wiley, 2000. | |
.. [3] J. Wenzel. Numerically stable sampling of the von Mises Fisher | |
distribution on S2. | |
https://www.mitsuba-renderer.org/~wenzel/files/vmf.pdf | |
.. [4] Wood, A. Simulation of the von mises fisher distribution. | |
Communications in statistics-simulation and computation 23, | |
1 (1994), 157-164. https://doi.org/10.1080/03610919408813161 | |
.. [5] geomstats, Github. MIT License. Accessed: 06.01.2023. | |
https://github.com/geomstats/geomstats | |
.. [6] Miolane, N. et al. Geomstats: A Python Package for Riemannian | |
Geometry in Machine Learning. Journal of Machine Learning Research | |
21 (2020). http://jmlr.org/papers/v21/19-027.html | |
Examples | |
-------- | |
**Visualization of the probability density** | |
Plot the probability density in three dimensions for increasing | |
concentration parameter. The density is calculated by the ``pdf`` | |
method. | |
>>> import numpy as np | |
>>> import matplotlib.pyplot as plt | |
>>> from scipy.stats import vonmises_fisher | |
>>> from matplotlib.colors import Normalize | |
>>> n_grid = 100 | |
>>> u = np.linspace(0, np.pi, n_grid) | |
>>> v = np.linspace(0, 2 * np.pi, n_grid) | |
>>> u_grid, v_grid = np.meshgrid(u, v) | |
>>> vertices = np.stack([np.cos(v_grid) * np.sin(u_grid), | |
... np.sin(v_grid) * np.sin(u_grid), | |
... np.cos(u_grid)], | |
... axis=2) | |
>>> x = np.outer(np.cos(v), np.sin(u)) | |
>>> y = np.outer(np.sin(v), np.sin(u)) | |
>>> z = np.outer(np.ones_like(u), np.cos(u)) | |
>>> def plot_vmf_density(ax, x, y, z, vertices, mu, kappa): | |
... vmf = vonmises_fisher(mu, kappa) | |
... pdf_values = vmf.pdf(vertices) | |
... pdfnorm = Normalize(vmin=pdf_values.min(), vmax=pdf_values.max()) | |
... ax.plot_surface(x, y, z, rstride=1, cstride=1, | |
... facecolors=plt.cm.viridis(pdfnorm(pdf_values)), | |
... linewidth=0) | |
... ax.set_aspect('equal') | |
... ax.view_init(azim=-130, elev=0) | |
... ax.axis('off') | |
... ax.set_title(rf"$\kappa={kappa}$") | |
>>> fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(9, 4), | |
... subplot_kw={"projection": "3d"}) | |
>>> left, middle, right = axes | |
>>> mu = np.array([-np.sqrt(0.5), -np.sqrt(0.5), 0]) | |
>>> plot_vmf_density(left, x, y, z, vertices, mu, 5) | |
>>> plot_vmf_density(middle, x, y, z, vertices, mu, 20) | |
>>> plot_vmf_density(right, x, y, z, vertices, mu, 100) | |
>>> plt.subplots_adjust(top=1, bottom=0.0, left=0.0, right=1.0, wspace=0.) | |
>>> plt.show() | |
As we increase the concentration parameter, the points are getting more | |
clustered together around the mean direction. | |
**Sampling** | |
Draw 5 samples from the distribution using the ``rvs`` method resulting | |
in a 5x3 array. | |
>>> rng = np.random.default_rng() | |
>>> mu = np.array([0, 0, 1]) | |
>>> samples = vonmises_fisher(mu, 20).rvs(5, random_state=rng) | |
>>> samples | |
array([[ 0.3884594 , -0.32482588, 0.86231516], | |
[ 0.00611366, -0.09878289, 0.99509023], | |
[-0.04154772, -0.01637135, 0.99900239], | |
[-0.14613735, 0.12553507, 0.98126695], | |
[-0.04429884, -0.23474054, 0.97104814]]) | |
These samples are unit vectors on the sphere :math:`S^2`. To verify, | |
let us calculate their euclidean norms: | |
>>> np.linalg.norm(samples, axis=1) | |
array([1., 1., 1., 1., 1.]) | |
Plot 20 observations drawn from the von Mises-Fisher distribution for | |
increasing concentration parameter :math:`\kappa`. The red dot highlights | |
the mean direction :math:`\mu`. | |
>>> def plot_vmf_samples(ax, x, y, z, mu, kappa): | |
... vmf = vonmises_fisher(mu, kappa) | |
... samples = vmf.rvs(20) | |
... ax.plot_surface(x, y, z, rstride=1, cstride=1, linewidth=0, | |
... alpha=0.2) | |
... ax.scatter(samples[:, 0], samples[:, 1], samples[:, 2], c='k', s=5) | |
... ax.scatter(mu[0], mu[1], mu[2], c='r', s=30) | |
... ax.set_aspect('equal') | |
... ax.view_init(azim=-130, elev=0) | |
... ax.axis('off') | |
... ax.set_title(rf"$\kappa={kappa}$") | |
>>> mu = np.array([-np.sqrt(0.5), -np.sqrt(0.5), 0]) | |
>>> fig, axes = plt.subplots(nrows=1, ncols=3, | |
... subplot_kw={"projection": "3d"}, | |
... figsize=(9, 4)) | |
>>> left, middle, right = axes | |
>>> plot_vmf_samples(left, x, y, z, mu, 5) | |
>>> plot_vmf_samples(middle, x, y, z, mu, 20) | |
>>> plot_vmf_samples(right, x, y, z, mu, 100) | |
>>> plt.subplots_adjust(top=1, bottom=0.0, left=0.0, | |
... right=1.0, wspace=0.) | |
>>> plt.show() | |
The plots show that with increasing concentration :math:`\kappa` the | |
resulting samples are centered more closely around the mean direction. | |
**Fitting the distribution parameters** | |
The distribution can be fitted to data using the ``fit`` method returning | |
the estimated parameters. As a toy example let's fit the distribution to | |
samples drawn from a known von Mises-Fisher distribution. | |
>>> mu, kappa = np.array([0, 0, 1]), 20 | |
>>> samples = vonmises_fisher(mu, kappa).rvs(1000, random_state=rng) | |
>>> mu_fit, kappa_fit = vonmises_fisher.fit(samples) | |
>>> mu_fit, kappa_fit | |
(array([0.01126519, 0.01044501, 0.99988199]), 19.306398751730995) | |
We see that the estimated parameters `mu_fit` and `kappa_fit` are | |
very close to the ground truth parameters. | |
""" | |
def __init__(self, seed=None): | |
super().__init__(seed) | |
def __call__(self, mu=None, kappa=1, seed=None): | |
"""Create a frozen von Mises-Fisher distribution. | |
See `vonmises_fisher_frozen` for more information. | |
""" | |
return vonmises_fisher_frozen(mu, kappa, seed=seed) | |
def _process_parameters(self, mu, kappa): | |
""" | |
Infer dimensionality from mu and ensure that mu is a one-dimensional | |
unit vector and kappa positive. | |
""" | |
mu = np.asarray(mu) | |
if mu.ndim > 1: | |
raise ValueError("'mu' must have one-dimensional shape.") | |
if not np.allclose(np.linalg.norm(mu), 1.): | |
raise ValueError("'mu' must be a unit vector of norm 1.") | |
if not mu.size > 1: | |
raise ValueError("'mu' must have at least two entries.") | |
kappa_error_msg = "'kappa' must be a positive scalar." | |
if not np.isscalar(kappa) or kappa < 0: | |
raise ValueError(kappa_error_msg) | |
if float(kappa) == 0.: | |
raise ValueError("For 'kappa=0' the von Mises-Fisher distribution " | |
"becomes the uniform distribution on the sphere " | |
"surface. Consider using " | |
"'scipy.stats.uniform_direction' instead.") | |
dim = mu.size | |
return dim, mu, kappa | |
def _check_data_vs_dist(self, x, dim): | |
if x.shape[-1] != dim: | |
raise ValueError("The dimensionality of the last axis of 'x' must " | |
"match the dimensionality of the " | |
"von Mises Fisher distribution.") | |
if not np.allclose(np.linalg.norm(x, axis=-1), 1.): | |
msg = "'x' must be unit vectors of norm 1 along last dimension." | |
raise ValueError(msg) | |
def _log_norm_factor(self, dim, kappa): | |
# normalization factor is given by | |
# c = kappa**(dim/2-1)/((2*pi)**(dim/2)*I[dim/2-1](kappa)) | |
# = kappa**(dim/2-1)*exp(-kappa) / | |
# ((2*pi)**(dim/2)*I[dim/2-1](kappa)*exp(-kappa) | |
# = kappa**(dim/2-1)*exp(-kappa) / | |
# ((2*pi)**(dim/2)*ive[dim/2-1](kappa) | |
# Then the log is given by | |
# log c = 1/2*(dim -1)*log(kappa) - kappa - -1/2*dim*ln(2*pi) - | |
# ive[dim/2-1](kappa) | |
halfdim = 0.5 * dim | |
return (0.5 * (dim - 2)*np.log(kappa) - halfdim * _LOG_2PI - | |
np.log(ive(halfdim - 1, kappa)) - kappa) | |
def _logpdf(self, x, dim, mu, kappa): | |
"""Log of the von Mises-Fisher probability density function. | |
As this function does no argument checking, it should not be | |
called directly; use 'logpdf' instead. | |
""" | |
x = np.asarray(x) | |
self._check_data_vs_dist(x, dim) | |
dotproducts = np.einsum('i,...i->...', mu, x) | |
return self._log_norm_factor(dim, kappa) + kappa * dotproducts | |
def logpdf(self, x, mu=None, kappa=1): | |
"""Log of the von Mises-Fisher probability density function. | |
Parameters | |
---------- | |
x : array_like | |
Points at which to evaluate the log of the probability | |
density function. The last axis of `x` must correspond | |
to unit vectors of the same dimensionality as the distribution. | |
mu : array_like, default: None | |
Mean direction of the distribution. Must be a one-dimensional unit | |
vector of norm 1. | |
kappa : float, default: 1 | |
Concentration parameter. Must be positive. | |
Returns | |
------- | |
logpdf : ndarray or scalar | |
Log of the probability density function evaluated at `x`. | |
""" | |
dim, mu, kappa = self._process_parameters(mu, kappa) | |
return self._logpdf(x, dim, mu, kappa) | |
def pdf(self, x, mu=None, kappa=1): | |
"""Von Mises-Fisher probability density function. | |
Parameters | |
---------- | |
x : array_like | |
Points at which to evaluate the probability | |
density function. The last axis of `x` must correspond | |
to unit vectors of the same dimensionality as the distribution. | |
mu : array_like | |
Mean direction of the distribution. Must be a one-dimensional unit | |
vector of norm 1. | |
kappa : float | |
Concentration parameter. Must be positive. | |
Returns | |
------- | |
pdf : ndarray or scalar | |
Probability density function evaluated at `x`. | |
""" | |
dim, mu, kappa = self._process_parameters(mu, kappa) | |
return np.exp(self._logpdf(x, dim, mu, kappa)) | |
def _rvs_2d(self, mu, kappa, size, random_state): | |
""" | |
In 2D, the von Mises-Fisher distribution reduces to the | |
von Mises distribution which can be efficiently sampled by numpy. | |
This method is much faster than the general rejection | |
sampling based algorithm. | |
""" | |
mean_angle = np.arctan2(mu[1], mu[0]) | |
angle_samples = random_state.vonmises(mean_angle, kappa, size=size) | |
samples = np.stack([np.cos(angle_samples), np.sin(angle_samples)], | |
axis=-1) | |
return samples | |
def _rvs_3d(self, kappa, size, random_state): | |
""" | |
Generate samples from a von Mises-Fisher distribution | |
with mu = [1, 0, 0] and kappa. Samples then have to be | |
rotated towards the desired mean direction mu. | |
This method is much faster than the general rejection | |
sampling based algorithm. | |
Reference: https://www.mitsuba-renderer.org/~wenzel/files/vmf.pdf | |
""" | |
if size is None: | |
sample_size = 1 | |
else: | |
sample_size = size | |
# compute x coordinate acc. to equation from section 3.1 | |
x = random_state.random(sample_size) | |
x = 1. + np.log(x + (1. - x) * np.exp(-2 * kappa))/kappa | |
# (y, z) are random 2D vectors that only have to be | |
# normalized accordingly. Then (x, y z) follow a VMF distribution | |
temp = np.sqrt(1. - np.square(x)) | |
uniformcircle = _sample_uniform_direction(2, sample_size, random_state) | |
samples = np.stack([x, temp * uniformcircle[..., 0], | |
temp * uniformcircle[..., 1]], | |
axis=-1) | |
if size is None: | |
samples = np.squeeze(samples) | |
return samples | |
def _rejection_sampling(self, dim, kappa, size, random_state): | |
""" | |
Generate samples from a n-dimensional von Mises-Fisher distribution | |
with mu = [1, 0, ..., 0] and kappa via rejection sampling. | |
Samples then have to be rotated towards the desired mean direction mu. | |
Reference: https://doi.org/10.1080/03610919408813161 | |
""" | |
dim_minus_one = dim - 1 | |
# calculate number of requested samples | |
if size is not None: | |
if not np.iterable(size): | |
size = (size, ) | |
n_samples = math.prod(size) | |
else: | |
n_samples = 1 | |
# calculate envelope for rejection sampler (eq. 4) | |
sqrt = np.sqrt(4 * kappa ** 2. + dim_minus_one ** 2) | |
envelop_param = (-2 * kappa + sqrt) / dim_minus_one | |
if envelop_param == 0: | |
# the regular formula suffers from loss of precision for high | |
# kappa. This can only be detected by checking for 0 here. | |
# Workaround: expansion for sqrt variable | |
# https://www.wolframalpha.com/input?i=sqrt%284*x%5E2%2Bd%5E2%29 | |
# e = (-2 * k + sqrt(k**2 + d**2)) / d | |
# ~ (-2 * k + 2 * k + d**2/(4 * k) - d**4/(64 * k**3)) / d | |
# = d/(4 * k) - d**3/(64 * k**3) | |
envelop_param = (dim_minus_one/4 * kappa**-1. | |
- dim_minus_one**3/64 * kappa**-3.) | |
# reference step 0 | |
node = (1. - envelop_param) / (1. + envelop_param) | |
# t = ln(1 - ((1-x)/(1+x))**2) | |
# = ln(4 * x / (1+x)**2) | |
# = ln(4) + ln(x) - 2*log1p(x) | |
correction = (kappa * node + dim_minus_one | |
* (np.log(4) + np.log(envelop_param) | |
- 2 * np.log1p(envelop_param))) | |
n_accepted = 0 | |
x = np.zeros((n_samples, )) | |
halfdim = 0.5 * dim_minus_one | |
# main loop | |
while n_accepted < n_samples: | |
# generate candidates acc. to reference step 1 | |
sym_beta = random_state.beta(halfdim, halfdim, | |
size=n_samples - n_accepted) | |
coord_x = (1 - (1 + envelop_param) * sym_beta) / ( | |
1 - (1 - envelop_param) * sym_beta) | |
# accept or reject: reference step 2 | |
# reformulation for numerical stability: | |
# t = ln(1 - (1-x)/(1+x) * y) | |
# = ln((1 + x - y +x*y)/(1 +x)) | |
accept_tol = random_state.random(n_samples - n_accepted) | |
criterion = ( | |
kappa * coord_x | |
+ dim_minus_one * (np.log((1 + envelop_param - coord_x | |
+ coord_x * envelop_param) / (1 + envelop_param))) | |
- correction) > np.log(accept_tol) | |
accepted_iter = np.sum(criterion) | |
x[n_accepted:n_accepted + accepted_iter] = coord_x[criterion] | |
n_accepted += accepted_iter | |
# concatenate x and remaining coordinates: step 3 | |
coord_rest = _sample_uniform_direction(dim_minus_one, n_accepted, | |
random_state) | |
coord_rest = np.einsum( | |
'...,...i->...i', np.sqrt(1 - x ** 2), coord_rest) | |
samples = np.concatenate([x[..., None], coord_rest], axis=1) | |
# reshape output to (size, dim) | |
if size is not None: | |
samples = samples.reshape(size + (dim, )) | |
else: | |
samples = np.squeeze(samples) | |
return samples | |
def _rotate_samples(self, samples, mu, dim): | |
"""A QR decomposition is used to find the rotation that maps the | |
north pole (1, 0,...,0) to the vector mu. This rotation is then | |
applied to all samples. | |
Parameters | |
---------- | |
samples: array_like, shape = [..., n] | |
mu : array-like, shape=[n, ] | |
Point to parametrise the rotation. | |
Returns | |
------- | |
samples : rotated samples | |
""" | |
base_point = np.zeros((dim, )) | |
base_point[0] = 1. | |
embedded = np.concatenate([mu[None, :], np.zeros((dim - 1, dim))]) | |
rotmatrix, _ = np.linalg.qr(np.transpose(embedded)) | |
if np.allclose(np.matmul(rotmatrix, base_point[:, None])[:, 0], mu): | |
rotsign = 1 | |
else: | |
rotsign = -1 | |
# apply rotation | |
samples = np.einsum('ij,...j->...i', rotmatrix, samples) * rotsign | |
return samples | |
def _rvs(self, dim, mu, kappa, size, random_state): | |
if dim == 2: | |
samples = self._rvs_2d(mu, kappa, size, random_state) | |
elif dim == 3: | |
samples = self._rvs_3d(kappa, size, random_state) | |
else: | |
samples = self._rejection_sampling(dim, kappa, size, | |
random_state) | |
if dim != 2: | |
samples = self._rotate_samples(samples, mu, dim) | |
return samples | |
def rvs(self, mu=None, kappa=1, size=1, random_state=None): | |
"""Draw random samples from a von Mises-Fisher distribution. | |
Parameters | |
---------- | |
mu : array_like | |
Mean direction of the distribution. Must be a one-dimensional unit | |
vector of norm 1. | |
kappa : float | |
Concentration parameter. Must be positive. | |
size : int or tuple of ints, optional | |
Given a shape of, for example, (m,n,k), m*n*k samples are | |
generated, and packed in an m-by-n-by-k arrangement. | |
Because each sample is N-dimensional, the output shape | |
is (m,n,k,N). If no shape is specified, a single (N-D) | |
sample is returned. | |
random_state : {None, int, np.random.RandomState, np.random.Generator}, | |
optional | |
Used for drawing random variates. | |
If `seed` is `None`, the `~np.random.RandomState` singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, seeded | |
with seed. | |
If `seed` is already a ``RandomState`` or ``Generator`` instance, | |
then that object is used. | |
Default is `None`. | |
Returns | |
------- | |
rvs : ndarray | |
Random variates of shape (`size`, `N`), where `N` is the | |
dimension of the distribution. | |
""" | |
dim, mu, kappa = self._process_parameters(mu, kappa) | |
random_state = self._get_random_state(random_state) | |
samples = self._rvs(dim, mu, kappa, size, random_state) | |
return samples | |
def _entropy(self, dim, kappa): | |
halfdim = 0.5 * dim | |
return (-self._log_norm_factor(dim, kappa) - kappa * | |
ive(halfdim, kappa) / ive(halfdim - 1, kappa)) | |
def entropy(self, mu=None, kappa=1): | |
"""Compute the differential entropy of the von Mises-Fisher | |
distribution. | |
Parameters | |
---------- | |
mu : array_like, default: None | |
Mean direction of the distribution. Must be a one-dimensional unit | |
vector of norm 1. | |
kappa : float, default: 1 | |
Concentration parameter. Must be positive. | |
Returns | |
------- | |
h : scalar | |
Entropy of the von Mises-Fisher distribution. | |
""" | |
dim, _, kappa = self._process_parameters(mu, kappa) | |
return self._entropy(dim, kappa) | |
def fit(self, x): | |
"""Fit the von Mises-Fisher distribution to data. | |
Parameters | |
---------- | |
x : array-like | |
Data the distribution is fitted to. Must be two dimensional. | |
The second axis of `x` must be unit vectors of norm 1 and | |
determine the dimensionality of the fitted | |
von Mises-Fisher distribution. | |
Returns | |
------- | |
mu : ndarray | |
Estimated mean direction. | |
kappa : float | |
Estimated concentration parameter. | |
""" | |
# validate input data | |
x = np.asarray(x) | |
if x.ndim != 2: | |
raise ValueError("'x' must be two dimensional.") | |
if not np.allclose(np.linalg.norm(x, axis=-1), 1.): | |
msg = "'x' must be unit vectors of norm 1 along last dimension." | |
raise ValueError(msg) | |
dim = x.shape[-1] | |
# mu is simply the directional mean | |
dirstats = directional_stats(x) | |
mu = dirstats.mean_direction | |
r = dirstats.mean_resultant_length | |
# kappa is the solution to the equation: | |
# r = I[dim/2](kappa) / I[dim/2 -1](kappa) | |
# = I[dim/2](kappa) * exp(-kappa) / I[dim/2 -1](kappa) * exp(-kappa) | |
# = ive(dim/2, kappa) / ive(dim/2 -1, kappa) | |
halfdim = 0.5 * dim | |
def solve_for_kappa(kappa): | |
bessel_vals = ive([halfdim, halfdim - 1], kappa) | |
return bessel_vals[0]/bessel_vals[1] - r | |
root_res = root_scalar(solve_for_kappa, method="brentq", | |
bracket=(1e-8, 1e9)) | |
kappa = root_res.root | |
return mu, kappa | |
vonmises_fisher = vonmises_fisher_gen() | |
class vonmises_fisher_frozen(multi_rv_frozen): | |
def __init__(self, mu=None, kappa=1, seed=None): | |
"""Create a frozen von Mises-Fisher distribution. | |
Parameters | |
---------- | |
mu : array_like, default: None | |
Mean direction of the distribution. | |
kappa : float, default: 1 | |
Concentration parameter. Must be positive. | |
seed : {None, int, `numpy.random.Generator`, | |
`numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance | |
then that instance is used. | |
""" | |
self._dist = vonmises_fisher_gen(seed) | |
self.dim, self.mu, self.kappa = ( | |
self._dist._process_parameters(mu, kappa) | |
) | |
def logpdf(self, x): | |
""" | |
Parameters | |
---------- | |
x : array_like | |
Points at which to evaluate the log of the probability | |
density function. The last axis of `x` must correspond | |
to unit vectors of the same dimensionality as the distribution. | |
Returns | |
------- | |
logpdf : ndarray or scalar | |
Log of probability density function evaluated at `x`. | |
""" | |
return self._dist._logpdf(x, self.dim, self.mu, self.kappa) | |
def pdf(self, x): | |
""" | |
Parameters | |
---------- | |
x : array_like | |
Points at which to evaluate the log of the probability | |
density function. The last axis of `x` must correspond | |
to unit vectors of the same dimensionality as the distribution. | |
Returns | |
------- | |
pdf : ndarray or scalar | |
Probability density function evaluated at `x`. | |
""" | |
return np.exp(self.logpdf(x)) | |
def rvs(self, size=1, random_state=None): | |
"""Draw random variates from the Von Mises-Fisher distribution. | |
Parameters | |
---------- | |
size : int or tuple of ints, optional | |
Given a shape of, for example, (m,n,k), m*n*k samples are | |
generated, and packed in an m-by-n-by-k arrangement. | |
Because each sample is N-dimensional, the output shape | |
is (m,n,k,N). If no shape is specified, a single (N-D) | |
sample is returned. | |
random_state : {None, int, `numpy.random.Generator`, | |
`numpy.random.RandomState`}, optional | |
If `seed` is None (or `np.random`), the `numpy.random.RandomState` | |
singleton is used. | |
If `seed` is an int, a new ``RandomState`` instance is used, | |
seeded with `seed`. | |
If `seed` is already a ``Generator`` or ``RandomState`` instance | |
then that instance is used. | |
Returns | |
------- | |
rvs : ndarray or scalar | |
Random variates of size (`size`, `N`), where `N` is the | |
dimension of the distribution. | |
""" | |
random_state = self._dist._get_random_state(random_state) | |
return self._dist._rvs(self.dim, self.mu, self.kappa, size, | |
random_state) | |
def entropy(self): | |
""" | |
Calculate the differential entropy of the von Mises-Fisher | |
distribution. | |
Returns | |
------- | |
h: float | |
Entropy of the Von Mises-Fisher distribution. | |
""" | |
return self._dist._entropy(self.dim, self.kappa) | |