| | |
| | |
| | |
| | import math |
| | import threading |
| | 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 import special |
| | from scipy._lib._util import check_random_state, _lazywhere |
| | from scipy.linalg.blas import drot, get_blas_funcs |
| | from ._continuous_distns import norm, invgamma |
| | 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', |
| | 'normal_inverse_gamma'] |
| |
|
| | _LOG_2PI = np.log(2 * np.pi) |
| | _LOG_2 = np.log(2) |
| | _LOG_PI = np.log(np.pi) |
| | MVN_LOCK = threading.Lock() |
| |
|
| |
|
| | _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) |
| |
|
| | |
| | |
| | |
| | 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)) |
| |
|
| | |
| | self.eps = 1e3*eps |
| | self.V = u[:, s <= eps] |
| |
|
| | |
| | self.rank = len(d) |
| | self.U = U |
| | self.log_pdet = np.sum(np.log(d)) |
| |
|
| | |
| | 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 |
| |
|
| | @property |
| | 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) |
| |
|
| | @property |
| | 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 |
| |
|
| | @random_state.setter |
| | 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. |
| | """ |
| | @property |
| | def random_state(self): |
| | return self._dist._random_state |
| |
|
| | @random_state.setter |
| | 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)) |
| | |
| | """ |
| |
|
| | 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: |
| | |
| | |
| | |
| | |
| | |
| | dim, mean, cov = self._process_parameters_psd(None, mean, cov) |
| | |
| | |
| | |
| | |
| | |
| | |
| | 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): |
| | |
| | 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.") |
| |
|
| | |
| | |
| | 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," |
| | f" but cov.shape = {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) |
| | |
| | |
| | |
| | |
| | b, a = np.broadcast_arrays(x, lower) |
| | i_swap = b < a |
| | signs = (-1)**(i_swap.sum(axis=-1)) |
| | 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): |
| | with MVN_LOCK: |
| | 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) |
| | |
| | |
| | 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 |
| | |
| | """ |
| | |
| | x = np.asarray(x) |
| | if x.ndim != 2: |
| | raise ValueError("`x` must be two-dimensional.") |
| |
|
| | n_vectors, dim = x.shape |
| |
|
| | |
| | |
| | if fix_mean is not None: |
| | |
| | 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: |
| | |
| | fix_cov = np.atleast_2d(fix_cov) |
| | |
| | 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) |
| | |
| | |
| | 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.]]) |
| | |
| | """ |
| | 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 |
| |
|
| | @property |
| | 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) |
| | |
| | |
| | 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) |
| |
|
| |
|
| | |
| | |
| | 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. |
| | """ |
| |
|
| | |
| | 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.") |
| |
|
| | |
| | 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] |
| |
|
| | |
| | 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] |
| |
|
| | |
| | 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) |
| | |
| | |
| | |
| | |
| | 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) |
| |
|
| |
|
| | |
| | |
| | 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.") |
| |
|
| | |
| | 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 " |
| | f"simplex. but np.sum(x, 0) = {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) |
| |
|
| |
|
| | |
| | |
| | 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," |
| | f" but scale.scale = {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," |
| | f" but x.shape = {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 " |
| | f"if they are three dimensional, but x.shape = {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) |
| |
|
| | |
| | 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.' |
| | f' Got size.ndim = {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 triangular. |
| | |
| | Notes |
| | ----- |
| | As this function does no argument checking, it should not be |
| | called directly; use 'logpdf' instead. |
| | |
| | """ |
| | |
| | |
| | |
| | |
| |
|
| | |
| | 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() |
| |
|
| | |
| | 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) |
| |
|
| | |
| | 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() |
| | 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. |
| | |
| | """ |
| | |
| | n_tril = dim * (dim-1) // 2 |
| | covariances = random_state.normal( |
| | size=n*n_tril).reshape(shape+(n_tril,)) |
| |
|
| | |
| | variances = (np.r_[[random_state.chisquare(df-(i+1)+1, size=n)**0.5 |
| | for i in range(dim)]].reshape((dim,) + |
| | shape[::-1]).T) |
| |
|
| | |
| | A = np.zeros(shape + (dim, dim)) |
| |
|
| | |
| | size_idx = tuple([slice(None, None, None)]*len(shape)) |
| | tril_idx = np.tril_indices(dim, k=-1) |
| | A[size_idx + tril_idx] = covariances |
| |
|
| | |
| | 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) |
| | |
| | |
| | A = self._standard_rvs(n, shape, dim, df, random_state) |
| |
|
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | 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) |
| |
|
| | |
| | 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) |
| |
|
| |
|
| | |
| | |
| | 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 triangular. |
| | |
| | Notes |
| | ----- |
| | As this function does no argument checking, it should not be |
| | called directly; use 'logpdf' instead. |
| | |
| | """ |
| | |
| | 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] |
| |
|
| | |
| | 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() |
| | 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)) |
| |
|
| | |
| | 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), |
| | ) |
| |
|
| | |
| | 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 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) |
| | |
| | A = self._inv_standard_rvs(n, shape, dim, df, random_state) |
| |
|
| | |
| | trsm = get_blas_funcs(('trsm'), (A,)) |
| | trmm = get_blas_funcs(('trmm'), (A,)) |
| |
|
| | for index in np.ndindex(A.shape[:-2]): |
| | if dim > 1: |
| | |
| | |
| | CA = trsm(1., A[index], C, side=1, lower=True) |
| | |
| | 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) |
| |
|
| | |
| | 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): |
| | |
| | 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 |
| | ) |
| |
|
| | |
| | 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) |
| |
|
| |
|
| | |
| | |
| | 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] |
| |
|
| | |
| | pcond = np.any(p < 0, axis=-1) |
| | pcond |= np.any(p > 1, axis=-1) |
| |
|
| | n = np.array(n, dtype=int, copy=True) |
| |
|
| | |
| | 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])) |
| |
|
| | |
| | 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) |
| |
|
| | |
| | |
| | xcond_ = xcond | np.zeros(npcond.shape, dtype=np.bool_) |
| | result = self._checkresult(result, xcond_, -np.inf) |
| |
|
| | |
| | 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) |
| |
|
| | |
| | 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) |
| |
|
| | |
| | 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) |
| |
|
| |
|
| | |
| | |
| | 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 = np.empty(size + (dim, dim)) |
| | H[..., :, :] = np.eye(dim) |
| | D = np.empty(size + (dim,)) |
| |
|
| | for n in range(dim-1): |
| |
|
| | |
| | |
| | |
| | |
| | x = random_state.normal(size=size + (dim-n,)) |
| | xrow = x[..., None, :] |
| | xcol = x[..., :, None] |
| |
|
| | |
| | |
| | |
| | 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) |
| |
|
| | |
| | |
| | x /= np.sqrt((norm2 - x0**2 + x[..., 0]**2) / 2.)[..., None] |
| |
|
| | |
| | |
| | H[..., :, n:] -= np.matmul(H[..., :, n:], xcol) * xrow |
| |
|
| | D[..., -1] = (-1)**(dim-1)*D[..., :-1].prod(axis=-1) |
| |
|
| | |
| | |
| | |
| | |
| | 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() |
| | |
| | """ |
| | 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) |
| | |
| | |
| | d = r.diagonal(offset=0, axis1=-2, axis2=-1) |
| | |
| | |
| | q *= (d/abs(d))[..., np.newaxis, :] |
| | 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() |
| | |
| | """ |
| | 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: |
| | |
| | return 0., 1. |
| |
|
| | dd = math.sqrt(max(aij**2 - aiid*ajjd, 0)) |
| |
|
| | |
| | t = (aij + math.copysign(dd, aij)) / ajjd |
| | c = 1. / math.sqrt(1. + t*t) |
| | if c == 0: |
| | |
| | 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 |
| | """ |
| | |
| | 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]) |
| |
|
| | |
| | |
| | |
| | |
| | |
| | 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) |
| | m = self._to_corr(m) |
| |
|
| | |
| | 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. |
| | """ |
| |
|
| | 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]]) # may vary |
| | |
| | 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) |
| | |
| | |
| | d = r.diagonal(offset=0, axis1=-2, axis2=-1) |
| | |
| | |
| | q *= (d/abs(d))[..., np.newaxis, :] |
| | 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() |
| | |
| | """ |
| | 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): |
| |
|
| | |
| | |
| | |
| | |
| | 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) |
| |
|
| | |
| | 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)) |
| | 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 |
| | |
| | |
| | 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): |
| | |
| | |
| | |
| | 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 |
| | )[()] |
| |
|
| | |
| | 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]]) |
| | |
| | """ |
| | |
| | |
| | |
| | |
| | |
| | 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," |
| | f" but cov.shape = {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) |
| |
|
| | |
| | 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() |
| |
|
| |
|
| | |
| | |
| | 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.") |
| |
|
| | |
| | if m.size != 0: |
| | n = n[..., np.newaxis] |
| |
|
| | m, n = np.broadcast_arrays(m, n) |
| |
|
| | |
| | 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]}.") |
| |
|
| | |
| | if m.size != 0: |
| | n = n[..., np.newaxis] |
| | M = M[..., np.newaxis] |
| |
|
| | x, m, n, M = np.broadcast_arrays(x, m, n, M) |
| |
|
| | |
| | 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): |
| | |
| | |
| | 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) |
| |
|
| | |
| | |
| | xcond_ = xcond_reduced | np.zeros(mncond.shape, dtype=np.bool_) |
| | result = self._checkresult(result, xcond_, -np.inf) |
| |
|
| | |
| | |
| | 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) |
| | |
| | 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) |
| | |
| | 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 |
| | """ |
| | |
| | |
| | M, m, n, _, _, mncond = self._process_parameters(m, n) |
| | |
| | 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)) |
| | |
| | if m.size != 0: |
| | M, n = M[..., 0, 0], n[..., 0, 0] |
| | cond = cond[..., 0, 0] |
| | dim = m.shape[-1] |
| | |
| | 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 |
| |
|
| | |
| | |
| | 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) |
| |
|
| | |
| | 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) |
| |
|
| |
|
| | |
| | |
| | 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") |
| |
|
| | |
| | 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) |
| |
|
| | @staticmethod |
| | 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 |
| |
|
| | @staticmethod |
| | 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 |
| |
|
| | @classmethod |
| | 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)}") |
| |
|
| | @classmethod |
| | def _rvs_select(cls, r, c, n): |
| | fac = 1.0 |
| | k = len(r) * len(c) |
| | |
| | if n > fac * np.log(n + 1) * k: |
| | return cls._rvs_patefield |
| | return cls._rvs_boyett |
| |
|
| | @staticmethod |
| | def _rvs_boyett(row, col, ntot, size, random_state): |
| | return _rcont.rvs_rcont1(row, col, ntot, size, random_state) |
| |
|
| | @staticmethod |
| | 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) |
| |
|
| | |
| | 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): |
| | |
| | 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) |
| |
|
| |
|
| | |
| | |
| | _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: |
| | |
| | |
| | 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) |
| |
|
| |
|
| | |
| | |
| | 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): |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | 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 |
| |
|
| | |
| | x = random_state.random(sample_size) |
| | x = 1. + np.log(x + (1. - x) * np.exp(-2 * kappa))/kappa |
| |
|
| | |
| | |
| | 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 |
| | |
| | if size is not None: |
| | if not np.iterable(size): |
| | size = (size, ) |
| | n_samples = math.prod(size) |
| | else: |
| | n_samples = 1 |
| | |
| | sqrt = np.sqrt(4 * kappa ** 2. + dim_minus_one ** 2) |
| | envelop_param = (-2 * kappa + sqrt) / dim_minus_one |
| | if envelop_param == 0: |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | envelop_param = (dim_minus_one/4 * kappa**-1. |
| | - dim_minus_one**3/64 * kappa**-3.) |
| | |
| | node = (1. - envelop_param) / (1. + envelop_param) |
| | |
| | |
| | |
| | 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 |
| | |
| | while n_accepted < n_samples: |
| | |
| | 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_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 |
| | |
| | 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) |
| | |
| | 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 |
| |
|
| | |
| | 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. |
| | |
| | """ |
| | |
| | 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] |
| |
|
| | |
| | dirstats = directional_stats(x) |
| | mu = dirstats.mean_direction |
| | r = dirstats.mean_resultant_length |
| |
|
| | |
| | |
| | |
| | |
| |
|
| | 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) |
| |
|
| |
|
| | class normal_inverse_gamma_gen(multi_rv_generic): |
| | r"""Normal-inverse-gamma distribution. |
| | |
| | The normal-inverse-gamma distribution is the conjugate prior of a normal |
| | distribution with unknown mean and variance. |
| | |
| | Methods |
| | ------- |
| | pdf(x, s2, mu=0, lmbda=1, a=1, b=1) |
| | Probability density function. |
| | logpdf(x, s2, mu=0, lmbda=1, a=1, b=1) |
| | Log of the probability density function. |
| | mean(mu=0, lmbda=1, a=1, b=1) |
| | Distribution mean. |
| | var(mu=0, lmbda=1, a=1, b=1) |
| | Distribution variance. |
| | rvs(mu=0, lmbda=1, a=1, b=1, size=None, random_state=None) |
| | Draw random samples. |
| | |
| | Parameters |
| | ---------- |
| | mu, lmbda, a, b : array_like |
| | Shape parameters of the distribution. See notes. |
| | 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 |
| | -------- |
| | norm |
| | invgamma |
| | |
| | Notes |
| | ----- |
| | |
| | The probability density function of `normal_inverse_gamma` is: |
| | |
| | .. math:: |
| | |
| | f(x, \sigma^2; \mu, \lambda, \alpha, \beta) = |
| | \frac{\sqrt{\lambda}}{\sqrt{2 \pi \sigma^2}} |
| | \frac{\beta^\alpha}{\Gamma(\alpha)} |
| | \left( \frac{1}{\sigma^2} \right)^{\alpha + 1} |
| | \exp \left(- \frac{2 \beta + \lambda (x - \mu)^2} {2 \sigma^2} \right) |
| | |
| | where all parameters are real and finite, and :math:`\sigma^2 > 0`, |
| | :math:`\lambda > 0`, :math:`\alpha > 0`, and :math:`\beta > 0`. |
| | |
| | Methods ``normal_inverse_gamma.pdf`` and ``normal_inverse_gamma.logpdf`` |
| | accept `x` and `s2` for arguments :math:`x` and :math:`\sigma^2`. |
| | All methods accept `mu`, `lmbda`, `a`, and `b` for shape parameters |
| | :math:`\mu`, :math:`\lambda`, :math:`\alpha`, and :math:`\beta`, |
| | respectively. |
| | |
| | .. versionadded:: 1.15 |
| | |
| | References |
| | ---------- |
| | .. [1] Normal-inverse-gamma distribution, Wikipedia, |
| | https://en.wikipedia.org/wiki/Normal-inverse-gamma_distribution |
| | |
| | Examples |
| | -------- |
| | Suppose we wish to investigate the relationship between the |
| | normal-inverse-gamma distribution and the inverse gamma distribution. |
| | |
| | >>> import numpy as np |
| | >>> from scipy import stats |
| | >>> import matplotlib.pyplot as plt |
| | >>> rng = np.random.default_rng(527484872345) |
| | >>> mu, lmbda, a, b = 0, 1, 20, 20 |
| | >>> norm_inv_gamma = stats.normal_inverse_gamma(mu, lmbda, a, b) |
| | >>> inv_gamma = stats.invgamma(a, scale=b) |
| | |
| | One approach is to compare the distribution of the `s2` elements of |
| | random variates against the PDF of an inverse gamma distribution. |
| | |
| | >>> _, s2 = norm_inv_gamma.rvs(size=10000, random_state=rng) |
| | >>> bins = np.linspace(s2.min(), s2.max(), 50) |
| | >>> plt.hist(s2, bins=bins, density=True, label='Frequency density') |
| | >>> s2 = np.linspace(s2.min(), s2.max(), 300) |
| | >>> plt.plot(s2, inv_gamma.pdf(s2), label='PDF') |
| | >>> plt.xlabel(r'$\sigma^2$') |
| | >>> plt.ylabel('Frequency density / PMF') |
| | >>> plt.show() |
| | |
| | Similarly, we can compare the marginal distribution of `s2` against |
| | an inverse gamma distribution. |
| | |
| | >>> from scipy.integrate import quad_vec |
| | >>> from scipy import integrate |
| | >>> s2 = np.linspace(0.5, 3, 6) |
| | >>> res = quad_vec(lambda x: norm_inv_gamma.pdf(x, s2), -np.inf, np.inf)[0] |
| | >>> np.allclose(res, inv_gamma.pdf(s2)) |
| | True |
| | |
| | The sample mean is comparable to the mean of the distribution. |
| | |
| | >>> x, s2 = norm_inv_gamma.rvs(size=10000, random_state=rng) |
| | >>> x.mean(), s2.mean() |
| | (np.float64(-0.005254750127304425), np.float64(1.050438111436508)) |
| | >>> norm_inv_gamma.mean() |
| | (np.float64(0.0), np.float64(1.0526315789473684)) |
| | |
| | Similarly, for the variance: |
| | |
| | >>> x.var(ddof=1), s2.var(ddof=1) |
| | (np.float64(1.0546150578185023), np.float64(0.061829865266330754)) |
| | >>> norm_inv_gamma.var() |
| | (np.float64(1.0526315789473684), np.float64(0.061557402277623886)) |
| | |
| | """ |
| | def rvs(self, mu=0, lmbda=1, a=1, b=1, size=None, random_state=None): |
| | """Draw random samples from the distribution. |
| | |
| | Parameters |
| | ---------- |
| | mu, lmbda, a, b : array_like, optional |
| | Shape parameters. `lmbda`, `a`, and `b` must be greater |
| | than zero. |
| | size : int or tuple of ints, optional |
| | Shape of samples to draw. |
| | random_state : {None, int, np.random.RandomState, np.random.Generator}, optional |
| | Used for drawing random variates. |
| | If `random_state` is `None`, the `~np.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 ``RandomState`` or ``Generator`` instance, |
| | then that object is used. |
| | Default is `None`. |
| | |
| | Returns |
| | ------- |
| | x, s2 : ndarray |
| | Random variates. |
| | |
| | """ |
| | random_state = self._get_random_state(random_state) |
| | s2 = invgamma(a, scale=b).rvs(size=size, random_state=random_state) |
| | scale = (s2 / lmbda)**0.5 |
| | x = norm(loc=mu, scale=scale).rvs(size=size, random_state=random_state) |
| | dtype = np.result_type(1.0, mu, lmbda, a, b) |
| | return x.astype(dtype), s2.astype(dtype) |
| |
|
| | def _logpdf(self, x, s2, mu, lmbda, a, b): |
| | t1 = 0.5 * (np.log(lmbda) - np.log(2 * np.pi * s2)) |
| | t2 = a*np.log(b) - special.gammaln(a).astype(a.dtype) |
| | t3 = -(a + 1) * np.log(s2) |
| | t4 = -(2*b + lmbda*(x - mu)**2) / (2*s2) |
| | return t1 + t2 + t3 + t4 |
| |
|
| | def logpdf(self, x, s2, mu=0, lmbda=1, a=1, b=1): |
| | """Log of the probability density function. |
| | |
| | Parameters |
| | ---------- |
| | x, s2 : array_like |
| | Arguments. `s2` must be greater than zero. |
| | mu, lmbda, a, b : array_like, optional |
| | Shape parameters. `lmbda`, `a`, and `b` must be greater |
| | than zero. |
| | |
| | Returns |
| | ------- |
| | logpdf : ndarray or scalar |
| | Log of the probability density function. |
| | |
| | """ |
| | invalid, args = self._process_parameters_pdf(x, s2, mu, lmbda, a, b) |
| | s2 = args[1] |
| | |
| | with np.errstate(all='ignore'): |
| | logpdf = np.asarray(self._logpdf(*args)) |
| | logpdf[s2 <= 0] = -np.inf |
| | logpdf[invalid] = np.nan |
| | return logpdf[()] |
| |
|
| | def _pdf(self, x, s2, mu, lmbda, a, b): |
| | t1 = np.sqrt(lmbda / (2 * np.pi * s2)) |
| | t2 = b**a / special.gamma(a).astype(a.dtype) |
| | t3 = (1 / s2)**(a + 1) |
| | t4 = np.exp(-(2*b + lmbda*(x - mu)**2) / (2*s2)) |
| | return t1 * t2 * t3 * t4 |
| |
|
| | def pdf(self, x, s2, mu=0, lmbda=1, a=1, b=1): |
| | """The probability density function. |
| | |
| | Parameters |
| | ---------- |
| | x, s2 : array_like |
| | Arguments. `s2` must be greater than zero. |
| | mu, lmbda, a, b : array_like, optional |
| | Shape parameters. `lmbda`, `a`, and `b` must be greater |
| | than zero. |
| | |
| | Returns |
| | ------- |
| | logpdf : ndarray or scalar |
| | The probability density function. |
| | |
| | """ |
| | invalid, args = self._process_parameters_pdf(x, s2, mu, lmbda, a, b) |
| | s2 = args[1] |
| | |
| | with np.errstate(all='ignore'): |
| | pdf = np.asarray(self._pdf(*args)) |
| | pdf[s2 <= 0] = 0 |
| | pdf[invalid] = np.nan |
| | return pdf[()] |
| |
|
| | def mean(self, mu=0, lmbda=1, a=1, b=1): |
| | """The mean of the distribution. |
| | |
| | Parameters |
| | ---------- |
| | mu, lmbda, a, b : array_like, optional |
| | Shape parameters. `lmbda` and `b` must be greater |
| | than zero, and `a` must be greater than one. |
| | |
| | Returns |
| | ------- |
| | x, s2 : ndarray |
| | The mean of the distribution. |
| | |
| | """ |
| | invalid, args = self._process_shapes(mu, lmbda, a, b) |
| | mu, lmbda, a, b = args |
| | invalid |= ~(a > 1) |
| | mean_x = np.asarray(mu).copy() |
| | mean_s2 = np.asarray(b / (a - 1)) |
| | mean_x[invalid] = np.nan |
| | mean_s2[invalid] = np.nan |
| | return mean_x[()], mean_s2[()] |
| |
|
| | def var(self, mu=0, lmbda=1, a=1, b=1): |
| | """The variance of the distribution. |
| | |
| | Parameters |
| | ---------- |
| | mu, lmbda, a, b : array_like, optional |
| | Shape parameters. `lmbda` and `b` must be greater |
| | than zero, and `a` must be greater than two. |
| | |
| | Returns |
| | ------- |
| | x, s2 : ndarray |
| | The variance of the distribution. |
| | |
| | """ |
| | invalid, args = self._process_shapes(mu, lmbda, a, b) |
| | mu, lmbda, a, b = args |
| | invalid_x = invalid | ~(a > 1) |
| | invalid_s2 = invalid | ~(a > 2) |
| | var_x = b / ((a - 1) * lmbda) |
| | var_s2 = b**2 / ((a - 1)**2 * (a - 2)) |
| | var_x, var_s2 = np.asarray(var_x), np.asarray(var_s2) |
| | var_x[invalid_x] = np.nan |
| | var_s2[invalid_s2] = np.nan |
| | return var_x[()], var_s2[()] |
| |
|
| | def _process_parameters_pdf(self, x, s2, mu, lmbda, a, b): |
| | args = np.broadcast_arrays(x, s2, mu, lmbda, a, b) |
| | dtype = np.result_type(1.0, *(arg.dtype for arg in args)) |
| | args = [arg.astype(dtype, copy=False) for arg in args] |
| | x, s2, mu, lmbda, a, b = args |
| | invalid = ~((lmbda > 0) & (a > 0) & (b > 0)) |
| | return invalid, args |
| |
|
| | def _process_shapes(self, mu, lmbda, a, b): |
| | args = np.broadcast_arrays(mu, lmbda, a, b) |
| | dtype = np.result_type(1.0, *(arg.dtype for arg in args)) |
| | args = [arg.astype(dtype, copy=False) for arg in args] |
| | mu, lmbda, a, b = args |
| | invalid = ~((lmbda > 0) & (a > 0) & (b > 0)) |
| | return invalid, args |
| |
|
| | def __call__(self, mu=0, lmbda=1, a=1, b=1, seed=None): |
| | return normal_inverse_gamma_frozen(mu, lmbda, a, b, seed=seed) |
| |
|
| |
|
| | normal_inverse_gamma = normal_inverse_gamma_gen() |
| |
|
| |
|
| | class normal_inverse_gamma_frozen(multi_rv_frozen): |
| |
|
| | def __init__(self, mu=0, lmbda=1, a=1, b=1, seed=None): |
| | self._dist = normal_inverse_gamma_gen(seed) |
| | self._shapes = mu, lmbda, a, b |
| |
|
| | def logpdf(self, x, s2): |
| | return self._dist.logpdf(x, s2, *self._shapes) |
| |
|
| | def pdf(self, x, s2): |
| | return self._dist.pdf(x, s2, *self._shapes) |
| |
|
| | def mean(self): |
| | return self._dist.mean(*self._shapes) |
| |
|
| | def var(self): |
| | return self._dist.var(*self._shapes) |
| |
|
| | def rvs(self, size=None, random_state=None): |
| | return self._dist.rvs(*self._shapes, size=size, random_state=random_state) |
| |
|
| |
|
| | |
| | |
| | for name in ['logpdf', 'pdf', 'mean', 'var', 'rvs']: |
| | method = normal_inverse_gamma_gen.__dict__[name] |
| | method_frozen = normal_inverse_gamma_frozen.__dict__[name] |
| | method_frozen.__doc__ = doccer.docformat(method.__doc__, |
| | mvn_docdict_noparams) |
| | method.__doc__ = doccer.docformat(method.__doc__, mvn_docdict_params) |
| |
|