pint.models.priors.GaussianRV_gen

class pint.models.priors.GaussianRV_gen(momtype=1, a=None, b=None, xtol=1e-14, badvalue=None, name=None, longname=None, shapes=None, seed=None)[source]

Bases: rv_continuous

A Gaussian prior between two bounds. If you just want a gaussian, use scipy.stats.norm This version is for generating bounded Gaussians

Parameters:

loc (number) – Mode of the gaussian (default=0.0)
scale (number) – Standard deviation of the gaussian (default=1.0)

Methods

`cdf`(x, args, *kwds)	Cumulative distribution function of the given RV.
`entropy`(args, *kwds)	Differential entropy of the RV.
`expect`([func, args, loc, scale, lb, ub, ...])	Calculate expected value of a function with respect to the distribution by numerical integration.
`fit`(data, args, *kwds)	Return estimates of shape (if applicable), location, and scale parameters from data.
`fit_loc_scale`(data, *args)	Estimate loc and scale parameters from data using 1st and 2nd moments.
`freeze`(args, *kwds)	Freeze the distribution for the given arguments.
`interval`(confidence, args, *kwds)	Confidence interval with equal areas around the median.
`isf`(q, args, *kwds)	Inverse survival function (inverse of sf) at q of the given RV.
`logcdf`(x, args, *kwds)	Log of the cumulative distribution function at x of the given RV.
`logpdf`(x, args, *kwds)	Log of the probability density function at x of the given RV.
`logsf`(x, args, *kwds)	Log of the survival function of the given RV.
`mean`(args, *kwds)	Mean of the distribution.
`median`(args, *kwds)	Median of the distribution.
`moment`(order, args, *kwds)	non-central moment of distribution of specified order.
`nnlf`(theta, x)	Negative loglikelihood function.
`pdf`(x, args, *kwds)	Probability density function at x of the given RV.
`ppf`(q, args, *kwds)	Percent point function (inverse of cdf) at q of the given RV.
`rvs`(args, *kwds)	Random variates of given type.
`sf`(x, args, *kwds)	Survival function (1 - cdf) at x of the given RV.
`stats`(args, *kwds)	Some statistics of the given RV.
`std`(args, *kwds)	Standard deviation of the distribution.
`support`(args, *kwargs)	Support of the distribution.
`var`(args, *kwds)	Variance of the distribution.

Attributes

random_state

Get or set the generator object for generating random variates.

__call__(*args, **kwds)

Freeze the distribution for the given arguments.

Parameters:

arg1 (array_like) – The shape parameter(s) for the distribution. Should include all the non-optional arguments, may include loc and scale.
arg2 (array_like) – The shape parameter(s) for the distribution. Should include all the non-optional arguments, may include loc and scale.
arg3 (array_like) – The shape parameter(s) for the distribution. Should include all the non-optional arguments, may include loc and scale.
... (array_like) – The shape parameter(s) for the distribution. Should include all the non-optional arguments, may include loc and scale.

Returns:

rv_frozen – The frozen distribution.

Return type:

rv_frozen instance

cdf(x, *args, **kwds)

Cumulative distribution function of the given RV.

Parameters:

x (array_like) – quantiles
arg1 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg2 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg3 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
... (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
loc (array_like, optional) – location parameter (default=0)
scale (array_like, optional) – scale parameter (default=1)

Returns:

cdf – Cumulative distribution function evaluated at x

Return type:

ndarray

entropy(*args, **kwds)

Differential entropy of the RV.

Parameters:

arg1 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information).
arg2 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information).
arg3 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information).
... (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information).
loc (array_like, optional) – Location parameter (default=0).
scale (array_like, optional (continuous distributions only).) – Scale parameter (default=1).

Notes

Entropy is defined base e:

>>> import numpy as np
>>> from scipy.stats._distn_infrastructure import rv_discrete
>>> drv = rv_discrete(values=((0, 1), (0.5, 0.5)))
>>> np.allclose(drv.entropy(), np.log(2.0))
True

expect(func=None, args=(), loc=0, scale=1, lb=None, ub=None, conditional=False, **kwds)

Calculate expected value of a function with respect to the distribution by numerical integration.

The expected value of a function f(x) with respect to a distribution dist is defined as:

        ub
E[f(x)] = Integral(f(x) * dist.pdf(x)),
        lb

where ub and lb are arguments and x has the dist.pdf(x) distribution. If the bounds lb and ub correspond to the support of the distribution, e.g. [-inf, inf] in the default case, then the integral is the unrestricted expectation of f(x). Also, the function f(x) may be defined such that f(x) is 0 outside a finite interval in which case the expectation is calculated within the finite range [lb, ub].

Parameters:

func (callable, optional) – Function for which integral is calculated. Takes only one argument. The default is the identity mapping f(x) = x.
args (tuple, optional) – Shape parameters of the distribution.
loc (float, optional) – Location parameter (default=0).
scale (float, optional) – Scale parameter (default=1).
lb (scalar, optional) – Lower and upper bound for integration. Default is set to the support of the distribution.
ub (scalar, optional) – Lower and upper bound for integration. Default is set to the support of the distribution.
conditional (bool, optional) – If True, the integral is corrected by the conditional probability of the integration interval. The return value is the expectation of the function, conditional on being in the given interval. Default is False.
routine. (Additional keyword arguments are passed to the integration) –

Returns:

expect – The calculated expected value.

Return type:

float

Notes

The integration behavior of this function is inherited from scipy.integrate.quad. Neither this function nor scipy.integrate.quad can verify whether the integral exists or is finite. For example cauchy(0).mean() returns np.nan and cauchy(0).expect() returns 0.0.

Likewise, the accuracy of results is not verified by the function. scipy.integrate.quad is typically reliable for integrals that are numerically favorable, but it is not guaranteed to converge to a correct value for all possible intervals and integrands. This function is provided for convenience; for critical applications, check results against other integration methods.

The function is not vectorized.

Examples

To understand the effect of the bounds of integration consider

>>> from scipy.stats import expon
>>> expon(1).expect(lambda x: 1, lb=0.0, ub=2.0)
0.6321205588285578

This is close to

>>> expon(1).cdf(2.0) - expon(1).cdf(0.0)
0.6321205588285577

If conditional=True

>>> expon(1).expect(lambda x: 1, lb=0.0, ub=2.0, conditional=True)
1.0000000000000002

The slight deviation from 1 is due to numerical integration.

The integrand can be treated as a complex-valued function by passing complex_func=True to scipy.integrate.quad .

>>> import numpy as np
>>> from scipy.stats import vonmises
>>> res = vonmises(loc=2, kappa=1).expect(lambda x: np.exp(1j*x),
...                                       complex_func=True)
>>> res
(-0.18576377217422957+0.40590124735052263j)

>>> np.angle(res)  # location of the (circular) distribution
2.0

fit(data, *args, **kwds)

Return estimates of shape (if applicable), location, and scale parameters from data. The default estimation method is Maximum Likelihood Estimation (MLE), but Method of Moments (MM) is also available.

Starting estimates for the fit are given by input arguments; for any arguments not provided with starting estimates, self._fitstart(data) is called to generate such.

One can hold some parameters fixed to specific values by passing in keyword arguments f0, f1, …, fn (for shape parameters) and floc and fscale (for location and scale parameters, respectively).

Parameters:

data (array_like or CensoredData instance) – Data to use in estimating the distribution parameters.
arg1 (floats, optional) – Starting value(s) for any shape-characterizing arguments (those not provided will be determined by a call to _fitstart(data)). No default value.
arg2 (floats, optional) – Starting value(s) for any shape-characterizing arguments (those not provided will be determined by a call to _fitstart(data)). No default value.
arg3 (floats, optional) – Starting value(s) for any shape-characterizing arguments (those not provided will be determined by a call to _fitstart(data)). No default value.
... (floats, optional) – Starting value(s) for any shape-characterizing arguments (those not provided will be determined by a call to _fitstart(data)). No default value.
**kwds (floats, optional) –
- loc: initial guess of the distribution’s location parameter.
- scale: initial guess of the distribution’s scale parameter.
Special keyword arguments are recognized as holding certain parameters fixed:
- f0…fn : hold respective shape parameters fixed. Alternatively, shape parameters to fix can be specified by name. For example, if self.shapes == "a, b", fa and fix_a are equivalent to f0, and fb and fix_b are equivalent to f1.
- floc : hold location parameter fixed to specified value.
- fscale : hold scale parameter fixed to specified value.
- optimizer : The optimizer to use. The optimizer must take func and starting position as the first two arguments, plus args (for extra arguments to pass to the function to be optimized) and disp. The fit method calls the optimizer with disp=0 to suppress output. The optimizer must return the estimated parameters.
- method : The method to use. The default is “MLE” (Maximum Likelihood Estimate); “MM” (Method of Moments) is also available.

Raises:

TypeError, ValueError – If an input is invalid
FitError – If fitting fails or the fit produced would be invalid

Returns:

parameter_tuple – Estimates for any shape parameters (if applicable), followed by those for location and scale. For most random variables, shape statistics will be returned, but there are exceptions (e.g. norm).

Return type:

tuple of floats

Notes

With method="MLE" (default), the fit is computed by minimizing the negative log-likelihood function. A large, finite penalty (rather than infinite negative log-likelihood) is applied for observations beyond the support of the distribution.

With method="MM", the fit is computed by minimizing the L2 norm of the relative errors between the first k raw (about zero) data moments and the corresponding distribution moments, where k is the number of non-fixed parameters. More precisely, the objective function is:

(((data_moments - dist_moments)
  / np.maximum(np.abs(data_moments), 1e-8))**2).sum()

where the constant 1e-8 avoids division by zero in case of vanishing data moments. Typically, this error norm can be reduced to zero. Note that the standard method of moments can produce parameters for which some data are outside the support of the fitted distribution; this implementation does nothing to prevent this.

For either method, the returned answer is not guaranteed to be globally optimal; it may only be locally optimal, or the optimization may fail altogether. If the data contain any of np.nan, np.inf, or -np.inf, the fit method will raise a RuntimeError.

When passing a CensoredData instance to data, the log-likelihood function is defined as:

\[\begin{split}l(\pmb{\theta}; k) & = \sum \log(f(k_u; \pmb{\theta})) + \sum \log(F(k_l; \pmb{\theta})) \\ & + \sum \log(1 - F(k_r; \pmb{\theta})) \\ & + \sum \log(F(k_{\text{high}, i}; \pmb{\theta}) - F(k_{\text{low}, i}; \pmb{\theta}))\end{split}\]

where \(f\) and \(F\) are the pdf and cdf, respectively, of the function being fitted, \(\pmb{\theta}\) is the parameter vector, \(u\) are the indices of uncensored observations, \(l\) are the indices of left-censored observations, \(r\) are the indices of right-censored observations, subscripts “low”/”high” denote endpoints of interval-censored observations, and \(i\) are the indices of interval-censored observations.

Examples

Generate some data to fit: draw random variates from the beta distribution

>>> import numpy as np
>>> from scipy.stats import beta
>>> a, b = 1., 2.
>>> rng = np.random.default_rng(172786373191770012695001057628748821561)
>>> x = beta.rvs(a, b, size=1000, random_state=rng)

Now we can fit all four parameters (a, b, loc and scale):

>>> a1, b1, loc1, scale1 = beta.fit(x)
>>> a1, b1, loc1, scale1
(1.0198945204435628, 1.9484708982737828, 4.372241314917588e-05, 0.9979078845964814)

The fit can be done also using a custom optimizer:

>>> from scipy.optimize import minimize
>>> def custom_optimizer(func, x0, args=(), disp=0):
...     res = minimize(func, x0, args, method="slsqp", options={"disp": disp})
...     if res.success:
...         return res.x
...     raise RuntimeError('optimization routine failed')
>>> a1, b1, loc1, scale1 = beta.fit(x, method="MLE", optimizer=custom_optimizer)
>>> a1, b1, loc1, scale1
(1.0198821087258905, 1.948484145914738, 4.3705304486881485e-05, 0.9979104663953395)

We can also use some prior knowledge about the dataset: let’s keep loc and scale fixed:

>>> a1, b1, loc1, scale1 = beta.fit(x, floc=0, fscale=1)
>>> loc1, scale1
(0, 1)

We can also keep shape parameters fixed by using f-keywords. To keep the zero-th shape parameter a equal 1, use f0=1 or, equivalently, fa=1:

>>> a1, b1, loc1, scale1 = beta.fit(x, fa=1, floc=0, fscale=1)
>>> a1
1

Not all distributions return estimates for the shape parameters. norm for example just returns estimates for location and scale:

>>> from scipy.stats import norm
>>> x = norm.rvs(a, b, size=1000, random_state=123)
>>> loc1, scale1 = norm.fit(x)
>>> loc1, scale1
(0.92087172783841631, 2.0015750750324668)

fit_loc_scale(data, *args)

Estimate loc and scale parameters from data using 1st and 2nd moments.

Parameters:

data (array_like) – Data to fit.
arg1 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information).
arg2 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information).
arg3 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information).
... (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information).

Returns:

Lhat (float) – Estimated location parameter for the data.
Shat (float) – Estimated scale parameter for the data.

freeze(*args, **kwds)

Freeze the distribution for the given arguments.

Parameters:

arg1 (array_like) – The shape parameter(s) for the distribution. Should include all the non-optional arguments, may include loc and scale.
arg2 (array_like) – The shape parameter(s) for the distribution. Should include all the non-optional arguments, may include loc and scale.
arg3 (array_like) – The shape parameter(s) for the distribution. Should include all the non-optional arguments, may include loc and scale.
... (array_like) – The shape parameter(s) for the distribution. Should include all the non-optional arguments, may include loc and scale.

Returns:

rv_frozen – The frozen distribution.

Return type:

rv_frozen instance

interval(confidence, *args, **kwds)

Confidence interval with equal areas around the median.

Parameters:

confidence (array_like of float) – Probability that an rv will be drawn from the returned range. Each value should be in the range [0, 1].
arg1 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information).
arg2 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information).
... (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information).
loc (array_like, optional) – location parameter, Default is 0.
scale (array_like, optional) – scale parameter, Default is 1.

Returns:

a, b – end-points of range that contain 100 * alpha % of the rv’s possible values.

Return type:

ndarray of float

Notes

This is implemented as ppf([p_tail, 1-p_tail]), where ppf is the inverse cumulative distribution function and p_tail = (1-confidence)/2. Suppose [c, d] is the support of a discrete distribution; then ppf([0, 1]) == (c-1, d). Therefore, when confidence=1 and the distribution is discrete, the left end of the interval will be beyond the support of the distribution. For discrete distributions, the interval will limit the probability in each tail to be less than or equal to p_tail (usually strictly less).

isf(q, *args, **kwds)

Inverse survival function (inverse of sf) at q of the given RV.

Parameters:

q (array_like) – upper tail probability
arg1 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg2 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg3 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
... (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
loc (array_like, optional) – location parameter (default=0)
scale (array_like, optional) – scale parameter (default=1)

Returns:

x – Quantile corresponding to the upper tail probability q.

Return type:

ndarray or scalar

logcdf(x, *args, **kwds)

Log of the cumulative distribution function at x of the given RV.

Parameters:

x (array_like) – quantiles
arg1 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg2 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg3 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
... (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
loc (array_like, optional) – location parameter (default=0)
scale (array_like, optional) – scale parameter (default=1)

Returns:

logcdf – Log of the cumulative distribution function evaluated at x

Return type:

array_like

logpdf(x, *args, **kwds)

Log of the probability density function at x of the given RV.

This uses a more numerically accurate calculation if available.

Parameters:

x (array_like) – quantiles
arg1 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg2 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg3 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
... (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
loc (array_like, optional) – location parameter (default=0)
scale (array_like, optional) – scale parameter (default=1)

Returns:

logpdf – Log of the probability density function evaluated at x

Return type:

array_like

logsf(x, *args, **kwds)

Log of the survival function of the given RV.

Returns the log of the “survival function,” defined as (1 - cdf), evaluated at x.

Parameters:

x (array_like) – quantiles
arg1 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg2 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg3 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
... (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
loc (array_like, optional) – location parameter (default=0)
scale (array_like, optional) – scale parameter (default=1)

Returns:

logsf – Log of the survival function evaluated at x.

Return type:

ndarray

mean(*args, **kwds)

Mean of the distribution.

Parameters:

arg1 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg2 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg3 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
... (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
loc (array_like, optional) – location parameter (default=0)
scale (array_like, optional) – scale parameter (default=1)

Returns:

mean – the mean of the distribution

Return type:

float

median(*args, **kwds)

Median of the distribution.

Parameters:

arg1 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg2 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
arg3 (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
... (array_like) – The shape parameter(s) for the distribution (see docstring of the instance object for more information)
loc (array_like, optional) – Location parameter, Default is 0.
scale (array_like, optional) – Scale parameter, Default is 1.

Returns:

median – The median of the distribution.

Return type:

float