revise-code-for-catchability-with-bias-correction

[Rick-Methot-NOAA]

• Resolves issue [Feature]: implement survey errtype that adds lognormal bias adjustment #535

What tests have been done?

<-- - [] Test files are in the issue. -->

What tests/review still need to be done?

needs close look by a math-stat whiz

Is there an input change for users to Stock Synthesis?

revision for T-dist

[Cole-Monnahan-NOAA]

The equations check out, although I must admit I did get a bit lost in the float options. But I feel confident the lognormal with bias correction and Q as a parameter is correct.

My minor comments are mostly about how this may break backward compatibility with t-distributions in use already.

Edit: I should add that I was also convinced by the performance in the test case in this comment.

[Rick-Methot-NOAA]

Thanks Cole for the good suggestions. I originally was going to retain T-dist exactly as you suggest. The reason I went with the distribution you reviewed is that it allowed for options >=0 to use log(surveyobs) and all options <0 would be in normal space. I have never seen anyone use the T-dist (and wish we had a database of all applications so I would know!) , so I felt that the risk was low. But the risk is not zero, so I will consider you recommendation.

[iantaylor-NOAA]

I found an email from 2020 in which Max Cardinale (@akatan999) referenced using the t-distribution for index likelihoods. It came up because the index plots in r4ss were not working correctly for t-distributed indices. I think the bug was present for at least 6 months and since nobody else reported the issue during that time, it's possible that nobody else was using the t-distribution feature.

[Rick-Methot-NOAA]

Thanks Ian. I will maintain backward compatibility.

[kellijohnson-NOAA]

We are attempting to use the t-distribution for the age-1 index of Pacific Hake abundance in the 2024 stock assessment per your recommendations @Rick-Methot-NOAA when I talked to you last year about trying to fit estimates of zero.

[kellijohnson-NOAA]

Also, regarding my review of this code. I am right in the middle of an assessment so if you need my review it will have to wait until at least next week. Sorry.

The merge-base changed after approval.