nmfs-ost / nmfs-ost/SSMSE

Two model input settings that aren't supported

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Dominant language
R
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Description

I finally took some time to work on issues identified by @JuanMatiasBraccini while testing the changes in PR https://github.com/nmfs-ost/SSMSE/pull/234 (now merged to the main branch).

I found 2 issues that caused problems (but informative error messages weren't being reported so it took some digging).

  1. the month (formerly seas) column in the CPUE input gets converted from 1 to 7 between the input data file and the data_echo.ss_new file and this mismatch causes problems in the check_avail_dat() function. Changing the input file to use month = 7 fixed it but a better error would be helpful.
  2. there are time-varying CPUE parameters with AUTOGEN = 0 in the control file. The AUTOGEN setting gets changed but the required parameter lines don't get added, causing an error. Copying the time-varying parameters from control.ss_new into the original input fixed the issue but a better solution would be helpful.

@JuanMatiasBraccini, let me know if you have any problems with these work-arounds or if they don't get the revised SSMSE working for you.

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the two cases described in the issue and compare the input data with data_echo.ss_new and control.ss_new. Inspect check_avail_dat() and the handling of time-varying CPUE parameters with AUTOGEN = 0. Done means both inputs are handled correctly and failures report an informative error instead of requiring manual workarounds.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
45/100

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