[feat]: compatability of r4ss::ss_output object into convert_output

[Schiano-NOAA]

This feature adds another functionality to allow users to input the "converted" output from a stock synthesis model that is run through the function ss_output in {r4ss}. This provides users multiple ways to convert the output for a stock synthesis model in the case they only have one or the other.

[github-actions]

New version checklist

• Package version in DESCRIPTION has been updated
• Release notes have been drafted/published
• Cheatsheet content has been updated (if applicable)
• Cheatsheet version has been updated

[github-actions]

Code Metrics Report

Coverage	Code to Test Ratio	Test Execution Time
66.2%	1:0.1	7m33s

Code coverage of files in pull request scope (47.6%)

Files	Coverage
R/convert_output.R	47.6%

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Reported by octocov

[Schiano-NOAA]

Remaining todo:

• Make alternative naming conventions sheet for r4ss names ---> no need now
• Testing on other SS3 examples
• ID why single_vals are not being added to conout
• Add version check --> no need now

[Copilot]

Pull request overview

This PR extends convert_output() to accept an r4ss::ss_output (list-like) object in addition to file-path inputs, and adds a regression test plus variable-name mappings to support this new input path.

Changes:

• Add support for r4ss::ss_output-style list inputs to be processed as SS3 output.
• Add a test fixture-based check that convert_output() can run on an r4ss object without error.
• Extend ss3_var_names.csv with additional label mappings for SS3/r4ss-derived fields.

Reviewed changes

Copilot reviewed 3 out of 4 changed files in this pull request and generated 4 comments.

File	Description
R/convert_output.R	Adds SS3 handling for list inputs (r4ss output) and adjusts parsing/normalization paths.
tests/testthat/test-convert_output.R	Adds a new test that exercises convert_output() with an r4ss object fixture.
inst/resources/ss3_var_names.csv	Adds/updates SS3 variable name mappings to support additional labels.

Comments suppressed due to low confidence (1)

R/convert_output.R:540

• grepl("?_month_[0-9]_?", ...) / grepl("?_area_[0-9]_?", ...) start with ?, which is an invalid regex ("nothing to repeat") in R. This can emit warnings or fail label normalization; the intended optional underscore should be expressed as _?.

                  label = dplyr::case_when(
                    grepl("?_month_[0-9]_?", label) ~ stringr::str_replace(label, "_?month_\\d?", ""),
                    grepl("?_area_[0-9]_?", label) ~ stringr::str_replace(label, "_?area_\\d?", ""),
                    TRUE ~ stringr::str_extract(label, "^.*?(?=_\\d|_gp|_fem|_mal|_sx|:|$)")

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[sbreitbart-NOAA]

@Schiano-NOAA I see your checklist above isn't fully checked-off. Still ready for a review?

[Schiano-NOAA]

@sbreitbart-NOAA oh thanks! Let me add a check for the version, otherwise feel free to review. I'm fairly confident this will work for all models.

[Schiano-NOAA]

@sbreitbart-NOAA good to go for review! I think all is well here

[sbreitbart-NOAA]

Most testing works well and quickly! Two plots don't work with the r4ss sample data, though: plot_abundance_at_age() and plot_biomass_at_age(). Both give this error:

plot_abundance_at_age(r4_out)
! Multiple module names found in data. 
ℹ Selection bypassed. Filtering by recruit.
Error in `column_data[[1]]` at stockplotr/R/process_data.R:305:5:
! Can't extract columns past the end.
ℹ Location 1 doesn't exist.
ℹ There are only 0 columns.
Run `rlang::last_trace()` to see where the error occurred.

[Schiano-NOAA]

@sbreitbart-NOAA thanks for looking at this! I will see what is going on and make adjustments 👍