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nmfs-ost / ss3-doc

Source code for the Stock Synthesis manual and other documentation
https://nmfs-ost.github.io/ss3-website/
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Remove section referencing TMB model for 2DAR1 #241

Closed e-perl-NOAA closed 3 months ago

e-perl-NOAA commented 3 months ago

We were made aware that there was a reference to a TMB model for estimating rho parameters in the 2DAR1 selectivity section of the user manual that we do not support.

It seems like we will need to delete the entire section of "Using the Two-Dimensional Autoregressive Selectivity" under section 14.2 since it goes through a process for tuning the parameters.

Rick-Methot-NOAA commented 3 months ago

Let's revise, not remove. It is not that we do not support the tuning method, it is just that we do not have the tools to implement the tuning method as described. I suggest we make a more generic endorsement of tuning the variance and rho parameters per the methods in Xu et al.

iantaylor-NOAA commented 3 months ago

I'll try to reword the text and make a new pull request for discussion.

HaikunXu commented 3 months ago

I have a TMB + R code to estimate the two rho parameters. Is there a proper way to share it with SS users when they want to explore 2DAR1 selectivity?

e-perl-NOAA commented 3 months ago

If the code is on GitHub then we can easily incorporate a link to that in the User Manual.

HaikunXu commented 3 months ago

Great - I will upload the TMB code and an example R code to Github and send you the link soon.