Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[FEATURE] Dirichlet-multinomial likelihood for composition data #112

Open
ChristineStawitz-NOAA opened this issue May 10, 2022 · 3 comments
Assignees
Labels
kind: feature New feature or request status: wishlist this will be moved to a later milestone theme: more features
Milestone

Comments

@ChristineStawitz-NOAA
Copy link
Contributor

ChristineStawitz-NOAA commented May 10, 2022

Is your feature request related to a problem? Please describe.
A Dirichlet multinomial distribution for composition data can help capture error more accurately

Describe the solution you'd like
A clear and concise description of what you want to happen.

Describe alternatives you've considered
Plain ol multinomial or multinomial robust (with small constant added)

Describe a reference describing the statistical validity of this approach
Thorson et al. 2017. Model-based estimates of effective sample size in stock assessment models using the Dirichlet-multinomial distribution.

Describe if this is needed for a management application
???

Additional context
@iantaylor-NOAA noted in issue 136 that measures of uncertainty specified in the input data might change based on what distribution is being used. For the Dirichlet-multinomial there still needs to be an input sample size but it is unclear if we should be using the same input sample size for the Dirichlet-multinomial as we do the multinomial. Something to think about when coding and advocating for a non-standard distribution. [Moved from #136 to this issue by @kellijohnson-NOAA].

@ChristineStawitz-NOAA ChristineStawitz-NOAA added the status: wishlist this will be moved to a later milestone label May 10, 2022
@ChristineStawitz-NOAA ChristineStawitz-NOAA added this to the 2 milestone May 10, 2022
@ChristineStawitz-NOAA ChristineStawitz-NOAA self-assigned this May 10, 2022
@k-doering-NOAA
Copy link
Member

related to this is the Tweedie distribution option: nmfs-ost/ss3-source-code#266 although this hasn't seen operational use yet (to my knowledge, maybe I am incorrect). It sounds like @timjmiller would be the most informed on this.

@timjmiller
Copy link
Contributor

timjmiller commented May 10, 2022 via email

@k-doering-NOAA
Copy link
Member

Another paper regarding the statistical validity for using the dirichlet multinomial: Fisch et al. 2022. Looks like the take home message was that in the 2 stock assessments, the linear formation of the Dirichlet multinomial performed best (although there are probably some nuances I'm not capturing with the statement). Looks like @KyleShertzer-NOAA is a coauthor on this one!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
kind: feature New feature or request status: wishlist this will be moved to a later milestone theme: more features
Projects
None yet
Development

No branches or pull requests

5 participants