[ADMB Users] negative binomial density

Mollie Brooks mbrooks at ufl.edu
Mon Jan 2 19:10:44 PST 2012

I see that r is the size parameter (a.k.a. alpha or k, or the shape parameter of underlying gamma heterogeneity), but I thought I should say something about what the 10^(-120) does to the behavior.

As tau gets close to 1, r goes toward infinity, but in this version it only goes to mu/(10^-120). 
I don't know much about the precision of calculations in ADMB. 
Is mu/(10^-120) less than infinity for any value of mu>0?


On 2 Jan 2012, at 9:33 PM, Mark Maunder wrote:

> I think var = u*(1+u/alpha)=u*tau  (e.g. tau = 1.0+ u/alpha);
> So you use loglike=log_negbinomial_density(Obs,u,tau);
> -----Original Message-----
> From: users-bounces at admb-project.org [mailto:users-bounces at admb-project.org] On Behalf Of Mollie Brooks
> Sent: Monday, January 02, 2012 12:31 PM
> To: John Sibert
> Cc: ADMB Users
> Subject: Re: [ADMB Users] negative binomial density
> I wrote the documentation that is there. I'm not familiar with this parameterization, so I left out the details and only filled in the formulas I read in the code. I'll look at it more carefully and ask Dave what he would say about the code he wrote. Then I'll try to remember how to use doxygen.
> cheers,
> Mollie
> Mollie Brooks
> Ph.D. Candidate
> NSF IGERT Fellow
> Biology Department
> University of Florida
> mbrooks at ufl.edu
> http://people.biology.ufl.edu/mbrooks
> On 2 Jan 2012, at 1:42 PM, John Sibert wrote:
>> I note that the documentation of the negative binomial density 
>> functions at http://admb-project.org/documentation/api/group__PDF.html
>> is incomplete. Also the the  "overdispersion" parameter appears to be scaled to the expected value.
>> It would be helpful if someone would complete the documentation and provide some rationale for the "r" variable.
>> Thanks,
>> John
>> --
>> John Sibert
>> Emeritus Researcher, SOEST
>> University of Hawaii at Manoa
>> Visit the ADMB project http://admb-project.org/
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