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@ -1,12 +1,14 @@
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import warnings
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from numpy import r_, minimum, maximum, atleast_1d, atleast_2d, mod, ones, floor, \
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random, eye, nonzero, where, repeat, sqrt, exp, inf, diag, zeros, sin, arcsin, nan #@UnresolvedImport
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from numpy import triu #@UnresolvedImport
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from scipy.special import ndtr as cdfnorm, ndtri as invnorm
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from wafo import mvn
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import numpy as np
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import numpy as np
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from numpy import (r_, minimum, maximum, atleast_1d, atleast_2d, mod, zeros, #@UnresolvedImport
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ones, floor, random, eye, nonzero, repeat, sqrt, exp, inf, diag, triu) #@UnresolvedImport
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from scipy.special import ndtri as invnorm
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from scipy.special import ndtr as cdfnorm
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import wafo.rindmod as rindmod
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import wafo.mvnprdmod as mvnprdmod
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import wafo.mvnprdmod as mvnprdmod
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from wafo import mvn
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import wafo.rindmod as rindmod
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import warnings
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from wafo.misc import common_shape
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from scipy.stats.stats import erfc
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class Rind(object):
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class Rind(object):
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'''
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'''
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@ -22,7 +24,7 @@ class Rind(object):
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Lower and upper barriers used to compute the integration limits, Hlo and Hup, respectively.
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Lower and upper barriers used to compute the integration limits, Hlo and Hup, respectively.
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indI : array-like, length Ni
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indI : array-like, length Ni
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vector of indices to the different barriers in the indicator function.
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vector of indices to the different barriers in the indicator function.
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(NB! restriction indI(1)=0, indI(NI)=Nt+Nd, Ni = Nb+1)
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(NB! restriction indI(1)=-1, indI(NI)=Nt+Nd, Ni = Nb+1)
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(default indI = 0:Nt+Nd)
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(default indI = 0:Nt+Nd)
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xc : values to condition on (default xc = zeros(0,1)), size Nc x Nx
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xc : values to condition on (default xc = zeros(0,1)), size Nc x Nx
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Nt : size of Xt (default Nt = Ntdc - Nc)
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Nt : size of Xt (default Nt = Ntdc - Nc)
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@ -361,7 +363,7 @@ def test_rind():
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Blo[0, ind] = maximum(Blo[0, ind], -infinity * dev[indI[ind + 1]])
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Blo[0, ind] = maximum(Blo[0, ind], -infinity * dev[indI[ind + 1]])
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E3 = rind(Sc, m, Blo, Bup, indI, xc, nt=1)
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E3 = rind(Sc, m, Blo, Bup, indI, xc, nt=1)
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def cdflomax(x,alpha,m0):
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def cdflomax(x, alpha, m0):
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'''
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'''
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Return CDF for local maxima for a zero-mean Gaussian process
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Return CDF for local maxima for a zero-mean Gaussian process
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@ -412,11 +414,11 @@ def cdflomax(x,alpha,m0):
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--------
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--------
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spec2mom, spec2bw
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spec2mom, spec2bw
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'''
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'''
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c1 = 1.0/(sqrt(1-alpha**2))*x/sqrt(m0)
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c1 = 1.0 / (sqrt(1 - alpha ** 2)) * x / sqrt(m0)
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c2 = alpha*c1
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c2 = alpha * c1
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return cdfnorm(c1)-alpha*exp(-x**2/2/m0)*cdfnorm(c2)
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return cdfnorm(c1) - alpha * exp(-x ** 2 / 2 / m0) * cdfnorm(c2)
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def prbnormtndpc(rho,a,b,D=None,df=0,abseps=1e-4,IERC=0,HNC=0.24):
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def prbnormtndpc(rho, a, b, D=None, df=0, abseps=1e-4, IERC=0, HNC=0.24):
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'''
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'''
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Return Multivariate normal or T probability with product correlation structure.
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Return Multivariate normal or T probability with product correlation structure.
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@ -490,11 +492,11 @@ def prbnormtndpc(rho,a,b,D=None,df=0,abseps=1e-4,IERC=0,HNC=0.24):
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if D is None:
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if D is None:
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D = zeros(len(rho))
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D = zeros(len(rho))
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# Make sure integration limits are finite
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# Make sure integration limits are finite
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A = np.clip(a-D,-100,100)
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A = np.clip(a - D, -100, 100)
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B = np.clip(b-D,-100,100)
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B = np.clip(b - D, -100, 100)
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return mvnprdmod.prbnormtndpc(rho,A,B,df,abseps,IERC,HNC)
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return mvnprdmod.prbnormtndpc(rho, A, B, df, abseps, IERC, HNC)
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def prbnormndpc(rho,a,b,abserr=1e-4,relerr=1e-4,usesimpson=True, usebreakpoints=False):
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def prbnormndpc(rho, a, b, abserr=1e-4, relerr=1e-4, usesimpson=True, usebreakpoints=False):
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'''
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'''
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Return Multivariate Normal probabilities with product correlation
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Return Multivariate Normal probabilities with product correlation
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@ -552,15 +554,15 @@ def prbnormndpc(rho,a,b,abserr=1e-4,relerr=1e-4,usesimpson=True, usebreakpoints=
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'''
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'''
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# Call fortran implementation
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# Call fortran implementation
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val,err,ier = mvnprdmod.prbnormndpc(rho,a,b,abserr,relerr,usebreakpoints,usesimpson);
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val, err, ier = mvnprdmod.prbnormndpc(rho, a, b, abserr, relerr, usebreakpoints, usesimpson);
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if ier>0:
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if ier > 0:
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warnings.warn('Abnormal termination ier = %d\n\n%s' % (ier,_ERRORMESSAGE[ier]))
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warnings.warn('Abnormal termination ier = %d\n\n%s' % (ier, _ERRORMESSAGE[ier]))
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return val, err, ier
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return val, err, ier
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_ERRORMESSAGE = {}
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_ERRORMESSAGE = {}
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_ERRORMESSAGE[0] = ''
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_ERRORMESSAGE[0] = ''
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_ERRORMESSAGE[1] ='''
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_ERRORMESSAGE[1] = '''
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Maximum number of subdivisions allowed has been achieved. one can allow
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Maximum number of subdivisions allowed has been achieved. one can allow
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more subdivisions by increasing the value of limit (and taking the
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more subdivisions by increasing the value of limit (and taking the
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according dimension adjustments into account). however, if this yields
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according dimension adjustments into account). however, if this yields
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@ -571,27 +573,27 @@ _ERRORMESSAGE[1] ='''
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the vector points. If necessary an appropriate special-purpose integrator
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the vector points. If necessary an appropriate special-purpose integrator
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must be used, which is designed for handling the type of difficulty involved.
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must be used, which is designed for handling the type of difficulty involved.
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'''
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'''
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_ERRORMESSAGE[2] ='''
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_ERRORMESSAGE[2] = '''
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the occurrence of roundoff error is detected, which prevents the requested
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the occurrence of roundoff error is detected, which prevents the requested
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tolerance from being achieved. The error may be under-estimated.'''
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tolerance from being achieved. The error may be under-estimated.'''
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_ERRORMESSAGE[3] ='''
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_ERRORMESSAGE[3] = '''
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Extremely bad integrand behaviour occurs at some points of the integration interval.'''
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Extremely bad integrand behaviour occurs at some points of the integration interval.'''
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_ERRORMESSAGE[4] ='''
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_ERRORMESSAGE[4] = '''
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The algorithm does not converge. Roundoff error is detected in the extrapolation table.
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The algorithm does not converge. Roundoff error is detected in the extrapolation table.
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It is presumed that the requested tolerance cannot be achieved, and that
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It is presumed that the requested tolerance cannot be achieved, and that
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the returned result is the best which can be obtained.'''
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the returned result is the best which can be obtained.'''
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_ERRORMESSAGE[5] ='''
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_ERRORMESSAGE[5] = '''
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The integral is probably divergent, or slowly convergent.
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The integral is probably divergent, or slowly convergent.
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It must be noted that divergence can occur with any other value of ier>0.'''
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It must be noted that divergence can occur with any other value of ier>0.'''
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_ERRORMESSAGE[6] ='''the input is invalid because:
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_ERRORMESSAGE[6] = '''the input is invalid because:
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1) npts2 < 2
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1) npts2 < 2
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2) break points are specified outside the integration range
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2) break points are specified outside the integration range
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3) (epsabs<=0 and epsrel<max(50*rel.mach.acc.,0.5d-28))
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3) (epsabs<=0 and epsrel<max(50*rel.mach.acc.,0.5d-28))
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4) limit < npts2.'''
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4) limit < npts2.'''
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def prbnormnd(correl,a,b,abseps=1e-4,releps=1e-3,maxpts=None,method=0):
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def prbnormnd(correl, a, b, abseps=1e-4, releps=1e-3, maxpts=None, method=0):
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'''
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'''
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Multivariate Normal probability by Genz' algorithm.
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Multivariate Normal probability by Genz' algorithm.
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@ -628,19 +630,30 @@ def prbnormnd(correl,a,b,abseps=1e-4,releps=1e-3,maxpts=None,method=0):
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decrease ERROR;
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decrease ERROR;
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if INFORM = 2, N > NMAX or N < 1. where NMAX depends on the
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if INFORM = 2, N > NMAX or N < 1. where NMAX depends on the
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integration method
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integration method
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Example:% Compute the probability that X1<0,X2<0,X3<0,X4<0,X5<0,
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Example
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% Xi are zero-mean Gaussian variables with variances one
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-------
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% and correlations Cov(X(i),X(j))=0.3:
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Compute the probability that X1<0,X2<0,X3<0,X4<0,X5<0,
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% indI=[0 5], and barriers B_lo=[-inf 0], B_lo=[0 inf]
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Xi are zero-mean Gaussian variables with variances one
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% gives H_lo = [-inf -inf -inf -inf -inf] H_lo = [0 0 0 0 0]
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and correlations Cov(X(i),X(j))=0.3:
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indI=[0 5], and barriers B_lo=[-inf 0], B_lo=[0 inf]
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gives H_lo = [-inf -inf -inf -inf -inf] H_lo = [0 0 0 0 0]
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N = 5; rho=0.3; NIT=3; Nt=N; indI=[0 N];
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>>> Et = 0.001946 # # exact prob.
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B_lo=-10; B_up=0; m=1.2*ones(N,1);
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>>> n = 5; nt = n
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Sc=(ones(N)-eye(N))*rho+eye(N);
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>>> Blo =-np.inf; Bup=0; indI=[-1, n-1] # Barriers
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E = rind(Sc,m,B_lo,B_up,indI,[],Nt) % exact prob. 0.00195
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>>> m = 1.2*np.ones(n); rho = 0.3;
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A = [-inf -inf -inf -inf -inf],
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>>> Sc =(np.ones((n,n))-np.eye(n))*rho+np.eye(n)
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B = [0 0 0 0 0]-m'
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>>> rind = Rind()
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[val,err,inform] = prbnormnd(Sc,A,B);
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>>> E0, err0, terr0 = rind(Sc,m,Blo,Bup,indI, nt=nt)
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>>> A = np.repeat(Blo,n)
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>>> B = np.repeat(Bup,n)-m
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>>> [val,err,inform] = prbnormnd(Sc,A,B);val;err;inform
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>>> np.abs(val-Et)< err0+terr0
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array([ True], dtype=bool)
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>>> 'val = %2.6f' % val
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'val = 0.001945'
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See also
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See also
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--------
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--------
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@ -648,16 +661,16 @@ def prbnormnd(correl,a,b,abseps=1e-4,releps=1e-3,maxpts=None,method=0):
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'''
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'''
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m,n = correl.shape
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m, n = correl.shape
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Na = len(a)
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Na = len(a)
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Nb = len(b)
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Nb = len(b)
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if (m!=n or m!=Na or m!=Nb):
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if (m != n or m != Na or m != Nb):
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raise ValueError('Size of input is inconsistent!')
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raise ValueError('Size of input is inconsistent!')
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if maxpts is None:
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if maxpts is None:
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maxpts = 1000*n
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maxpts = 1000 * n
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maxpts = max(round(maxpts),10*n);
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maxpts = max(round(maxpts), 10 * n);
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# % array of correlation coefficients; the correlation
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# % array of correlation coefficients; the correlation
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# % coefficient in row I column J of the correlation matrix
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# % coefficient in row I column J of the correlation matrix
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@ -665,16 +678,21 @@ def prbnormnd(correl,a,b,abseps=1e-4,releps=1e-3,maxpts=None,method=0):
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# % The correlation matrix must be positive semidefinite.
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# % The correlation matrix must be positive semidefinite.
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D = np.diag(correl)
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D = np.diag(correl)
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if (any(D!=1)):
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if (any(D != 1)):
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raise ValueError('This is not a correlation matrix')
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raise ValueError('This is not a correlation matrix')
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# Make sure integration limits are finite
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# Make sure integration limits are finite
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A = np.clip(a,-100,100)
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A = np.clip(a, -100, 100)
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B = np.clip(b,-100, 100)
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B = np.clip(b, -100, 100)
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ix = np.where(np.triu(np.ones((m, m)), 1) != 0)
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L = correl[ix].ravel() #% return only off diagonal elements
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infinity = 37
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infin = np.repeat(2, n) - (B > infinity) - 2 * (A < -infinity)
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err, val, inform = mvn.mvndst(A, B, infin, L, maxpts, abseps, releps)
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#L = correl((triu(ones(m),1)~=0)); % return only off diagonal elements
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return val, err, inform
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return mvn.mvnun(A,B, correl,maxpts, abseps, releps)
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#CALL the mexroutine
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#CALL the mexroutine
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# t0 = clock;
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# t0 = clock;
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@ -688,7 +706,253 @@ def prbnormnd(correl,a,b,abseps=1e-4,releps=1e-3,maxpts=None,method=0):
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# [value, err,inform] = mexGenzMvnPrb(L,A,B,abseps,releps,maxpts,method);
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# [value, err,inform] = mexGenzMvnPrb(L,A,B,abseps,releps,maxpts,method);
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# end
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# end
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# exTime = etime(clock,t0);
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# exTime = etime(clock,t0);
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#
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# '
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#% gauss legendre points and weights, n = 6
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_W6 = [ 0.1713244923791705e+00, 0.3607615730481384e+00, 0.4679139345726904e+00]
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_X6 = [-0.9324695142031522e+00, -0.6612093864662647e+00, -0.2386191860831970e+00]
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#% gauss legendre points and weights, n = 12
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_W12 = [ 0.4717533638651177e-01, 0.1069393259953183e+00, 0.1600783285433464e+00,
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0.2031674267230659e+00, 0.2334925365383547e+00, 0.2491470458134029e+00]
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_X12 = [ -0.9815606342467191e+00, -0.9041172563704750e+00, -0.7699026741943050e+00,
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- 0.5873179542866171e+00, -0.3678314989981802e+00, -0.1252334085114692e+00]
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#% gauss legendre points and weights, n = 20
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_W20 = [ 0.1761400713915212e-01, 0.4060142980038694e-01,
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0.6267204833410906e-01, 0.8327674157670475e-01,
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0.1019301198172404e+00, 0.1181945319615184e+00,
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0.1316886384491766e+00, 0.1420961093183821e+00,
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0.1491729864726037e+00, 0.1527533871307259e+00]
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_X20 = [ -0.9931285991850949e+00, -0.9639719272779138e+00,
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- 0.9122344282513259e+00, -0.8391169718222188e+00,
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- 0.7463319064601508e+00, -0.6360536807265150e+00,
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- 0.5108670019508271e+00, -0.3737060887154196e+00,
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- 0.2277858511416451e+00, -0.7652652113349733e-01]
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def cdfnorm2d(b1, b2, r):
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'''
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Returnc Bivariate Normal cumulative distribution function
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Parameters
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----------
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b1, b2 : array-like
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upper integration limits
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r : real scalar
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correlation coefficient (-1 <= r <= 1).
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Returns
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-------
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bvn : ndarray
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distribution function evaluated at b1, b2.
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Notes
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-----
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CDFNORM2D computes bivariate normal probabilities, i.e., the probability
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Prob(X1 <= B1 and X2 <= B2) with an absolute error less than 1e-15.
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This function is based on the method described by Drezner, z and
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G.O. Wesolowsky, (1989), with major modifications for double precision,
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and for |r| close to 1.
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Example
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-------
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>>> x = np.linspace(-5,5,20)
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>>> [B1,B2] = np.meshgrid(x, x)
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>>> r = 0.3;
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>>> F = cdfnorm2d(B1,B2,r);
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surf(x,x,F)
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See also
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cdfnorm
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Reference
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---------
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Drezner, z and g.o. Wesolowsky, (1989),
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"On the computation of the bivariate normal integral",
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Journal of statist. comput. simul. 35, pp. 101-107,
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'''
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# Translated into Python
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# Per A. Brodtkorb
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#
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# Original code
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# by alan genz
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# department of mathematics
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# washington state university
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# pullman, wa 99164-3113
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# email : alangenz@wsu.edu
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cshape = common_shape(b1, b2, r, shape=[1, ])
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one = ones(cshape)
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h, k, r = (-b1 * one).ravel(), (-b2 * one).ravel(), (r * one).ravel()
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bvn = where(abs(r) > 1, nan, 0.0)
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two = 2.e0;
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twopi = 6.283185307179586e0;
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hk = h * k
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k0, = nonzero(abs(r) < 0.925e0)
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if len(k0) > 0:
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hs = (h[k0] ** 2 + k[k0] ** 2) / two
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asr = arcsin(r[k0])
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k1, = nonzero(r[k0] >= 0.75)
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if len(k1) > 0:
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k01 = k0[k1]
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for i in range(10):
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for sign in - 1, 1:
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sn = sin(asr[k1] * (sign * _X20[i] + 1) / 2)
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bvn[k01] = bvn[k01] + _W20[i] * exp((sn * hk[k01] - hs[k1]) / (1 - sn * sn));
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k1, = nonzero((0.3 <= r[k0]) & (r[k0] < 0.75))
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if len(k1) > 0:
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k01 = k0[k1];
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for i in range(6):
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for sign in - 1, 1:
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sn = sin(asr[k1] * (sign * _X12[i] + 1) / 2);
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bvn[k01] = bvn[k01] + _W12[i] * exp((sn * hk[k01] - hs[k1]) / (1 - sn * sn));
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k1, = nonzero(r[k0] < 0.3);
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if len(k1) > 0:
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k01 = k0[k1]
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for i in range(3):
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for sign in - 1, 1:
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sn = sin(asr[k1] * (sign * _X6[i] + 1) / 2)
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bvn[k01] = bvn[k01] + _W6[i] * exp((sn * hk[k01] - hs[k1]) / (1 - sn * sn))
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bvn[k0] *= asr / (two * twopi)
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bvn[k0] += fi(-h[k0]) * fi(-k[k0])
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k1, = nonzero((0.925 <= abs(r)) & (abs(r) <= 1));
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if len(k1) > 0:
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k2, = nonzero(r[k1] < 0);
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if len(k2) > 0:
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k12 = k1[k2];
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k[k12] = -k[k12];
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hk[k12] = -hk[k12];
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k3, = nonzero(abs(r[k1]) < 1);
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if len(k3) > 0:
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k13 = k1[k3];
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a2 = (1 - r[k13]) * (1 + r[k13]);
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a = sqrt(a2)
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b = abs(h[k13] - k[k13]);
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bs = b * b;
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c = (4.e0 - hk[k13]) / 8.e0;
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d = (12.e0 - hk[k13]) / 16.e0;
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asr = -(bs / a2 + hk[k13]) / 2.e0;
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k4, = nonzero(asr > -100.e0);
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if len(k4) > 0:
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bvn[k13[k4]] = a[k4] * exp(asr[k4]) * (1 - c[k4] *
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(bs[k4] - a2[k4]) * (1 - d[k4] * bs[k4] / 5) / 3
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+ c[k4] * d[k4] * a2[k4] ** 2 / 5);
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k5, = nonzero(hk[k13] < 100.e0);
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if len(k5) > 0:
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#% b = sqrt(bs);
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k135 = k13[k5];
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bvn[k135] = bvn[k135] - exp(-hk[k135] / 2) * sqrt(twopi) * fi(-b[k5] / a[k5]) * b[k5] * (1 - c[k5] * bs[k5] * (1 - d[k5] * bs[k5] / 5) / 3)
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a /= two
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for i in range(10):
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for sign in - 1, 1:
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xs = (a * (sign * _X20[i] + 1)) ** 2;
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rs = sqrt(1 - xs);
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asr = -(bs / xs + hk[k13]) / 2;
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k6, = nonzero(asr > -100.e0) ;
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if len(k6) > 0:
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k136 = k13[k6]
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bvn[k136] += (a[k6] * _W20[i] * exp(asr[k6]) *
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(exp(-hk[k136] * (1 - rs[k6]) / (2 * (1 + rs[k6]))) / rs[k6] -
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(1 + c[k6] * xs[k6] * (1 + d[k6] * xs[k6]))))
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bvn[k3] = -bvn[k3] / twopi;
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k7, = nonzero(r[k1] > 0);
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if len(k7):
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k17 = k1[k7]
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bvn[k17] += fi(-np.maximum(h[k17], k[k17]));
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k8, = nonzero(r[k1] < 0);
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if len(k8) > 0:
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k18 = k1[k8];
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bvn[k18] = -bvn[k18] + np.maximum(0, fi(-h[k18]) - fi(-k[k18]));
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bvn.shape = cshape
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return bvn
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def fi(x):
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return 0.5 * (erfc((-x) / sqrt(2)))
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def prbnorm2d(a, b, r):
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'''
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Returns Bivariate Normal probability
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Parameters
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---------
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a, b : array-like, size==2
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vector with lower and upper integration limits, respectively.
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r : real scalar
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correlation coefficient
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Returns
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-------
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prb : real scalar
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computed probability Prob(A[0] <= X1 <= B[0] and A[1] <= X2 <= B[1])
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with an absolute error less than 1e-15.
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Example
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-------
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>>> a = [-1, -2]
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>>> b = [1, 1]
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>>> r = 0.3
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>>> prbnorm2d(a,b,r)
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See also
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--------
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cdfnorm2d,
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cdfnorm,
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prbnormndpc
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'''
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infinity = 37
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lower = np.asarray(a)
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upper = np.asarray(b)
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if np.all((lower <= -infinity) & (infinity<=upper)):
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return 1.0
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if (lower >= upper).any():
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return 0.0
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correl = r
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infin = np.repeat(2, 2) - (upper > infinity) - 2 * (lower < -infinity)
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if np.all(infin == 2):
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return (bvd(lower[0], lower[1], correl)
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- bvd(upper[0], lower[1], correl)
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- bvd(lower[0], upper[1], correl)
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+ bvd(upper[0], upper[1], correl))
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elif (infin[0] == 2 and infin[1] == 1):
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return bvd(lower[0], lower[1], correl) - bvd(upper[0], lower[1], correl)
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elif (infin[0] == 1 and infin[1] == 2) :
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return bvd(lower[0], lower[1], correl) - bvd(lower[0], upper[1], correl)
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elif (infin[0] == 2 and infin[1] == 0) :
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return bvd(-upper[0], -upper[1], correl) - bvd(-lower[0], -upper[1], correl)
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elif (infin[0] == 0 and infin[1] == 2):
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return bvd(-upper[0], -upper[1], correl) - bvd(-upper[0], -lower[1], correl)
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elif (infin[0] == 1 and infin[1] == 0) :
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return bvd(lower[0], -upper[1], -correl)
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elif (infin[0] == 0 and infin[1] == 1) :
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return bvd(-upper[0], lower[1], -correl)
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elif (infin[0] == 1 and infin[1] == 1):
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return bvd(lower[0], lower[1], correl)
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elif (infin[0] == 0 and infin[1] == 0) :
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return bvd(-upper[0], -upper[1], correl)
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return 1
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def bvd(lo, up, r):
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return cdfnorm2d(-lo, -up, r)
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if __name__ == '__main__':
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if __name__ == '__main__':
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if False: #True: #
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if False: #True: #
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|