add options other than retained catch into om F search loop
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- Dominant language
- R
- Stars
- 21
- Forks
- 14
- PR merge metrics
- No merged PRs in 30d
Description
The variable https://github.com/nmfs-fish-tools/SSMSE/blob/04ae5e507abd8cdcf06206a544939538b431d40f/R/extendOM.R#L38
can be used to pick if only retained catch is used, or all dead biomass is used. However, this functionality is only available within the extend_OM, and doesn't feed through so the user can pick it, so the default is just to use the retained catch.
Give users more options on what type of catch they are fitting. This is somewhat related to the discussion on #51 , as users can add in discards to the data frame coming from the MS, but it is not currently used by SSMSE: currently only catch or catch_F (which is really catch in terms of F) , are possible to be used by SSMSE, and either of these are assumed to be JUST retained catch.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in R/extendOM.R around line 38 and trace how the retained-catch choice is passed through extend_OM and SSMSE. Review the handling of catch and catch_F, including the possible discard data mentioned in the issue. Done means users can select among the supported catch types when fitting, rather than defaulting only to retained catch.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 40/100