Source code for statsmodels.sandbox.distributions.extras

'''Various extensions to distributions

* skew normal and skew t distribution by Azzalini, A. & Capitanio, A.
* Gram-Charlier expansion distribution (using 4 moments),
* distributions based on non-linear transformation
  - Transf_gen
  - ExpTransf_gen, LogTransf_gen
  - TransfTwo_gen
    (defines as examples: square, negative square and abs transformations)
  - this versions are without __new__
* mnvormcdf, mvstdnormcdf : cdf, rectangular integral for multivariate normal
  distribution

TODO:
* Where is Transf_gen for general monotonic transformation ? found and added it
* write some docstrings, some parts I don't remember
* add Box-Cox transformation, parameterized ?


this is only partially cleaned, still includes test examples as functions

main changes
* add transf_gen (2010-05-09)
* added separate example and tests (2010-05-09)
* collect transformation function into classes

Example
-------

>>> logtg = Transf_gen(stats.t, np.exp, np.log,
                numargs = 1, a=0, name = 'lnnorm',
                longname = 'Exp transformed normal',
                extradoc = '\ndistribution of y = exp(x), with x standard normal'
                'precision for moment andstats is not very high, 2-3 decimals')
>>> logtg.cdf(5, 6)
0.92067704211191848
>>> stats.t.cdf(np.log(5), 6)
0.92067704211191848

>>> logtg.pdf(5, 6)
0.021798547904239293
>>> stats.t.pdf(np.log(5), 6)
0.10899273954837908
>>> stats.t.pdf(np.log(5), 6)/5.  #derivative
0.021798547909675815


Author: josef-pktd
License: BSD

'''

#note copied from distr_skewnorm_0.py

from __future__ import print_function
from statsmodels.compat.python import range, iteritems
from scipy import stats, special, integrate  # integrate is for scipy 0.6.0 ???
from scipy.stats import distributions
from statsmodels.stats.moment_helpers import mvsk2mc, mc2mvsk
import numpy as np

[docs]class SkewNorm_gen(distributions.rv_continuous): '''univariate Skew-Normal distribution of Azzalini class follows scipy.stats.distributions pattern but with __init__ ''' def __init__(self): #super(SkewNorm_gen,self).__init__( distributions.rv_continuous.__init__(self, name = 'Skew Normal distribution', shapes = 'alpha', extradoc = ''' ''' ) def _argcheck(self, alpha): return 1 #(alpha >= 0) def _rvs(self, alpha): # see http://azzalini.stat.unipd.it/SN/faq.html delta = alpha/np.sqrt(1+alpha**2) u0 = stats.norm.rvs(size=self._size) u1 = delta*u0 + np.sqrt(1-delta**2)*stats.norm.rvs(size=self._size) return np.where(u0>0, u1, -u1) def _munp(self, n, alpha): # use pdf integration with _mom0_sc if only _pdf is defined. # default stats calculation uses ppf, which is much slower return self._mom0_sc(n, alpha) def _pdf(self,x,alpha): # 2*normpdf(x)*normcdf(alpha*x) return 2.0/np.sqrt(2*np.pi)*np.exp(-x**2/2.0) * special.ndtr(alpha*x) def _stats_skip(self,x,alpha,moments='mvsk'): #skip for now to force moment integration as check pass
skewnorm = SkewNorm_gen() # generated the same way as distributions in stats.distributions
[docs]class SkewNorm2_gen(distributions.rv_continuous): '''univariate Skew-Normal distribution of Azzalini class follows scipy.stats.distributions pattern ''' def _argcheck(self, alpha): return 1 #where(alpha>=0, 1, 0) def _pdf(self,x,alpha): # 2*normpdf(x)*normcdf(alpha*x return 2.0/np.sqrt(2*np.pi)*np.exp(-x**2/2.0) * special.ndtr(alpha*x)
skewnorm2 = SkewNorm2_gen(name = 'Skew Normal distribution', shapes = 'alpha', extradoc = ''' -inf < alpha < inf''')
[docs]class ACSkewT_gen(distributions.rv_continuous): '''univariate Skew-T distribution of Azzalini class follows scipy.stats.distributions pattern but with __init__ ''' def __init__(self): #super(SkewT_gen,self).__init__( distributions.rv_continuous.__init__(self, name = 'Skew T distribution', shapes = 'df, alpha', extradoc = ''' Skewed T distribution by Azzalini, A. & Capitanio, A. (2003)_ the pdf is given by: pdf(x) = 2.0 * t.pdf(x, df) * t.cdf(df+1, alpha*x*np.sqrt((1+df)/(x**2+df))) with alpha >=0 Note: different from skewed t distribution by Hansen 1999 .._ Azzalini, A. & Capitanio, A. (2003), Distributions generated by perturbation of symmetry with emphasis on a multivariate skew-t distribution, appears in J.Roy.Statist.Soc, series B, vol.65, pp.367-389 ''' ) def _argcheck(self, df, alpha): return (alpha == alpha)*(df>0) ## def _arg_check(self, alpha): ## return np.where(alpha>=0, 0, 1) ## def _argcheck(self, alpha): ## return np.where(alpha>=0, 1, 0) def _rvs(self, df, alpha): # see http://azzalini.stat.unipd.it/SN/faq.html #delta = alpha/np.sqrt(1+alpha**2) V = stats.chi2.rvs(df, size=self._size) z = skewnorm.rvs(alpha, size=self._size) return z/np.sqrt(V/df) def _munp(self, n, df, alpha): # use pdf integration with _mom0_sc if only _pdf is defined. # default stats calculation uses ppf return self._mom0_sc(n, df, alpha) def _pdf(self, x, df, alpha): # 2*normpdf(x)*normcdf(alpha*x) return 2.0*distributions.t._pdf(x, df) * special.stdtr(df+1, alpha*x*np.sqrt((1+df)/(x**2+df)))
## ##def mvsk2cm(*args): ## mu,sig,sk,kur = args ## # Get central moments ## cnt = [None]*4 ## cnt[0] = mu ## cnt[1] = sig #*sig ## cnt[2] = sk * sig**1.5 ## cnt[3] = (kur+3.0) * sig**2.0 ## return cnt ## ## ##def mvsk2m(args): ## mc, mc2, skew, kurt = args#= self._stats(*args,**mdict) ## mnc = mc ## mnc2 = mc2 + mc*mc ## mc3 = skew*(mc2**1.5) # 3rd central moment ## mnc3 = mc3+3*mc*mc2+mc**3 # 3rd non-central moment ## mc4 = (kurt+3.0)*(mc2**2.0) # 4th central moment ## mnc4 = mc4+4*mc*mc3+6*mc*mc*mc2+mc**4 ## return (mc, mc2, mc3, mc4), (mnc, mnc2, mnc3, mnc4) ## ##def mc2mvsk(args): ## mc, mc2, mc3, mc4 = args ## skew = mc3 / mc2**1.5 ## kurt = mc4 / mc2**2.0 - 3.0 ## return (mc, mc2, skew, kurt) ## ##def m2mc(args): ## mnc, mnc2, mnc3, mnc4 = args ## mc = mnc ## mc2 = mnc2 - mnc*mnc ## #mc3 = skew*(mc2**1.5) # 3rd central moment ## mc3 = mnc3 - (3*mc*mc2+mc**3) # 3rd central moment ## #mc4 = (kurt+3.0)*(mc2**2.0) # 4th central moment ## mc4 = mnc4 - (4*mc*mc3+6*mc*mc*mc2+mc**4) ## return (mc, mc2, mc3, mc4) from numpy import poly1d,sqrt, exp import scipy def _hermnorm(N): # return the negatively normalized hermite polynomials up to order N-1 # (inclusive) # using the recursive relationship # p_n+1 = p_n(x)' - x*p_n(x) # and p_0(x) = 1 plist = [None]*N plist[0] = poly1d(1) for n in range(1,N): plist[n] = plist[n-1].deriv() - poly1d([1,0])*plist[n-1] return plist
[docs]def pdf_moments_st(cnt): """Return the Gaussian expanded pdf function given the list of central moments (first one is mean). version of scipy.stats, any changes ? the scipy.stats version has a bug and returns normal distribution """ N = len(cnt) if N < 2: raise ValueError("At least two moments must be given to " "approximate the pdf.") totp = poly1d(1) sig = sqrt(cnt[1]) mu = cnt[0] if N > 2: Dvals = _hermnorm(N+1) for k in range(3,N+1): # Find Ck Ck = 0.0 for n in range((k-3)/2): m = k-2*n if m % 2: # m is odd momdiff = cnt[m-1] else: momdiff = cnt[m-1] - sig*sig*scipy.factorial2(m-1) Ck += Dvals[k][m] / sig**m * momdiff # Add to totp raise SystemError print(Dvals) print(Ck) totp = totp + Ck*Dvals[k] def thisfunc(x): xn = (x-mu)/sig return totp(xn)*exp(-xn*xn/2.0)/sqrt(2*np.pi)/sig return thisfunc, totp
[docs]def pdf_mvsk(mvsk): """Return the Gaussian expanded pdf function given the list of 1st, 2nd moment and skew and Fisher (excess) kurtosis. Parameters ---------- mvsk : list of mu, mc2, skew, kurt distribution is matched to these four moments Returns ------- pdffunc : function function that evaluates the pdf(x), where x is the non-standardized random variable. Notes ----- Changed so it works only if four arguments are given. Uses explicit formula, not loop. This implements a Gram-Charlier expansion of the normal distribution where the first 2 moments coincide with those of the normal distribution but skew and kurtosis can deviate from it. In the Gram-Charlier distribution it is possible that the density becomes negative. This is the case when the deviation from the normal distribution is too large. References ---------- http://en.wikipedia.org/wiki/Edgeworth_series Johnson N.L., S. Kotz, N. Balakrishnan: Continuous Univariate Distributions, Volume 1, 2nd ed., p.30 """ N = len(mvsk) if N < 4: raise ValueError("Four moments must be given to " "approximate the pdf.") mu, mc2, skew, kurt = mvsk totp = poly1d(1) sig = sqrt(mc2) if N > 2: Dvals = _hermnorm(N+1) C3 = skew/6.0 C4 = kurt/24.0 # Note: Hermite polynomial for order 3 in _hermnorm is negative # instead of positive totp = totp - C3*Dvals[3] + C4*Dvals[4] def pdffunc(x): xn = (x-mu)/sig return totp(xn)*np.exp(-xn*xn/2.0)/np.sqrt(2*np.pi)/sig return pdffunc
[docs]def pdf_moments(cnt): """Return the Gaussian expanded pdf function given the list of central moments (first one is mean). Changed so it works only if four arguments are given. Uses explicit formula, not loop. Notes ----- This implements a Gram-Charlier expansion of the normal distribution where the first 2 moments coincide with those of the normal distribution but skew and kurtosis can deviate from it. In the Gram-Charlier distribution it is possible that the density becomes negative. This is the case when the deviation from the normal distribution is too large. References ---------- http://en.wikipedia.org/wiki/Edgeworth_series Johnson N.L., S. Kotz, N. Balakrishnan: Continuous Univariate Distributions, Volume 1, 2nd ed., p.30 """ N = len(cnt) if N < 2: raise ValueError("At least two moments must be given to " "approximate the pdf.") mc, mc2, mc3, mc4 = cnt skew = mc3 / mc2**1.5 kurt = mc4 / mc2**2.0 - 3.0 # Fisher kurtosis, excess kurtosis totp = poly1d(1) sig = sqrt(cnt[1]) mu = cnt[0] if N > 2: Dvals = _hermnorm(N+1) ## for k in range(3,N+1): ## # Find Ck ## Ck = 0.0 ## for n in range((k-3)/2): ## m = k-2*n ## if m % 2: # m is odd ## momdiff = cnt[m-1] ## else: ## momdiff = cnt[m-1] - sig*sig*scipy.factorial2(m-1) ## Ck += Dvals[k][m] / sig**m * momdiff ## # Add to totp ## raise ## print Dvals ## print Ck ## totp = totp + Ck*Dvals[k] C3 = skew/6.0 C4 = kurt/24.0 totp = totp - C3*Dvals[3] + C4*Dvals[4] def thisfunc(x): xn = (x-mu)/sig return totp(xn)*np.exp(-xn*xn/2.0)/np.sqrt(2*np.pi)/sig return thisfunc
[docs]class NormExpan_gen(distributions.rv_continuous): '''Gram-Charlier Expansion of Normal distribution class follows scipy.stats.distributions pattern but with __init__ ''' def __init__(self,args, **kwds): #todo: replace with super call distributions.rv_continuous.__init__(self, name = 'Normal Expansion distribution', shapes = ' ', extradoc = ''' The distribution is defined as the Gram-Charlier expansion of the normal distribution using the first four moments. The pdf is given by pdf(x) = (1+ skew/6.0 * H(xc,3) + kurt/24.0 * H(xc,4))*normpdf(xc) where xc = (x-mu)/sig is the standardized value of the random variable and H(xc,3) and H(xc,4) are Hermite polynomials Note: This distribution has to be parameterized during initialization and instantiation, and does not have a shape parameter after instantiation (similar to frozen distribution except for location and scale.) Location and scale can be used as with other distributions, however note, that they are relative to the initialized distribution. ''' ) #print args, kwds mode = kwds.get('mode', 'sample') if mode == 'sample': mu,sig,sk,kur = stats.describe(args)[2:] self.mvsk = (mu,sig,sk,kur) cnt = mvsk2mc((mu,sig,sk,kur)) elif mode == 'mvsk': cnt = mvsk2mc(args) self.mvsk = args elif mode == 'centmom': cnt = args self.mvsk = mc2mvsk(cnt) else: raise ValueError("mode must be 'mvsk' or centmom") self.cnt = cnt #self.mvsk = (mu,sig,sk,kur) #self._pdf = pdf_moments(cnt) self._pdf = pdf_mvsk(self.mvsk) def _munp(self,n): # use pdf integration with _mom0_sc if only _pdf is defined. # default stats calculation uses ppf return self._mom0_sc(n) def _stats_skip(self): # skip for now to force numerical integration of pdf for testing return self.mvsk
## copied from nonlinear_transform_gen.py ''' A class for the distribution of a non-linear monotonic transformation of a continuous random variable simplest usage: example: create log-gamma distribution, i.e. y = log(x), where x is gamma distributed (also available in scipy.stats) loggammaexpg = Transf_gen(stats.gamma, np.log, np.exp) example: what is the distribution of the discount factor y=1/(1+x) where interest rate x is normally distributed with N(mux,stdx**2)')? (just to come up with a story that implies a nice transformation) invnormalg = Transf_gen(stats.norm, inversew, inversew_inv, decr=True, a=-np.inf) This class does not work well for distributions with difficult shapes, e.g. 1/x where x is standard normal, because of the singularity and jump at zero. Note: I'm working from my version of scipy.stats.distribution. But this script runs under scipy 0.6.0 (checked with numpy: 1.2.0rc2 and python 2.4) This is not yet thoroughly tested, polished or optimized TODO: * numargs handling is not yet working properly, numargs needs to be specified (default = 0 or 1) * feeding args and kwargs to underlying distribution is untested and incomplete * distinguish args and kwargs for the transformed and the underlying distribution - currently all args and no kwargs are transmitted to underlying distribution - loc and scale only work for transformed, but not for underlying distribution - possible to separate args for transformation and underlying distribution parameters * add _rvs as method, will be faster in many cases Created on Tuesday, October 28, 2008, 12:40:37 PM Author: josef-pktd License: BSD ''' from scipy import integrate # for scipy 0.6.0 from scipy import stats, info from scipy.stats import distributions def get_u_argskwargs(**kwargs): #Todo: What's this? wrong spacing, used in Transf_gen TransfTwo_gen u_kwargs = dict((k.replace('u_','',1),v) for k,v in iteritems(kwargs) if k.startswith('u_')) u_args = u_kwargs.pop('u_args',None) return u_args, u_kwargs class Transf_gen(distributions.rv_continuous): '''a class for non-linear monotonic transformation of a continuous random variable ''' def __init__(self, kls, func, funcinv, *args, **kwargs): #print args #print kwargs self.func = func self.funcinv = funcinv #explicit for self.__dict__.update(kwargs) #need to set numargs because inspection does not work self.numargs = kwargs.pop('numargs', 0) #print self.numargs name = kwargs.pop('name','transfdist') longname = kwargs.pop('longname','Non-linear transformed distribution') extradoc = kwargs.pop('extradoc',None) a = kwargs.pop('a', -np.inf) b = kwargs.pop('b', np.inf) self.decr = kwargs.pop('decr', False) #defines whether it is a decreasing (True) # or increasing (False) monotonic transformation self.u_args, self.u_kwargs = get_u_argskwargs(**kwargs) self.kls = kls #(self.u_args, self.u_kwargs) # possible to freeze the underlying distribution super(Transf_gen,self).__init__(a=a, b=b, name = name, longname = longname, extradoc = extradoc) def _rvs(self, *args, **kwargs): self.kls._size = self._size return self.funcinv(self.kls._rvs(*args)) def _cdf(self,x,*args, **kwargs): #print args if not self.decr: return self.kls._cdf(self.funcinv(x),*args, **kwargs) #note scipy _cdf only take *args not *kwargs else: return 1.0 - self.kls._cdf(self.funcinv(x),*args, **kwargs) def _ppf(self, q, *args, **kwargs): if not self.decr: return self.func(self.kls._ppf(q,*args, **kwargs)) else: return self.func(self.kls._ppf(1-q,*args, **kwargs)) def inverse(x): return np.divide(1.0,x) mux, stdx = 0.05, 0.1 mux, stdx = 9.0, 1.0 def inversew(x): return 1.0/(1+mux+x*stdx) def inversew_inv(x): return (1.0/x - 1.0 - mux)/stdx #.np.divide(1.0,x)-10 def identit(x): return x invdnormalg = Transf_gen(stats.norm, inversew, inversew_inv, decr=True, #a=-np.inf, numargs = 0, name = 'discf', longname = 'normal-based discount factor', extradoc = '\ndistribution of discount factor y=1/(1+x)) with x N(0.05,0.1**2)') lognormalg = Transf_gen(stats.norm, np.exp, np.log, numargs = 2, a=0, name = 'lnnorm', longname = 'Exp transformed normal', extradoc = '\ndistribution of y = exp(x), with x standard normal' 'precision for moment andstats is not very high, 2-3 decimals') loggammaexpg = Transf_gen(stats.gamma, np.log, np.exp, numargs=1) ## copied form nonlinear_transform_short.py '''univariate distribution of a non-linear monotonic transformation of a random variable ''' from scipy import stats from scipy.stats import distributions import numpy as np class ExpTransf_gen(distributions.rv_continuous): '''Distribution based on log/exp transformation the constructor can be called with a distribution class and generates the distribution of the transformed random variable ''' def __init__(self, kls, *args, **kwargs): #print args #print kwargs #explicit for self.__dict__.update(kwargs) if 'numargs' in kwargs: self.numargs = kwargs['numargs'] else: self.numargs = 1 if 'name' in kwargs: name = kwargs['name'] else: name = 'Log transformed distribution' if 'a' in kwargs: a = kwargs['a'] else: a = 0 super(ExpTransf_gen,self).__init__(a=0, name = name) self.kls = kls def _cdf(self,x,*args): pass #print args return self.kls.cdf(np.log(x),*args) def _ppf(self, q, *args): return np.exp(self.kls.ppf(q,*args)) class LogTransf_gen(distributions.rv_continuous): '''Distribution based on log/exp transformation the constructor can be called with a distribution class and generates the distribution of the transformed random variable ''' def __init__(self, kls, *args, **kwargs): #explicit for self.__dict__.update(kwargs) if 'numargs' in kwargs: self.numargs = kwargs['numargs'] else: self.numargs = 1 if 'name' in kwargs: name = kwargs['name'] else: name = 'Log transformed distribution' if 'a' in kwargs: a = kwargs['a'] else: a = 0 super(LogTransf_gen,self).__init__(a=a, name = name) self.kls = kls def _cdf(self,x, *args): #print args return self.kls._cdf(np.exp(x),*args) def _ppf(self, q, *args): return np.log(self.kls._ppf(q,*args)) ## copied from transformtwo.py ''' Created on Apr 28, 2009 @author: Josef Perktold ''' ''' A class for the distribution of a non-linear u-shaped or hump shaped transformation of a continuous random variable This is a companion to the distributions of non-linear monotonic transformation to the case when the inverse mapping is a 2-valued correspondence, for example for absolute value or square simplest usage: example: create squared distribution, i.e. y = x**2, where x is normal or t distributed This class does not work well for distributions with difficult shapes, e.g. 1/x where x is standard normal, because of the singularity and jump at zero. This verifies for normal - chi2, normal - halfnorm, foldnorm, and t - F TODO: * numargs handling is not yet working properly, numargs needs to be specified (default = 0 or 1) * feeding args and kwargs to underlying distribution works in t distribution example * distinguish args and kwargs for the transformed and the underlying distribution - currently all args and no kwargs are transmitted to underlying distribution - loc and scale only work for transformed, but not for underlying distribution - possible to separate args for transformation and underlying distribution parameters * add _rvs as method, will be faster in many cases ''' class TransfTwo_gen(distributions.rv_continuous): '''Distribution based on a non-monotonic (u- or hump-shaped transformation) the constructor can be called with a distribution class, and functions that define the non-linear transformation. and generates the distribution of the transformed random variable Note: the transformation, it's inverse and derivatives need to be fully specified: func, funcinvplus, funcinvminus, derivplus, derivminus. Currently no numerical derivatives or inverse are calculated This can be used to generate distribution instances similar to the distributions in scipy.stats. ''' #a class for non-linear non-monotonic transformation of a continuous random variable def __init__(self, kls, func, funcinvplus, funcinvminus, derivplus, derivminus, *args, **kwargs): #print args #print kwargs self.func = func self.funcinvplus = funcinvplus self.funcinvminus = funcinvminus self.derivplus = derivplus self.derivminus = derivminus #explicit for self.__dict__.update(kwargs) #need to set numargs because inspection does not work self.numargs = kwargs.pop('numargs', 0) #print self.numargs name = kwargs.pop('name','transfdist') longname = kwargs.pop('longname','Non-linear transformed distribution') extradoc = kwargs.pop('extradoc',None) a = kwargs.pop('a', -np.inf) # attached to self in super b = kwargs.pop('b', np.inf) # self.a, self.b would be overwritten self.shape = kwargs.pop('shape', False) #defines whether it is a `u` shaped or `hump' shaped # transformation self.u_args, self.u_kwargs = get_u_argskwargs(**kwargs) self.kls = kls #(self.u_args, self.u_kwargs) # possible to freeze the underlying distribution super(TransfTwo_gen,self).__init__(a=a, b=b, name = name, shapes = kls.shapes, longname = longname, extradoc = extradoc) # add enough info for self.freeze() to be able to reconstruct the instance try: self._ctor_param.update(dict(kls=kls, func=func, funcinvplus=funcinvplus, funcinvminus=funcinvminus, derivplus=derivplus, derivminus=derivminus, shape=self.shape)) except AttributeError: # scipy < 0.14 does not have this, ignore and do nothing pass def _rvs(self, *args): self.kls._size = self._size #size attached to self, not function argument return self.func(self.kls._rvs(*args)) def _pdf(self,x,*args, **kwargs): #print args if self.shape == 'u': signpdf = 1 elif self.shape == 'hump': signpdf = -1 else: raise ValueError('shape can only be `u` or `hump`') return signpdf * (self.derivplus(x)*self.kls._pdf(self.funcinvplus(x),*args, **kwargs) - self.derivminus(x)*self.kls._pdf(self.funcinvminus(x),*args, **kwargs)) #note scipy _cdf only take *args not *kwargs def _cdf(self,x,*args, **kwargs): #print args if self.shape == 'u': return self.kls._cdf(self.funcinvplus(x),*args, **kwargs) - \ self.kls._cdf(self.funcinvminus(x),*args, **kwargs) #note scipy _cdf only take *args not *kwargs else: return 1.0 - self._sf(x,*args, **kwargs) def _sf(self,x,*args, **kwargs): #print args if self.shape == 'hump': return self.kls._cdf(self.funcinvplus(x),*args, **kwargs) - \ self.kls._cdf(self.funcinvminus(x),*args, **kwargs) #note scipy _cdf only take *args not *kwargs else: return 1.0 - self._cdf(x, *args, **kwargs) def _munp(self, n,*args, **kwargs): return self._mom0_sc(n,*args) # ppf might not be possible in general case? # should be possible in symmetric case # def _ppf(self, q, *args, **kwargs): # if self.shape == 'u': # return self.func(self.kls._ppf(q,*args, **kwargs)) # elif self.shape == 'hump': # return self.func(self.kls._ppf(1-q,*args, **kwargs)) #TODO: rename these functions to have unique names class SquareFunc(object): '''class to hold quadratic function with inverse function and derivative using instance methods instead of class methods, if we want extension to parameterized function ''' def inverseplus(self, x): return np.sqrt(x) def inverseminus(self, x): return 0.0 - np.sqrt(x) def derivplus(self, x): return 0.5/np.sqrt(x) def derivminus(self, x): return 0.0 - 0.5/np.sqrt(x) def squarefunc(self, x): return np.power(x,2) sqfunc = SquareFunc() squarenormalg = TransfTwo_gen(stats.norm, sqfunc.squarefunc, sqfunc.inverseplus, sqfunc.inverseminus, sqfunc.derivplus, sqfunc.derivminus, shape='u', a=0.0, b=np.inf, numargs = 0, name = 'squarenorm', longname = 'squared normal distribution', extradoc = '\ndistribution of the square of a normal random variable' +\ ' y=x**2 with x N(0.0,1)') #u_loc=l, u_scale=s) squaretg = TransfTwo_gen(stats.t, sqfunc.squarefunc, sqfunc.inverseplus, sqfunc.inverseminus, sqfunc.derivplus, sqfunc.derivminus, shape='u', a=0.0, b=np.inf, numargs = 1, name = 'squarenorm', longname = 'squared t distribution', extradoc = '\ndistribution of the square of a t random variable' +\ ' y=x**2 with x t(dof,0.0,1)') def inverseplus(x): return np.sqrt(-x) def inverseminus(x): return 0.0 - np.sqrt(-x) def derivplus(x): return 0.0 - 0.5/np.sqrt(-x) def derivminus(x): return 0.5/np.sqrt(-x) def negsquarefunc(x): return -np.power(x,2) negsquarenormalg = TransfTwo_gen(stats.norm, negsquarefunc, inverseplus, inverseminus, derivplus, derivminus, shape='hump', a=-np.inf, b=0.0, numargs = 0, name = 'negsquarenorm', longname = 'negative squared normal distribution', extradoc = '\ndistribution of the negative square of a normal random variable' +\ ' y=-x**2 with x N(0.0,1)') #u_loc=l, u_scale=s) def inverseplus(x): return x def inverseminus(x): return 0.0 - x def derivplus(x): return 1.0 def derivminus(x): return 0.0 - 1.0 def absfunc(x): return np.abs(x) absnormalg = TransfTwo_gen(stats.norm, np.abs, inverseplus, inverseminus, derivplus, derivminus, shape='u', a=0.0, b=np.inf, numargs = 0, name = 'absnorm', longname = 'absolute of normal distribution', extradoc = '\ndistribution of the absolute value of a normal random variable' +\ ' y=abs(x) with x N(0,1)') #copied from mvncdf.py '''multivariate normal probabilities and cumulative distribution function a wrapper for scipy.stats.kde.mvndst SUBROUTINE MVNDST( N, LOWER, UPPER, INFIN, CORREL, MAXPTS, & ABSEPS, RELEPS, ERROR, VALUE, INFORM ) * * A subroutine for computing multivariate normal probabilities. * This subroutine uses an algorithm given in the paper * "Numerical Computation of Multivariate Normal Probabilities", in * J. of Computational and Graphical Stat., 1(1992), pp. 141-149, by * Alan Genz * Department of Mathematics * Washington State University * Pullman, WA 99164-3113 * Email : AlanGenz@wsu.edu * * Parameters * * N INTEGER, the number of variables. * LOWER REAL, array of lower integration limits. * UPPER REAL, array of upper integration limits. * INFIN INTEGER, array of integration limits flags: * if INFIN(I) < 0, Ith limits are (-infinity, infinity); * if INFIN(I) = 0, Ith limits are (-infinity, UPPER(I)]; * if INFIN(I) = 1, Ith limits are [LOWER(I), infinity); * if INFIN(I) = 2, Ith limits are [LOWER(I), UPPER(I)]. * CORREL REAL, array of correlation coefficients; the correlation * coefficient in row I column J of the correlation matrix * should be stored in CORREL( J + ((I-2)*(I-1))/2 ), for J < I. * THe correlation matrix must be positive semidefinite. * MAXPTS INTEGER, maximum number of function values allowed. This * parameter can be used to limit the time. A sensible * strategy is to start with MAXPTS = 1000*N, and then * increase MAXPTS if ERROR is too large. * ABSEPS REAL absolute error tolerance. * RELEPS REAL relative error tolerance. * ERROR REAL estimated absolute error, with 99% confidence level. * VALUE REAL estimated value for the integral * INFORM INTEGER, termination status parameter: * if INFORM = 0, normal completion with ERROR < EPS; * if INFORM = 1, completion with ERROR > EPS and MAXPTS * function vaules used; increase MAXPTS to * decrease ERROR; * if INFORM = 2, N > 500 or N < 1. * >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[10.0,10.0],[0,0],[0.5]) (2e-016, 1.0, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[100.0,100.0],[0,0],[0.0]) (2e-016, 1.0, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[1.0,1.0],[0,0],[0.0]) (2e-016, 0.70786098173714096, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[0.001,1.0],[0,0],[0.0]) (2e-016, 0.42100802096993045, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[0.001,10.0],[0,0],[0.0]) (2e-016, 0.50039894221391101, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[0.001,100.0],[0,0],[0.0]) (2e-016, 0.50039894221391101, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[0.01,100.0],[0,0],[0.0]) (2e-016, 0.5039893563146316, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[0.1,100.0],[0,0],[0.0]) (2e-016, 0.53982783727702899, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[0.1,100.0],[2,2],[0.0]) (2e-016, 0.019913918638514494, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[0.0,0.0],[0,0],[0.0]) (2e-016, 0.25, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[0.0,0.0],[-1,0],[0.0]) (2e-016, 0.5, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[0.0,0.0],[-1,0],[0.5]) (2e-016, 0.5, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[0.0,0.0],[0,0],[0.5]) (2e-016, 0.33333333333333337, 0) >>> scipy.stats.kde.mvn.mvndst([0.0,0.0],[0.0,0.0],[0,0],[0.99]) (2e-016, 0.47747329317779391, 0) ''' #from scipy.stats import kde informcode = {0: 'normal completion with ERROR < EPS', 1: '''completion with ERROR > EPS and MAXPTS function values used; increase MAXPTS to decrease ERROR;''', 2: 'N > 500 or N < 1'}
[docs]def mvstdnormcdf(lower, upper, corrcoef, **kwds): '''standardized multivariate normal cumulative distribution function This is a wrapper for scipy.stats.kde.mvn.mvndst which calculates a rectangular integral over a standardized multivariate normal distribution. This function assumes standardized scale, that is the variance in each dimension is one, but correlation can be arbitrary, covariance = correlation matrix Parameters ---------- lower, upper : array_like, 1d lower and upper integration limits with length equal to the number of dimensions of the multivariate normal distribution. It can contain -np.inf or np.inf for open integration intervals corrcoef : float or array_like specifies correlation matrix in one of three ways, see notes optional keyword parameters to influence integration * maxpts : int, maximum number of function values allowed. This parameter can be used to limit the time. A sensible strategy is to start with `maxpts` = 1000*N, and then increase `maxpts` if ERROR is too large. * abseps : float absolute error tolerance. * releps : float relative error tolerance. Returns ------- cdfvalue : float value of the integral Notes ----- The correlation matrix corrcoef can be given in 3 different ways If the multivariate normal is two-dimensional than only the correlation coefficient needs to be provided. For general dimension the correlation matrix can be provided either as a one-dimensional array of the upper triangular correlation coefficients stacked by rows, or as full square correlation matrix See Also -------- mvnormcdf : cdf of multivariate normal distribution without standardization Examples -------- >>> print(mvstdnormcdf([-np.inf,-np.inf], [0.0,np.inf], 0.5)) 0.5 >>> corr = [[1.0, 0, 0.5],[0,1,0],[0.5,0,1]] >>> print(mvstdnormcdf([-np.inf,-np.inf,-100.0], [0.0,0.0,0.0], corr, abseps=1e-6)) 0.166666399198 >>> print(mvstdnormcdf([-np.inf,-np.inf,-100.0],[0.0,0.0,0.0],corr, abseps=1e-8)) something wrong completion with ERROR > EPS and MAXPTS function values used; increase MAXPTS to decrease ERROR; 1.048330348e-006 0.166666546218 >>> print(mvstdnormcdf([-np.inf,-np.inf,-100.0],[0.0,0.0,0.0], corr, \ maxpts=100000, abseps=1e-8)) 0.166666588293 ''' n = len(lower) #don't know if converting to array is necessary, #but it makes ndim check possible lower = np.array(lower) upper = np.array(upper) corrcoef = np.array(corrcoef) correl = np.zeros(int(n*(n-1)/2.0)) #dtype necessary? if (lower.ndim != 1) or (upper.ndim != 1): raise ValueError('can handle only 1D bounds') if len(upper) != n: raise ValueError('bounds have different lengths') if n==2 and corrcoef.size==1: correl = corrcoef #print 'case scalar rho', n elif corrcoef.ndim == 1 and len(corrcoef) == n*(n-1)/2.0: #print 'case flat corr', corrcoeff.shape correl = corrcoef elif corrcoef.shape == (n,n): #print 'case square corr', correl.shape correl = corrcoef[np.tril_indices(n, -1)] # for ii in range(n): # for jj in range(ii): # correl[ jj + ((ii-2)*(ii-1))/2] = corrcoef[ii,jj] else: raise ValueError('corrcoef has incorrect dimension') if not 'maxpts' in kwds: if n >2: kwds['maxpts'] = 10000*n lowinf = np.isneginf(lower) uppinf = np.isposinf(upper) infin = 2.0*np.ones(n) np.putmask(infin,lowinf,0)# infin.putmask(0,lowinf) np.putmask(infin,uppinf,1) #infin.putmask(1,uppinf) #this has to be last np.putmask(infin,lowinf*uppinf,-1) ## #remove infs ## np.putmask(lower,lowinf,-100)# infin.putmask(0,lowinf) ## np.putmask(upper,uppinf,100) #infin.putmask(1,uppinf) #print lower,',',upper,',',infin,',',correl #print correl.shape #print kwds.items() error, cdfvalue, inform = scipy.stats.kde.mvn.mvndst(lower,upper,infin,correl,**kwds) if inform: print('something wrong', informcode[inform], error) return cdfvalue
[docs]def mvnormcdf(upper, mu, cov, lower=None, **kwds): '''multivariate normal cumulative distribution function This is a wrapper for scipy.stats.kde.mvn.mvndst which calculates a rectangular integral over a multivariate normal distribution. Parameters ---------- lower, upper : array_like, 1d lower and upper integration limits with length equal to the number of dimensions of the multivariate normal distribution. It can contain -np.inf or np.inf for open integration intervals mu : array_lik, 1d list or array of means cov : array_like, 2d specifies covariance matrix optional keyword parameters to influence integration * maxpts : int, maximum number of function values allowed. This parameter can be used to limit the time. A sensible strategy is to start with `maxpts` = 1000*N, and then increase `maxpts` if ERROR is too large. * abseps : float absolute error tolerance. * releps : float relative error tolerance. Returns ------- cdfvalue : float value of the integral Notes ----- This function normalizes the location and scale of the multivariate normal distribution and then uses `mvstdnormcdf` to call the integration. See Also -------- mvstdnormcdf : location and scale standardized multivariate normal cdf ''' upper = np.array(upper) if lower is None: lower = -np.ones(upper.shape) * np.inf else: lower = np.array(lower) cov = np.array(cov) stdev = np.sqrt(np.diag(cov)) # standard deviation vector #do I need to make sure stdev is float and not int? #is this correct to normalize to corr? lower = (lower - mu)/stdev upper = (upper - mu)/stdev divrow = np.atleast_2d(stdev) corr = cov/divrow/divrow.T #v/np.sqrt(np.atleast_2d(np.diag(covv)))/np.sqrt(np.atleast_2d(np.diag(covv))).T return mvstdnormcdf(lower, upper, corr, **kwds)