[SciPy-user] computing Bayesian credible intervals : help on constrained optimisation schemes?
Mon May 5 10:13:09 CDT 2008
I think that you need an alternative approach here because:
1) The Poisson is a discrete distribution not continuous (so can not use
2) The Poisson is also a skewed distribution so finding points such that
p(a)=p(b) is impossible unless the Poisson parameter is sufficiently large.
3) Depending on the parameters, it is impossible to get exact
probabilities like 5% or 95% from discrete distributions.
These issues probably are reflected in the reported problems.
Depending on your parameter and hence how accurate do you want for your
interval, Normal/Gaussian can provide a suitable approximation.
If you must stay with the Poisson, you need to solve it by brute force
and allow for p(a) != p(b).
> I have tried to solve your problem via openopt.NSLP solver nssolve &
> openopt.GLP solver galileo, both give maxResidual=0.885, that is far
> from desired zero, so your system (with required non-negative solution)
> seems to have no solution.
> As for using fsolve or other smooth-funcs intended tools, it (AFAIK) is
> senseless wrt non-smooth funcs, like your numerical integration yields.
> Regards, D.
> Johann Cohen-Tanugi wrote:
>> I am attaching my script. I followed Neil's suggestion but it fails to
>> converge, due seemingly to issues with the fact that a and b must be
>> positive, which I cannot enforce with fsolve, AFAIK.
>> I am ready to dive into constrained schemes, especially in openOpt,
>> but I was hoping for some suggestions beforehand as to which path to
>> follow to solve this problem now.
>> I remind that I am trying to find a and b so that :
>> integral from a to b of p(x) = Q
>> and p(a)=p(b)
>> where Q is given (0.95 in my script) and p is a Poisson posterior pdf
>> for ON/OFF source experiments. a,b, and x are source rates, and as
>> such are positive.
>> People will have recognized the computation of a Bayesian credible
>> interval here!!
>> thanks a lot in advance,
>> Neil Martinsen-Burrell wrote:
>>> Johann Cohen-Tanugi <cohen <at> slac.stanford.edu> writes:
>>>> hi Neil, thanks for your answer and sorry I was not clear enough. Of
>>>> course I require the 2 conditions. 1) defines *a* credible interval
>>>> if p is a posterior pdf; and 2) sets a constraint that for common
>>>> situation yield *the* standard Bayesian credible interval. I will
>>>> have a look at brentq, I do not know what it refers to.
>>> scipy.optimize.brentq is Brent's method for finding a root of a given
>>> equation. Since you are looking for two values, a and b, with two
>>> then Brent's method is not appropriate (barring some symmetry-based
>>> reduction to
>>> one variable). I like to use scipy.optimize.fsolve to find roots of
>>> multivariable equations, such as
>>> def solve_me(x): # x is an array of the values you are solving for
>>> a,b = x
>>> integral_error = quad(density, a , b) - q
>>> prob_difference = density(b) - density(a)
>>> return np.array([integral_error, prob_difference])
>>> fsolve(solve_me, [0.0, 1.0]) # initial guess is a = 0, b = 1
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