# # Author: Travis Oliphant 2002-2011 with contributions from # SciPy Developers 2004-2011 # from functools import partial from scipy import special from scipy.special import entr, logsumexp, betaln, gammaln as gamln, zeta from scipy._lib._util import _lazywhere, rng_integers from scipy.interpolate import interp1d from numpy import floor, ceil, log, exp, sqrt, log1p, expm1, tanh, cosh, sinh import numpy as np from ._distn_infrastructure import (rv_discrete, get_distribution_names, _check_shape, _ShapeInfo) import scipy.stats._boost as _boost from ._biasedurn import (_PyFishersNCHypergeometric, _PyWalleniusNCHypergeometric, _PyStochasticLib3) def _isintegral(x): return x == np.round(x) class binom_gen(rv_discrete): r"""A binomial discrete random variable. %(before_notes)s Notes ----- The probability mass function for `binom` is: .. math:: f(k) = \binom{n}{k} p^k (1-p)^{n-k} for :math:`k \in \{0, 1, \dots, n\}`, :math:`0 \leq p \leq 1` `binom` takes :math:`n` and :math:`p` as shape parameters, where :math:`p` is the probability of a single success and :math:`1-p` is the probability of a single failure. %(after_notes)s %(example)s See Also -------- hypergeom, nbinom, nhypergeom """ def _shape_info(self): return [_ShapeInfo("n", True, (0, np.inf), (True, False)), _ShapeInfo("p", False, (0, 1), (True, True))] def _rvs(self, n, p, size=None, random_state=None): return random_state.binomial(n, p, size) def _argcheck(self, n, p): return (n >= 0) & _isintegral(n) & (p >= 0) & (p <= 1) def _get_support(self, n, p): return self.a, n def _logpmf(self, x, n, p): k = floor(x) combiln = (gamln(n+1) - (gamln(k+1) + gamln(n-k+1))) return combiln + special.xlogy(k, p) + special.xlog1py(n-k, -p) def _pmf(self, x, n, p): # binom.pmf(k) = choose(n, k) * p**k * (1-p)**(n-k) return _boost._binom_pdf(x, n, p) def _cdf(self, x, n, p): k = floor(x) return _boost._binom_cdf(k, n, p) def _sf(self, x, n, p): k = floor(x) return _boost._binom_sf(k, n, p) def _isf(self, x, n, p): return _boost._binom_isf(x, n, p) def _ppf(self, q, n, p): return _boost._binom_ppf(q, n, p) def _stats(self, n, p, moments='mv'): mu = _boost._binom_mean(n, p) var = _boost._binom_variance(n, p) g1, g2 = None, None if 's' in moments: g1 = _boost._binom_skewness(n, p) if 'k' in moments: g2 = _boost._binom_kurtosis_excess(n, p) return mu, var, g1, g2 def _entropy(self, n, p): k = np.r_[0:n + 1] vals = self._pmf(k, n, p) return np.sum(entr(vals), axis=0) binom = binom_gen(name='binom') class bernoulli_gen(binom_gen): r"""A Bernoulli discrete random variable. %(before_notes)s Notes ----- The probability mass function for `bernoulli` is: .. math:: f(k) = \begin{cases}1-p &\text{if } k = 0\\ p &\text{if } k = 1\end{cases} for :math:`k` in :math:`\{0, 1\}`, :math:`0 \leq p \leq 1` `bernoulli` takes :math:`p` as shape parameter, where :math:`p` is the probability of a single success and :math:`1-p` is the probability of a single failure. %(after_notes)s %(example)s """ def _shape_info(self): return [_ShapeInfo("p", False, (0, 1), (True, True))] def _rvs(self, p, size=None, random_state=None): return binom_gen._rvs(self, 1, p, size=size, random_state=random_state) def _argcheck(self, p): return (p >= 0) & (p <= 1) def _get_support(self, p): # Overrides binom_gen._get_support!x return self.a, self.b def _logpmf(self, x, p): return binom._logpmf(x, 1, p) def _pmf(self, x, p): # bernoulli.pmf(k) = 1-p if k = 0 # = p if k = 1 return binom._pmf(x, 1, p) def _cdf(self, x, p): return binom._cdf(x, 1, p) def _sf(self, x, p): return binom._sf(x, 1, p) def _isf(self, x, p): return binom._isf(x, 1, p) def _ppf(self, q, p): return binom._ppf(q, 1, p) def _stats(self, p): return binom._stats(1, p) def _entropy(self, p): return entr(p) + entr(1-p) bernoulli = bernoulli_gen(b=1, name='bernoulli') class betabinom_gen(rv_discrete): r"""A beta-binomial discrete random variable. %(before_notes)s Notes ----- The beta-binomial distribution is a binomial distribution with a probability of success `p` that follows a beta distribution. The probability mass function for `betabinom` is: .. math:: f(k) = \binom{n}{k} \frac{B(k + a, n - k + b)}{B(a, b)} for :math:`k \in \{0, 1, \dots, n\}`, :math:`n \geq 0`, :math:`a > 0`, :math:`b > 0`, where :math:`B(a, b)` is the beta function. `betabinom` takes :math:`n`, :math:`a`, and :math:`b` as shape parameters. References ---------- .. [1] https://en.wikipedia.org/wiki/Beta-binomial_distribution %(after_notes)s .. versionadded:: 1.4.0 See Also -------- beta, binom %(example)s """ def _shape_info(self): return [_ShapeInfo("n", True, (0, np.inf), (True, False)), _ShapeInfo("a", False, (0, np.inf), (False, False)), _ShapeInfo("b", False, (0, np.inf), (False, False))] def _rvs(self, n, a, b, size=None, random_state=None): p = random_state.beta(a, b, size) return random_state.binomial(n, p, size) def _get_support(self, n, a, b): return 0, n def _argcheck(self, n, a, b): return (n >= 0) & _isintegral(n) & (a > 0) & (b > 0) def _logpmf(self, x, n, a, b): k = floor(x) combiln = -log(n + 1) - betaln(n - k + 1, k + 1) return combiln + betaln(k + a, n - k + b) - betaln(a, b) def _pmf(self, x, n, a, b): return exp(self._logpmf(x, n, a, b)) def _stats(self, n, a, b, moments='mv'): e_p = a / (a + b) e_q = 1 - e_p mu = n * e_p var = n * (a + b + n) * e_p * e_q / (a + b + 1) g1, g2 = None, None if 's' in moments: g1 = 1.0 / sqrt(var) g1 *= (a + b + 2 * n) * (b - a) g1 /= (a + b + 2) * (a + b) if 'k' in moments: g2 = (a + b).astype(e_p.dtype) g2 *= (a + b - 1 + 6 * n) g2 += 3 * a * b * (n - 2) g2 += 6 * n ** 2 g2 -= 3 * e_p * b * n * (6 - n) g2 -= 18 * e_p * e_q * n ** 2 g2 *= (a + b) ** 2 * (1 + a + b) g2 /= (n * a * b * (a + b + 2) * (a + b + 3) * (a + b + n)) g2 -= 3 return mu, var, g1, g2 betabinom = betabinom_gen(name='betabinom') class nbinom_gen(rv_discrete): r"""A negative binomial discrete random variable. %(before_notes)s Notes ----- Negative binomial distribution describes a sequence of i.i.d. Bernoulli trials, repeated until a predefined, non-random number of successes occurs. The probability mass function of the number of failures for `nbinom` is: .. math:: f(k) = \binom{k+n-1}{n-1} p^n (1-p)^k for :math:`k \ge 0`, :math:`0 < p \leq 1` `nbinom` takes :math:`n` and :math:`p` as shape parameters where :math:`n` is the number of successes, :math:`p` is the probability of a single success, and :math:`1-p` is the probability of a single failure. Another common parameterization of the negative binomial distribution is in terms of the mean number of failures :math:`\mu` to achieve :math:`n` successes. The mean :math:`\mu` is related to the probability of success as .. math:: p = \frac{n}{n + \mu} The number of successes :math:`n` may also be specified in terms of a "dispersion", "heterogeneity", or "aggregation" parameter :math:`\alpha`, which relates the mean :math:`\mu` to the variance :math:`\sigma^2`, e.g. :math:`\sigma^2 = \mu + \alpha \mu^2`. Regardless of the convention used for :math:`\alpha`, .. math:: p &= \frac{\mu}{\sigma^2} \\ n &= \frac{\mu^2}{\sigma^2 - \mu} %(after_notes)s %(example)s See Also -------- hypergeom, binom, nhypergeom """ def _shape_info(self): return [_ShapeInfo("n", True, (0, np.inf), (True, False)), _ShapeInfo("p", False, (0, 1), (True, True))] def _rvs(self, n, p, size=None, random_state=None): return random_state.negative_binomial(n, p, size) def _argcheck(self, n, p): return (n > 0) & (p > 0) & (p <= 1) def _pmf(self, x, n, p): # nbinom.pmf(k) = choose(k+n-1, n-1) * p**n * (1-p)**k return _boost._nbinom_pdf(x, n, p) def _logpmf(self, x, n, p): coeff = gamln(n+x) - gamln(x+1) - gamln(n) return coeff + n*log(p) + special.xlog1py(x, -p) def _cdf(self, x, n, p): k = floor(x) return _boost._nbinom_cdf(k, n, p) def _logcdf(self, x, n, p): k = floor(x) k, n, p = np.broadcast_arrays(k, n, p) cdf = self._cdf(k, n, p) cond = cdf > 0.5 def f1(k, n, p): return np.log1p(-special.betainc(k + 1, n, 1 - p)) # do calc in place logcdf = cdf with np.errstate(divide='ignore'): logcdf[cond] = f1(k[cond], n[cond], p[cond]) logcdf[~cond] = np.log(cdf[~cond]) return logcdf def _sf(self, x, n, p): k = floor(x) return _boost._nbinom_sf(k, n, p) def _isf(self, x, n, p): with np.errstate(over='ignore'): # see gh-17432 return _boost._nbinom_isf(x, n, p) def _ppf(self, q, n, p): with np.errstate(over='ignore'): # see gh-17432 return _boost._nbinom_ppf(q, n, p) def _stats(self, n, p): return ( _boost._nbinom_mean(n, p), _boost._nbinom_variance(n, p), _boost._nbinom_skewness(n, p), _boost._nbinom_kurtosis_excess(n, p), ) nbinom = nbinom_gen(name='nbinom') class betanbinom_gen(rv_discrete): r"""A beta-negative-binomial discrete random variable. %(before_notes)s Notes ----- The beta-negative-binomial distribution is a negative binomial distribution with a probability of success `p` that follows a beta distribution. The probability mass function for `betanbinom` is: .. math:: f(k) = \binom{n + k - 1}{k} \frac{B(a + n, b + k)}{B(a, b)} for :math:`k \ge 0`, :math:`n \geq 0`, :math:`a > 0`, :math:`b > 0`, where :math:`B(a, b)` is the beta function. `betanbinom` takes :math:`n`, :math:`a`, and :math:`b` as shape parameters. References ---------- .. [1] https://en.wikipedia.org/wiki/Beta_negative_binomial_distribution %(after_notes)s .. versionadded:: 1.12.0 See Also -------- betabinom : Beta binomial distribution %(example)s """ def _shape_info(self): return [_ShapeInfo("n", True, (0, np.inf), (True, False)), _ShapeInfo("a", False, (0, np.inf), (False, False)), _ShapeInfo("b", False, (0, np.inf), (False, False))] def _rvs(self, n, a, b, size=None, random_state=None): p = random_state.beta(a, b, size) return random_state.negative_binomial(n, p, size) def _argcheck(self, n, a, b): return (n >= 0) & _isintegral(n) & (a > 0) & (b > 0) def _logpmf(self, x, n, a, b): k = floor(x) combiln = -np.log(n + k) - betaln(n, k + 1) return combiln + betaln(a + n, b + k) - betaln(a, b) def _pmf(self, x, n, a, b): return exp(self._logpmf(x, n, a, b)) def _stats(self, n, a, b, moments='mv'): # reference: Wolfram Alpha input # BetaNegativeBinomialDistribution[a, b, n] def mean(n, a, b): return n * b / (a - 1.) mu = _lazywhere(a > 1, (n, a, b), f=mean, fillvalue=np.inf) def var(n, a, b): return (n * b * (n + a - 1.) * (a + b - 1.) / ((a - 2.) * (a - 1.)**2.)) var = _lazywhere(a > 2, (n, a, b), f=var, fillvalue=np.inf) g1, g2 = None, None def skew(n, a, b): return ((2 * n + a - 1.) * (2 * b + a - 1.) / (a - 3.) / sqrt(n * b * (n + a - 1.) * (b + a - 1.) / (a - 2.))) if 's' in moments: g1 = _lazywhere(a > 3, (n, a, b), f=skew, fillvalue=np.inf) def kurtosis(n, a, b): term = (a - 2.) term_2 = ((a - 1.)**2. * (a**2. + a * (6 * b - 1.) + 6. * (b - 1.) * b) + 3. * n**2. * ((a + 5.) * b**2. + (a + 5.) * (a - 1.) * b + 2. * (a - 1.)**2) + 3 * (a - 1.) * n * ((a + 5.) * b**2. + (a + 5.) * (a - 1.) * b + 2. * (a - 1.)**2.)) denominator = ((a - 4.) * (a - 3.) * b * n * (a + b - 1.) * (a + n - 1.)) # Wolfram Alpha uses Pearson kurtosis, so we substract 3 to get # scipy's Fisher kurtosis return term * term_2 / denominator - 3. if 'k' in moments: g2 = _lazywhere(a > 4, (n, a, b), f=kurtosis, fillvalue=np.inf) return mu, var, g1, g2 betanbinom = betanbinom_gen(name='betanbinom') class geom_gen(rv_discrete): r"""A geometric discrete random variable. %(before_notes)s Notes ----- The probability mass function for `geom` is: .. math:: f(k) = (1-p)^{k-1} p for :math:`k \ge 1`, :math:`0 < p \leq 1` `geom` takes :math:`p` as shape parameter, where :math:`p` is the probability of a single success and :math:`1-p` is the probability of a single failure. %(after_notes)s See Also -------- planck %(example)s """ def _shape_info(self): return [_ShapeInfo("p", False, (0, 1), (True, True))] def _rvs(self, p, size=None, random_state=None): return random_state.geometric(p, size=size) def _argcheck(self, p): return (p <= 1) & (p > 0) def _pmf(self, k, p): return np.power(1-p, k-1) * p def _logpmf(self, k, p): return special.xlog1py(k - 1, -p) + log(p) def _cdf(self, x, p): k = floor(x) return -expm1(log1p(-p)*k) def _sf(self, x, p): return np.exp(self._logsf(x, p)) def _logsf(self, x, p): k = floor(x) return k*log1p(-p) def _ppf(self, q, p): vals = ceil(log1p(-q) / log1p(-p)) temp = self._cdf(vals-1, p) return np.where((temp >= q) & (vals > 0), vals-1, vals) def _stats(self, p): mu = 1.0/p qr = 1.0-p var = qr / p / p g1 = (2.0-p) / sqrt(qr) g2 = np.polyval([1, -6, 6], p)/(1.0-p) return mu, var, g1, g2 def _entropy(self, p): return -np.log(p) - np.log1p(-p) * (1.0-p) / p geom = geom_gen(a=1, name='geom', longname="A geometric") class hypergeom_gen(rv_discrete): r"""A hypergeometric discrete random variable. The hypergeometric distribution models drawing objects from a bin. `M` is the total number of objects, `n` is total number of Type I objects. The random variate represents the number of Type I objects in `N` drawn without replacement from the total population. %(before_notes)s Notes ----- The symbols used to denote the shape parameters (`M`, `n`, and `N`) are not universally accepted. See the Examples for a clarification of the definitions used here. The probability mass function is defined as, .. math:: p(k, M, n, N) = \frac{\binom{n}{k} \binom{M - n}{N - k}} {\binom{M}{N}} for :math:`k \in [\max(0, N - M + n), \min(n, N)]`, where the binomial coefficients are defined as, .. math:: \binom{n}{k} \equiv \frac{n!}{k! (n - k)!}. %(after_notes)s Examples -------- >>> import numpy as np >>> from scipy.stats import hypergeom >>> import matplotlib.pyplot as plt Suppose we have a collection of 20 animals, of which 7 are dogs. Then if we want to know the probability of finding a given number of dogs if we choose at random 12 of the 20 animals, we can initialize a frozen distribution and plot the probability mass function: >>> [M, n, N] = [20, 7, 12] >>> rv = hypergeom(M, n, N) >>> x = np.arange(0, n+1) >>> pmf_dogs = rv.pmf(x) >>> fig = plt.figure() >>> ax = fig.add_subplot(111) >>> ax.plot(x, pmf_dogs, 'bo') >>> ax.vlines(x, 0, pmf_dogs, lw=2) >>> ax.set_xlabel('# of dogs in our group of chosen animals') >>> ax.set_ylabel('hypergeom PMF') >>> plt.show() Instead of using a frozen distribution we can also use `hypergeom` methods directly. To for example obtain the cumulative distribution function, use: >>> prb = hypergeom.cdf(x, M, n, N) And to generate random numbers: >>> R = hypergeom.rvs(M, n, N, size=10) See Also -------- nhypergeom, binom, nbinom """ def _shape_info(self): return [_ShapeInfo("M", True, (0, np.inf), (True, False)), _ShapeInfo("n", True, (0, np.inf), (True, False)), _ShapeInfo("N", True, (0, np.inf), (True, False))] def _rvs(self, M, n, N, size=None, random_state=None): return random_state.hypergeometric(n, M-n, N, size=size) def _get_support(self, M, n, N): return np.maximum(N-(M-n), 0), np.minimum(n, N) def _argcheck(self, M, n, N): cond = (M > 0) & (n >= 0) & (N >= 0) cond &= (n <= M) & (N <= M) cond &= _isintegral(M) & _isintegral(n) & _isintegral(N) return cond def _logpmf(self, k, M, n, N): tot, good = M, n bad = tot - good result = (betaln(good+1, 1) + betaln(bad+1, 1) + betaln(tot-N+1, N+1) - betaln(k+1, good-k+1) - betaln(N-k+1, bad-N+k+1) - betaln(tot+1, 1)) return result def _pmf(self, k, M, n, N): return _boost._hypergeom_pdf(k, n, N, M) def _cdf(self, k, M, n, N): return _boost._hypergeom_cdf(k, n, N, M) def _stats(self, M, n, N): M, n, N = 1. * M, 1. * n, 1. * N m = M - n # Boost kurtosis_excess doesn't return the same as the value # computed here. g2 = M * (M + 1) - 6. * N * (M - N) - 6. * n * m g2 *= (M - 1) * M * M g2 += 6. * n * N * (M - N) * m * (5. * M - 6) g2 /= n * N * (M - N) * m * (M - 2.) * (M - 3.) return ( _boost._hypergeom_mean(n, N, M), _boost._hypergeom_variance(n, N, M), _boost._hypergeom_skewness(n, N, M), g2, ) def _entropy(self, M, n, N): k = np.r_[N - (M - n):min(n, N) + 1] vals = self.pmf(k, M, n, N) return np.sum(entr(vals), axis=0) def _sf(self, k, M, n, N): return _boost._hypergeom_sf(k, n, N, M) def _logsf(self, k, M, n, N): res = [] for quant, tot, good, draw in zip(*np.broadcast_arrays(k, M, n, N)): if (quant + 0.5) * (tot + 0.5) < (good - 0.5) * (draw - 0.5): # Less terms to sum if we calculate log(1-cdf) res.append(log1p(-exp(self.logcdf(quant, tot, good, draw)))) else: # Integration over probability mass function using logsumexp k2 = np.arange(quant + 1, draw + 1) res.append(logsumexp(self._logpmf(k2, tot, good, draw))) return np.asarray(res) def _logcdf(self, k, M, n, N): res = [] for quant, tot, good, draw in zip(*np.broadcast_arrays(k, M, n, N)): if (quant + 0.5) * (tot + 0.5) > (good - 0.5) * (draw - 0.5): # Less terms to sum if we calculate log(1-sf) res.append(log1p(-exp(self.logsf(quant, tot, good, draw)))) else: # Integration over probability mass function using logsumexp k2 = np.arange(0, quant + 1) res.append(logsumexp(self._logpmf(k2, tot, good, draw))) return np.asarray(res) hypergeom = hypergeom_gen(name='hypergeom') class nhypergeom_gen(rv_discrete): r"""A negative hypergeometric discrete random variable. Consider a box containing :math:`M` balls:, :math:`n` red and :math:`M-n` blue. We randomly sample balls from the box, one at a time and *without* replacement, until we have picked :math:`r` blue balls. `nhypergeom` is the distribution of the number of red balls :math:`k` we have picked. %(before_notes)s Notes ----- The symbols used to denote the shape parameters (`M`, `n`, and `r`) are not universally accepted. See the Examples for a clarification of the definitions used here. The probability mass function is defined as, .. math:: f(k; M, n, r) = \frac{{{k+r-1}\choose{k}}{{M-r-k}\choose{n-k}}} {{M \choose n}} for :math:`k \in [0, n]`, :math:`n \in [0, M]`, :math:`r \in [0, M-n]`, and the binomial coefficient is: .. math:: \binom{n}{k} \equiv \frac{n!}{k! (n - k)!}. It is equivalent to observing :math:`k` successes in :math:`k+r-1` samples with :math:`k+r`'th sample being a failure. The former can be modelled as a hypergeometric distribution. The probability of the latter is simply the number of failures remaining :math:`M-n-(r-1)` divided by the size of the remaining population :math:`M-(k+r-1)`. This relationship can be shown as: .. math:: NHG(k;M,n,r) = HG(k;M,n,k+r-1)\frac{(M-n-(r-1))}{(M-(k+r-1))} where :math:`NHG` is probability mass function (PMF) of the negative hypergeometric distribution and :math:`HG` is the PMF of the hypergeometric distribution. %(after_notes)s Examples -------- >>> import numpy as np >>> from scipy.stats import nhypergeom >>> import matplotlib.pyplot as plt Suppose we have a collection of 20 animals, of which 7 are dogs. Then if we want to know the probability of finding a given number of dogs (successes) in a sample with exactly 12 animals that aren't dogs (failures), we can initialize a frozen distribution and plot the probability mass function: >>> M, n, r = [20, 7, 12] >>> rv = nhypergeom(M, n, r) >>> x = np.arange(0, n+2) >>> pmf_dogs = rv.pmf(x) >>> fig = plt.figure() >>> ax = fig.add_subplot(111) >>> ax.plot(x, pmf_dogs, 'bo') >>> ax.vlines(x, 0, pmf_dogs, lw=2) >>> ax.set_xlabel('# of dogs in our group with given 12 failures') >>> ax.set_ylabel('nhypergeom PMF') >>> plt.show() Instead of using a frozen distribution we can also use `nhypergeom` methods directly. To for example obtain the probability mass function, use: >>> prb = nhypergeom.pmf(x, M, n, r) And to generate random numbers: >>> R = nhypergeom.rvs(M, n, r, size=10) To verify the relationship between `hypergeom` and `nhypergeom`, use: >>> from scipy.stats import hypergeom, nhypergeom >>> M, n, r = 45, 13, 8 >>> k = 6 >>> nhypergeom.pmf(k, M, n, r) 0.06180776620271643 >>> hypergeom.pmf(k, M, n, k+r-1) * (M - n - (r-1)) / (M - (k+r-1)) 0.06180776620271644 See Also -------- hypergeom, binom, nbinom References ---------- .. [1] Negative Hypergeometric Distribution on Wikipedia https://en.wikipedia.org/wiki/Negative_hypergeometric_distribution .. [2] Negative Hypergeometric Distribution from http://www.math.wm.edu/~leemis/chart/UDR/PDFs/Negativehypergeometric.pdf """ def _shape_info(self): return [_ShapeInfo("M", True, (0, np.inf), (True, False)), _ShapeInfo("n", True, (0, np.inf), (True, False)), _ShapeInfo("r", True, (0, np.inf), (True, False))] def _get_support(self, M, n, r): return 0, n def _argcheck(self, M, n, r): cond = (n >= 0) & (n <= M) & (r >= 0) & (r <= M-n) cond &= _isintegral(M) & _isintegral(n) & _isintegral(r) return cond def _rvs(self, M, n, r, size=None, random_state=None): @_vectorize_rvs_over_shapes def _rvs1(M, n, r, size, random_state): # invert cdf by calculating all values in support, scalar M, n, r a, b = self.support(M, n, r) ks = np.arange(a, b+1) cdf = self.cdf(ks, M, n, r) ppf = interp1d(cdf, ks, kind='next', fill_value='extrapolate') rvs = ppf(random_state.uniform(size=size)).astype(int) if size is None: return rvs.item() return rvs return _rvs1(M, n, r, size=size, random_state=random_state) def _logpmf(self, k, M, n, r): cond = ((r == 0) & (k == 0)) result = _lazywhere(~cond, (k, M, n, r), lambda k, M, n, r: (-betaln(k+1, r) + betaln(k+r, 1) - betaln(n-k+1, M-r-n+1) + betaln(M-r-k+1, 1) + betaln(n+1, M-n+1) - betaln(M+1, 1)), fillvalue=0.0) return result def _pmf(self, k, M, n, r): # same as the following but numerically more precise # return comb(k+r-1, k) * comb(M-r-k, n-k) / comb(M, n) return exp(self._logpmf(k, M, n, r)) def _stats(self, M, n, r): # Promote the datatype to at least float # mu = rn / (M-n+1) M, n, r = 1.*M, 1.*n, 1.*r mu = r*n / (M-n+1) var = r*(M+1)*n / ((M-n+1)*(M-n+2)) * (1 - r / (M-n+1)) # The skew and kurtosis are mathematically # intractable so return `None`. See [2]_. g1, g2 = None, None return mu, var, g1, g2 nhypergeom = nhypergeom_gen(name='nhypergeom') # FIXME: Fails _cdfvec class logser_gen(rv_discrete): r"""A Logarithmic (Log-Series, Series) discrete random variable. %(before_notes)s Notes ----- The probability mass function for `logser` is: .. math:: f(k) = - \frac{p^k}{k \log(1-p)} for :math:`k \ge 1`, :math:`0 < p < 1` `logser` takes :math:`p` as shape parameter, where :math:`p` is the probability of a single success and :math:`1-p` is the probability of a single failure. %(after_notes)s %(example)s """ def _shape_info(self): return [_ShapeInfo("p", False, (0, 1), (True, True))] def _rvs(self, p, size=None, random_state=None): # looks wrong for p>0.5, too few k=1 # trying to use generic is worse, no k=1 at all return random_state.logseries(p, size=size) def _argcheck(self, p): return (p > 0) & (p < 1) def _pmf(self, k, p): # logser.pmf(k) = - p**k / (k*log(1-p)) return -np.power(p, k) * 1.0 / k / special.log1p(-p) def _stats(self, p): r = special.log1p(-p) mu = p / (p - 1.0) / r mu2p = -p / r / (p - 1.0)**2 var = mu2p - mu*mu mu3p = -p / r * (1.0+p) / (1.0 - p)**3 mu3 = mu3p - 3*mu*mu2p + 2*mu**3 g1 = mu3 / np.power(var, 1.5) mu4p = -p / r * ( 1.0 / (p-1)**2 - 6*p / (p - 1)**3 + 6*p*p / (p-1)**4) mu4 = mu4p - 4*mu3p*mu + 6*mu2p*mu*mu - 3*mu**4 g2 = mu4 / var**2 - 3.0 return mu, var, g1, g2 logser = logser_gen(a=1, name='logser', longname='A logarithmic') class poisson_gen(rv_discrete): r"""A Poisson discrete random variable. %(before_notes)s Notes ----- The probability mass function for `poisson` is: .. math:: f(k) = \exp(-\mu) \frac{\mu^k}{k!} for :math:`k \ge 0`. `poisson` takes :math:`\mu \geq 0` as shape parameter. When :math:`\mu = 0`, the ``pmf`` method returns ``1.0`` at quantile :math:`k = 0`. %(after_notes)s %(example)s """ def _shape_info(self): return [_ShapeInfo("mu", False, (0, np.inf), (True, False))] # Override rv_discrete._argcheck to allow mu=0. def _argcheck(self, mu): return mu >= 0 def _rvs(self, mu, size=None, random_state=None): return random_state.poisson(mu, size) def _logpmf(self, k, mu): Pk = special.xlogy(k, mu) - gamln(k + 1) - mu return Pk def _pmf(self, k, mu): # poisson.pmf(k) = exp(-mu) * mu**k / k! return exp(self._logpmf(k, mu)) def _cdf(self, x, mu): k = floor(x) return special.pdtr(k, mu) def _sf(self, x, mu): k = floor(x) return special.pdtrc(k, mu) def _ppf(self, q, mu): vals = ceil(special.pdtrik(q, mu)) vals1 = np.maximum(vals - 1, 0) temp = special.pdtr(vals1, mu) return np.where(temp >= q, vals1, vals) def _stats(self, mu): var = mu tmp = np.asarray(mu) mu_nonzero = tmp > 0 g1 = _lazywhere(mu_nonzero, (tmp,), lambda x: sqrt(1.0/x), np.inf) g2 = _lazywhere(mu_nonzero, (tmp,), lambda x: 1.0/x, np.inf) return mu, var, g1, g2 poisson = poisson_gen(name="poisson", longname='A Poisson') class planck_gen(rv_discrete): r"""A Planck discrete exponential random variable. %(before_notes)s Notes ----- The probability mass function for `planck` is: .. math:: f(k) = (1-\exp(-\lambda)) \exp(-\lambda k) for :math:`k \ge 0` and :math:`\lambda > 0`. `planck` takes :math:`\lambda` as shape parameter. The Planck distribution can be written as a geometric distribution (`geom`) with :math:`p = 1 - \exp(-\lambda)` shifted by ``loc = -1``. %(after_notes)s See Also -------- geom %(example)s """ def _shape_info(self): return [_ShapeInfo("lambda", False, (0, np.inf), (False, False))] def _argcheck(self, lambda_): return lambda_ > 0 def _pmf(self, k, lambda_): return -expm1(-lambda_)*exp(-lambda_*k) def _cdf(self, x, lambda_): k = floor(x) return -expm1(-lambda_*(k+1)) def _sf(self, x, lambda_): return exp(self._logsf(x, lambda_)) def _logsf(self, x, lambda_): k = floor(x) return -lambda_*(k+1) def _ppf(self, q, lambda_): vals = ceil(-1.0/lambda_ * log1p(-q)-1) vals1 = (vals-1).clip(*(self._get_support(lambda_))) temp = self._cdf(vals1, lambda_) return np.where(temp >= q, vals1, vals) def _rvs(self, lambda_, size=None, random_state=None): # use relation to geometric distribution for sampling p = -expm1(-lambda_) return random_state.geometric(p, size=size) - 1.0 def _stats(self, lambda_): mu = 1/expm1(lambda_) var = exp(-lambda_)/(expm1(-lambda_))**2 g1 = 2*cosh(lambda_/2.0) g2 = 4+2*cosh(lambda_) return mu, var, g1, g2 def _entropy(self, lambda_): C = -expm1(-lambda_) return lambda_*exp(-lambda_)/C - log(C) planck = planck_gen(a=0, name='planck', longname='A discrete exponential ') class boltzmann_gen(rv_discrete): r"""A Boltzmann (Truncated Discrete Exponential) random variable. %(before_notes)s Notes ----- The probability mass function for `boltzmann` is: .. math:: f(k) = (1-\exp(-\lambda)) \exp(-\lambda k) / (1-\exp(-\lambda N)) for :math:`k = 0,..., N-1`. `boltzmann` takes :math:`\lambda > 0` and :math:`N > 0` as shape parameters. %(after_notes)s %(example)s """ def _shape_info(self): return [_ShapeInfo("lambda_", False, (0, np.inf), (False, False)), _ShapeInfo("N", True, (0, np.inf), (False, False))] def _argcheck(self, lambda_, N): return (lambda_ > 0) & (N > 0) & _isintegral(N) def _get_support(self, lambda_, N): return self.a, N - 1 def _pmf(self, k, lambda_, N): # boltzmann.pmf(k) = # (1-exp(-lambda_)*exp(-lambda_*k)/(1-exp(-lambda_*N)) fact = (1-exp(-lambda_))/(1-exp(-lambda_*N)) return fact*exp(-lambda_*k) def _cdf(self, x, lambda_, N): k = floor(x) return (1-exp(-lambda_*(k+1)))/(1-exp(-lambda_*N)) def _ppf(self, q, lambda_, N): qnew = q*(1-exp(-lambda_*N)) vals = ceil(-1.0/lambda_ * log(1-qnew)-1) vals1 = (vals-1).clip(0.0, np.inf) temp = self._cdf(vals1, lambda_, N) return np.where(temp >= q, vals1, vals) def _stats(self, lambda_, N): z = exp(-lambda_) zN = exp(-lambda_*N) mu = z/(1.0-z)-N*zN/(1-zN) var = z/(1.0-z)**2 - N*N*zN/(1-zN)**2 trm = (1-zN)/(1-z) trm2 = (z*trm**2 - N*N*zN) g1 = z*(1+z)*trm**3 - N**3*zN*(1+zN) g1 = g1 / trm2**(1.5) g2 = z*(1+4*z+z*z)*trm**4 - N**4 * zN*(1+4*zN+zN*zN) g2 = g2 / trm2 / trm2 return mu, var, g1, g2 boltzmann = boltzmann_gen(name='boltzmann', a=0, longname='A truncated discrete exponential ') class randint_gen(rv_discrete): r"""A uniform discrete random variable. %(before_notes)s Notes ----- The probability mass function for `randint` is: .. math:: f(k) = \frac{1}{\texttt{high} - \texttt{low}} for :math:`k \in \{\texttt{low}, \dots, \texttt{high} - 1\}`. `randint` takes :math:`\texttt{low}` and :math:`\texttt{high}` as shape parameters. %(after_notes)s Examples -------- >>> import numpy as np >>> from scipy.stats import randint >>> import matplotlib.pyplot as plt >>> fig, ax = plt.subplots(1, 1) Calculate the first four moments: >>> low, high = 7, 31 >>> mean, var, skew, kurt = randint.stats(low, high, moments='mvsk') Display the probability mass function (``pmf``): >>> x = np.arange(low - 5, high + 5) >>> ax.plot(x, randint.pmf(x, low, high), 'bo', ms=8, label='randint pmf') >>> ax.vlines(x, 0, randint.pmf(x, low, high), colors='b', lw=5, alpha=0.5) Alternatively, the distribution object can be called (as a function) to fix the shape and location. This returns a "frozen" RV object holding the given parameters fixed. Freeze the distribution and display the frozen ``pmf``: >>> rv = randint(low, high) >>> ax.vlines(x, 0, rv.pmf(x), colors='k', linestyles='-', ... lw=1, label='frozen pmf') >>> ax.legend(loc='lower center') >>> plt.show() Check the relationship between the cumulative distribution function (``cdf``) and its inverse, the percent point function (``ppf``): >>> q = np.arange(low, high) >>> p = randint.cdf(q, low, high) >>> np.allclose(q, randint.ppf(p, low, high)) True Generate random numbers: >>> r = randint.rvs(low, high, size=1000) """ def _shape_info(self): return [_ShapeInfo("low", True, (-np.inf, np.inf), (False, False)), _ShapeInfo("high", True, (-np.inf, np.inf), (False, False))] def _argcheck(self, low, high): return (high > low) & _isintegral(low) & _isintegral(high) def _get_support(self, low, high): return low, high-1 def _pmf(self, k, low, high): # randint.pmf(k) = 1./(high - low) p = np.ones_like(k) / (high - low) return np.where((k >= low) & (k < high), p, 0.) def _cdf(self, x, low, high): k = floor(x) return (k - low + 1.) / (high - low) def _ppf(self, q, low, high): vals = ceil(q * (high - low) + low) - 1 vals1 = (vals - 1).clip(low, high) temp = self._cdf(vals1, low, high) return np.where(temp >= q, vals1, vals) def _stats(self, low, high): m2, m1 = np.asarray(high), np.asarray(low) mu = (m2 + m1 - 1.0) / 2 d = m2 - m1 var = (d*d - 1) / 12.0 g1 = 0.0 g2 = -6.0/5.0 * (d*d + 1.0) / (d*d - 1.0) return mu, var, g1, g2 def _rvs(self, low, high, size=None, random_state=None): """An array of *size* random integers >= ``low`` and < ``high``.""" if np.asarray(low).size == 1 and np.asarray(high).size == 1: # no need to vectorize in that case return rng_integers(random_state, low, high, size=size) if size is not None: # NumPy's RandomState.randint() doesn't broadcast its arguments. # Use `broadcast_to()` to extend the shapes of low and high # up to size. Then we can use the numpy.vectorize'd # randint without needing to pass it a `size` argument. low = np.broadcast_to(low, size) high = np.broadcast_to(high, size) randint = np.vectorize(partial(rng_integers, random_state), otypes=[np.dtype(int)]) return randint(low, high) def _entropy(self, low, high): return log(high - low) randint = randint_gen(name='randint', longname='A discrete uniform ' '(random integer)') # FIXME: problems sampling. class zipf_gen(rv_discrete): r"""A Zipf (Zeta) discrete random variable. %(before_notes)s See Also -------- zipfian Notes ----- The probability mass function for `zipf` is: .. math:: f(k, a) = \frac{1}{\zeta(a) k^a} for :math:`k \ge 1`, :math:`a > 1`. `zipf` takes :math:`a > 1` as shape parameter. :math:`\zeta` is the Riemann zeta function (`scipy.special.zeta`) The Zipf distribution is also known as the zeta distribution, which is a special case of the Zipfian distribution (`zipfian`). %(after_notes)s References ---------- .. [1] "Zeta Distribution", Wikipedia, https://en.wikipedia.org/wiki/Zeta_distribution %(example)s Confirm that `zipf` is the large `n` limit of `zipfian`. >>> import numpy as np >>> from scipy.stats import zipf, zipfian >>> k = np.arange(11) >>> np.allclose(zipf.pmf(k, a), zipfian.pmf(k, a, n=10000000)) True """ def _shape_info(self): return [_ShapeInfo("a", False, (1, np.inf), (False, False))] def _rvs(self, a, size=None, random_state=None): return random_state.zipf(a, size=size) def _argcheck(self, a): return a > 1 def _pmf(self, k, a): k = k.astype(np.float64) # zipf.pmf(k, a) = 1/(zeta(a) * k**a) Pk = 1.0 / special.zeta(a, 1) * k**-a return Pk def _munp(self, n, a): return _lazywhere( a > n + 1, (a, n), lambda a, n: special.zeta(a - n, 1) / special.zeta(a, 1), np.inf) zipf = zipf_gen(a=1, name='zipf', longname='A Zipf') def _gen_harmonic_gt1(n, a): """Generalized harmonic number, a > 1""" # See https://en.wikipedia.org/wiki/Harmonic_number; search for "hurwitz" return zeta(a, 1) - zeta(a, n+1) def _gen_harmonic_leq1(n, a): """Generalized harmonic number, a <= 1""" if not np.size(n): return n n_max = np.max(n) # loop starts at maximum of all n out = np.zeros_like(a, dtype=float) # add terms of harmonic series; starting from smallest to avoid roundoff for i in np.arange(n_max, 0, -1, dtype=float): mask = i <= n # don't add terms after nth out[mask] += 1/i**a[mask] return out def _gen_harmonic(n, a): """Generalized harmonic number""" n, a = np.broadcast_arrays(n, a) return _lazywhere(a > 1, (n, a), f=_gen_harmonic_gt1, f2=_gen_harmonic_leq1) class zipfian_gen(rv_discrete): r"""A Zipfian discrete random variable. %(before_notes)s See Also -------- zipf Notes ----- The probability mass function for `zipfian` is: .. math:: f(k, a, n) = \frac{1}{H_{n,a} k^a} for :math:`k \in \{1, 2, \dots, n-1, n\}`, :math:`a \ge 0`, :math:`n \in \{1, 2, 3, \dots\}`. `zipfian` takes :math:`a` and :math:`n` as shape parameters. :math:`H_{n,a}` is the :math:`n`:sup:`th` generalized harmonic number of order :math:`a`. The Zipfian distribution reduces to the Zipf (zeta) distribution as :math:`n \rightarrow \infty`. %(after_notes)s References ---------- .. [1] "Zipf's Law", Wikipedia, https://en.wikipedia.org/wiki/Zipf's_law .. [2] Larry Leemis, "Zipf Distribution", Univariate Distribution Relationships. http://www.math.wm.edu/~leemis/chart/UDR/PDFs/Zipf.pdf %(example)s Confirm that `zipfian` reduces to `zipf` for large `n`, `a > 1`. >>> import numpy as np >>> from scipy.stats import zipf, zipfian >>> k = np.arange(11) >>> np.allclose(zipfian.pmf(k, a=3.5, n=10000000), zipf.pmf(k, a=3.5)) True """ def _shape_info(self): return [_ShapeInfo("a", False, (0, np.inf), (True, False)), _ShapeInfo("n", True, (0, np.inf), (False, False))] def _argcheck(self, a, n): # we need np.asarray here because moment (maybe others) don't convert return (a >= 0) & (n > 0) & (n == np.asarray(n, dtype=int)) def _get_support(self, a, n): return 1, n def _pmf(self, k, a, n): k = k.astype(np.float64) return 1.0 / _gen_harmonic(n, a) * k**-a def _cdf(self, k, a, n): return _gen_harmonic(k, a) / _gen_harmonic(n, a) def _sf(self, k, a, n): k = k + 1 # # to match SciPy convention # see http://www.math.wm.edu/~leemis/chart/UDR/PDFs/Zipf.pdf return ((k**a*(_gen_harmonic(n, a) - _gen_harmonic(k, a)) + 1) / (k**a*_gen_harmonic(n, a))) def _stats(self, a, n): # see # see http://www.math.wm.edu/~leemis/chart/UDR/PDFs/Zipf.pdf Hna = _gen_harmonic(n, a) Hna1 = _gen_harmonic(n, a-1) Hna2 = _gen_harmonic(n, a-2) Hna3 = _gen_harmonic(n, a-3) Hna4 = _gen_harmonic(n, a-4) mu1 = Hna1/Hna mu2n = (Hna2*Hna - Hna1**2) mu2d = Hna**2 mu2 = mu2n / mu2d g1 = (Hna3/Hna - 3*Hna1*Hna2/Hna**2 + 2*Hna1**3/Hna**3)/mu2**(3/2) g2 = (Hna**3*Hna4 - 4*Hna**2*Hna1*Hna3 + 6*Hna*Hna1**2*Hna2 - 3*Hna1**4) / mu2n**2 g2 -= 3 return mu1, mu2, g1, g2 zipfian = zipfian_gen(a=1, name='zipfian', longname='A Zipfian') class dlaplace_gen(rv_discrete): r"""A Laplacian discrete random variable. %(before_notes)s Notes ----- The probability mass function for `dlaplace` is: .. math:: f(k) = \tanh(a/2) \exp(-a |k|) for integers :math:`k` and :math:`a > 0`. `dlaplace` takes :math:`a` as shape parameter. %(after_notes)s %(example)s """ def _shape_info(self): return [_ShapeInfo("a", False, (0, np.inf), (False, False))] def _pmf(self, k, a): # dlaplace.pmf(k) = tanh(a/2) * exp(-a*abs(k)) return tanh(a/2.0) * exp(-a * abs(k)) def _cdf(self, x, a): k = floor(x) def f(k, a): return 1.0 - exp(-a * k) / (exp(a) + 1) def f2(k, a): return exp(a * (k + 1)) / (exp(a) + 1) return _lazywhere(k >= 0, (k, a), f=f, f2=f2) def _ppf(self, q, a): const = 1 + exp(a) vals = ceil(np.where(q < 1.0 / (1 + exp(-a)), log(q*const) / a - 1, -log((1-q) * const) / a)) vals1 = vals - 1 return np.where(self._cdf(vals1, a) >= q, vals1, vals) def _stats(self, a): ea = exp(a) mu2 = 2.*ea/(ea-1.)**2 mu4 = 2.*ea*(ea**2+10.*ea+1.) / (ea-1.)**4 return 0., mu2, 0., mu4/mu2**2 - 3. def _entropy(self, a): return a / sinh(a) - log(tanh(a/2.0)) def _rvs(self, a, size=None, random_state=None): # The discrete Laplace is equivalent to the two-sided geometric # distribution with PMF: # f(k) = (1 - alpha)/(1 + alpha) * alpha^abs(k) # Reference: # https://www.sciencedirect.com/science/ # article/abs/pii/S0378375804003519 # Furthermore, the two-sided geometric distribution is # equivalent to the difference between two iid geometric # distributions. # Reference (page 179): # https://pdfs.semanticscholar.org/61b3/ # b99f466815808fd0d03f5d2791eea8b541a1.pdf # Thus, we can leverage the following: # 1) alpha = e^-a # 2) probability_of_success = 1 - alpha (Bernoulli trial) probOfSuccess = -np.expm1(-np.asarray(a)) x = random_state.geometric(probOfSuccess, size=size) y = random_state.geometric(probOfSuccess, size=size) return x - y dlaplace = dlaplace_gen(a=-np.inf, name='dlaplace', longname='A discrete Laplacian') class skellam_gen(rv_discrete): r"""A Skellam discrete random variable. %(before_notes)s Notes ----- Probability distribution of the difference of two correlated or uncorrelated Poisson random variables. Let :math:`k_1` and :math:`k_2` be two Poisson-distributed r.v. with expected values :math:`\lambda_1` and :math:`\lambda_2`. Then, :math:`k_1 - k_2` follows a Skellam distribution with parameters :math:`\mu_1 = \lambda_1 - \rho \sqrt{\lambda_1 \lambda_2}` and :math:`\mu_2 = \lambda_2 - \rho \sqrt{\lambda_1 \lambda_2}`, where :math:`\rho` is the correlation coefficient between :math:`k_1` and :math:`k_2`. If the two Poisson-distributed r.v. are independent then :math:`\rho = 0`. Parameters :math:`\mu_1` and :math:`\mu_2` must be strictly positive. For details see: https://en.wikipedia.org/wiki/Skellam_distribution `skellam` takes :math:`\mu_1` and :math:`\mu_2` as shape parameters. %(after_notes)s %(example)s """ def _shape_info(self): return [_ShapeInfo("mu1", False, (0, np.inf), (False, False)), _ShapeInfo("mu2", False, (0, np.inf), (False, False))] def _rvs(self, mu1, mu2, size=None, random_state=None): n = size return (random_state.poisson(mu1, n) - random_state.poisson(mu2, n)) def _pmf(self, x, mu1, mu2): with np.errstate(over='ignore'): # see gh-17432 px = np.where(x < 0, _boost._ncx2_pdf(2*mu2, 2*(1-x), 2*mu1)*2, _boost._ncx2_pdf(2*mu1, 2*(1+x), 2*mu2)*2) # ncx2.pdf() returns nan's for extremely low probabilities return px def _cdf(self, x, mu1, mu2): x = floor(x) with np.errstate(over='ignore'): # see gh-17432 px = np.where(x < 0, _boost._ncx2_cdf(2*mu2, -2*x, 2*mu1), 1 - _boost._ncx2_cdf(2*mu1, 2*(x+1), 2*mu2)) return px def _stats(self, mu1, mu2): mean = mu1 - mu2 var = mu1 + mu2 g1 = mean / sqrt((var)**3) g2 = 1 / var return mean, var, g1, g2 skellam = skellam_gen(a=-np.inf, name="skellam", longname='A Skellam') class yulesimon_gen(rv_discrete): r"""A Yule-Simon discrete random variable. %(before_notes)s Notes ----- The probability mass function for the `yulesimon` is: .. math:: f(k) = \alpha B(k, \alpha+1) for :math:`k=1,2,3,...`, where :math:`\alpha>0`. Here :math:`B` refers to the `scipy.special.beta` function. The sampling of random variates is based on pg 553, Section 6.3 of [1]_. Our notation maps to the referenced logic via :math:`\alpha=a-1`. For details see the wikipedia entry [2]_. References ---------- .. [1] Devroye, Luc. "Non-uniform Random Variate Generation", (1986) Springer, New York. .. [2] https://en.wikipedia.org/wiki/Yule-Simon_distribution %(after_notes)s %(example)s """ def _shape_info(self): return [_ShapeInfo("alpha", False, (0, np.inf), (False, False))] def _rvs(self, alpha, size=None, random_state=None): E1 = random_state.standard_exponential(size) E2 = random_state.standard_exponential(size) ans = ceil(-E1 / log1p(-exp(-E2 / alpha))) return ans def _pmf(self, x, alpha): return alpha * special.beta(x, alpha + 1) def _argcheck(self, alpha): return (alpha > 0) def _logpmf(self, x, alpha): return log(alpha) + special.betaln(x, alpha + 1) def _cdf(self, x, alpha): return 1 - x * special.beta(x, alpha + 1) def _sf(self, x, alpha): return x * special.beta(x, alpha + 1) def _logsf(self, x, alpha): return log(x) + special.betaln(x, alpha + 1) def _stats(self, alpha): mu = np.where(alpha <= 1, np.inf, alpha / (alpha - 1)) mu2 = np.where(alpha > 2, alpha**2 / ((alpha - 2.0) * (alpha - 1)**2), np.inf) mu2 = np.where(alpha <= 1, np.nan, mu2) g1 = np.where(alpha > 3, sqrt(alpha - 2) * (alpha + 1)**2 / (alpha * (alpha - 3)), np.inf) g1 = np.where(alpha <= 2, np.nan, g1) g2 = np.where(alpha > 4, alpha + 3 + ((11 * alpha**3 - 49 * alpha - 22) / (alpha * (alpha - 4) * (alpha - 3))), np.inf) g2 = np.where(alpha <= 2, np.nan, g2) return mu, mu2, g1, g2 yulesimon = yulesimon_gen(name='yulesimon', a=1) def _vectorize_rvs_over_shapes(_rvs1): """Decorator that vectorizes _rvs method to work on ndarray shapes""" # _rvs1 must be a _function_ that accepts _scalar_ args as positional # arguments, `size` and `random_state` as keyword arguments. # _rvs1 must return a random variate array with shape `size`. If `size` is # None, _rvs1 must return a scalar. # When applied to _rvs1, this decorator broadcasts ndarray args # and loops over them, calling _rvs1 for each set of scalar args. # For usage example, see _nchypergeom_gen def _rvs(*args, size, random_state): _rvs1_size, _rvs1_indices = _check_shape(args[0].shape, size) size = np.array(size) _rvs1_size = np.array(_rvs1_size) _rvs1_indices = np.array(_rvs1_indices) if np.all(_rvs1_indices): # all args are scalars return _rvs1(*args, size, random_state) out = np.empty(size) # out.shape can mix dimensions associated with arg_shape and _rvs1_size # Sort them to arg_shape + _rvs1_size for easy indexing of dimensions # corresponding with the different sets of scalar args j0 = np.arange(out.ndim) j1 = np.hstack((j0[~_rvs1_indices], j0[_rvs1_indices])) out = np.moveaxis(out, j1, j0) for i in np.ndindex(*size[~_rvs1_indices]): # arg can be squeezed because singleton dimensions will be # associated with _rvs1_size, not arg_shape per _check_shape out[i] = _rvs1(*[np.squeeze(arg)[i] for arg in args], _rvs1_size, random_state) return np.moveaxis(out, j0, j1) # move axes back before returning return _rvs class _nchypergeom_gen(rv_discrete): r"""A noncentral hypergeometric discrete random variable. For subclassing by nchypergeom_fisher_gen and nchypergeom_wallenius_gen. """ rvs_name = None dist = None def _shape_info(self): return [_ShapeInfo("M", True, (0, np.inf), (True, False)), _ShapeInfo("n", True, (0, np.inf), (True, False)), _ShapeInfo("N", True, (0, np.inf), (True, False)), _ShapeInfo("odds", False, (0, np.inf), (False, False))] def _get_support(self, M, n, N, odds): N, m1, n = M, n, N # follow Wikipedia notation m2 = N - m1 x_min = np.maximum(0, n - m2) x_max = np.minimum(n, m1) return x_min, x_max def _argcheck(self, M, n, N, odds): M, n = np.asarray(M), np.asarray(n), N, odds = np.asarray(N), np.asarray(odds) cond1 = (M.astype(int) == M) & (M >= 0) cond2 = (n.astype(int) == n) & (n >= 0) cond3 = (N.astype(int) == N) & (N >= 0) cond4 = odds > 0 cond5 = N <= M cond6 = n <= M return cond1 & cond2 & cond3 & cond4 & cond5 & cond6 def _rvs(self, M, n, N, odds, size=None, random_state=None): @_vectorize_rvs_over_shapes def _rvs1(M, n, N, odds, size, random_state): length = np.prod(size) urn = _PyStochasticLib3() rv_gen = getattr(urn, self.rvs_name) rvs = rv_gen(N, n, M, odds, length, random_state) rvs = rvs.reshape(size) return rvs return _rvs1(M, n, N, odds, size=size, random_state=random_state) def _pmf(self, x, M, n, N, odds): x, M, n, N, odds = np.broadcast_arrays(x, M, n, N, odds) if x.size == 0: # np.vectorize doesn't work with zero size input return np.empty_like(x) @np.vectorize def _pmf1(x, M, n, N, odds): urn = self.dist(N, n, M, odds, 1e-12) return urn.probability(x) return _pmf1(x, M, n, N, odds) def _stats(self, M, n, N, odds, moments): @np.vectorize def _moments1(M, n, N, odds): urn = self.dist(N, n, M, odds, 1e-12) return urn.moments() m, v = (_moments1(M, n, N, odds) if ("m" in moments or "v" in moments) else (None, None)) s, k = None, None return m, v, s, k class nchypergeom_fisher_gen(_nchypergeom_gen): r"""A Fisher's noncentral hypergeometric discrete random variable. Fisher's noncentral hypergeometric distribution models drawing objects of two types from a bin. `M` is the total number of objects, `n` is the number of Type I objects, and `odds` is the odds ratio: the odds of selecting a Type I object rather than a Type II object when there is only one object of each type. The random variate represents the number of Type I objects drawn if we take a handful of objects from the bin at once and find out afterwards that we took `N` objects. %(before_notes)s See Also -------- nchypergeom_wallenius, hypergeom, nhypergeom Notes ----- Let mathematical symbols :math:`N`, :math:`n`, and :math:`M` correspond with parameters `N`, `n`, and `M` (respectively) as defined above. The probability mass function is defined as .. math:: p(x; M, n, N, \omega) = \frac{\binom{n}{x}\binom{M - n}{N-x}\omega^x}{P_0}, for :math:`x \in [x_l, x_u]`, :math:`M \in {\mathbb N}`, :math:`n \in [0, M]`, :math:`N \in [0, M]`, :math:`\omega > 0`, where :math:`x_l = \max(0, N - (M - n))`, :math:`x_u = \min(N, n)`, .. math:: P_0 = \sum_{y=x_l}^{x_u} \binom{n}{y}\binom{M - n}{N-y}\omega^y, and the binomial coefficients are defined as .. math:: \binom{n}{k} \equiv \frac{n!}{k! (n - k)!}. `nchypergeom_fisher` uses the BiasedUrn package by Agner Fog with permission for it to be distributed under SciPy's license. The symbols used to denote the shape parameters (`N`, `n`, and `M`) are not universally accepted; they are chosen for consistency with `hypergeom`. Note that Fisher's noncentral hypergeometric distribution is distinct from Wallenius' noncentral hypergeometric distribution, which models drawing a pre-determined `N` objects from a bin one by one. When the odds ratio is unity, however, both distributions reduce to the ordinary hypergeometric distribution. %(after_notes)s References ---------- .. [1] Agner Fog, "Biased Urn Theory". https://cran.r-project.org/web/packages/BiasedUrn/vignettes/UrnTheory.pdf .. [2] "Fisher's noncentral hypergeometric distribution", Wikipedia, https://en.wikipedia.org/wiki/Fisher's_noncentral_hypergeometric_distribution %(example)s """ rvs_name = "rvs_fisher" dist = _PyFishersNCHypergeometric nchypergeom_fisher = nchypergeom_fisher_gen( name='nchypergeom_fisher', longname="A Fisher's noncentral hypergeometric") class nchypergeom_wallenius_gen(_nchypergeom_gen): r"""A Wallenius' noncentral hypergeometric discrete random variable. Wallenius' noncentral hypergeometric distribution models drawing objects of two types from a bin. `M` is the total number of objects, `n` is the number of Type I objects, and `odds` is the odds ratio: the odds of selecting a Type I object rather than a Type II object when there is only one object of each type. The random variate represents the number of Type I objects drawn if we draw a pre-determined `N` objects from a bin one by one. %(before_notes)s See Also -------- nchypergeom_fisher, hypergeom, nhypergeom Notes ----- Let mathematical symbols :math:`N`, :math:`n`, and :math:`M` correspond with parameters `N`, `n`, and `M` (respectively) as defined above. The probability mass function is defined as .. math:: p(x; N, n, M) = \binom{n}{x} \binom{M - n}{N-x} \int_0^1 \left(1-t^{\omega/D}\right)^x\left(1-t^{1/D}\right)^{N-x} dt for :math:`x \in [x_l, x_u]`, :math:`M \in {\mathbb N}`, :math:`n \in [0, M]`, :math:`N \in [0, M]`, :math:`\omega > 0`, where :math:`x_l = \max(0, N - (M - n))`, :math:`x_u = \min(N, n)`, .. math:: D = \omega(n - x) + ((M - n)-(N-x)), and the binomial coefficients are defined as .. math:: \binom{n}{k} \equiv \frac{n!}{k! (n - k)!}. `nchypergeom_wallenius` uses the BiasedUrn package by Agner Fog with permission for it to be distributed under SciPy's license. The symbols used to denote the shape parameters (`N`, `n`, and `M`) are not universally accepted; they are chosen for consistency with `hypergeom`. Note that Wallenius' noncentral hypergeometric distribution is distinct from Fisher's noncentral hypergeometric distribution, which models take a handful of objects from the bin at once, finding out afterwards that `N` objects were taken. When the odds ratio is unity, however, both distributions reduce to the ordinary hypergeometric distribution. %(after_notes)s References ---------- .. [1] Agner Fog, "Biased Urn Theory". https://cran.r-project.org/web/packages/BiasedUrn/vignettes/UrnTheory.pdf .. [2] "Wallenius' noncentral hypergeometric distribution", Wikipedia, https://en.wikipedia.org/wiki/Wallenius'_noncentral_hypergeometric_distribution %(example)s """ rvs_name = "rvs_wallenius" dist = _PyWalleniusNCHypergeometric nchypergeom_wallenius = nchypergeom_wallenius_gen( name='nchypergeom_wallenius', longname="A Wallenius' noncentral hypergeometric") # Collect names of classes and objects in this module. pairs = list(globals().copy().items()) _distn_names, _distn_gen_names = get_distribution_names(pairs, rv_discrete) __all__ = _distn_names + _distn_gen_names