Fix plot_biomass and update naming convention for catch in SS3 converter

[Schiano-NOAA]

Goal:

Fixing a bug identified in #185 which initially (and incorrectly) displayed biomass but it was actually catch. This makes sense since the landings and biomass plots were extremely similar.

What has been changed:

The following fixes are implemented in this PR:

• Adjust extraction of biomass from the standard output so it only pulls biomass
• Adjust standard naming conventions in the converter to be accurate to the true quantities/estimates
• Minor addition to example in table_landings (reviewer can ignore this)

The resulting plot should show biomass over time with error as a cloud if applicable. Another issue was identified when plotting multiple model results. Feel free to test on multiple results, but the primary focus is the accuracy in the estimate plotted. Issues regarding plotting multiple output on the same plot will be addressed in a new PR.

Actions:

To review this PR:

• Test the convert_output() function on a Report.sso file
• Test the plot_biomass() function using the example data sett found in the package and converted output in the first bullet
• Test plot_biomass(dat = list("a"=data1, "b"=data2)) to see if any errors occur when multiple datasets are provided

The maintainers @Schiano-NOAA and @sbreitbart-NOAA will handle any package checks and testing errors that might occur and make adjustments if there are any more issues found after these changes were made. Thanks for contributing the {stockplotr}!

[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
71.1%	1:0.1	4m47s

Code coverage of files in pull request scope (92.3%)

Files	Coverage
R/plot_biomass.R	90.1%
R/table_landings.R	95.1%

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Reported by octocov

[Schiano-NOAA]

@Ovec8hkin would you be willing to review this PR? This addressed the issue you opened regarding the plot_biomass function. It was a relatively straight forward fix and should hopefully work well now!

I tried assigning you and adding you to the repository, but your name would not populate. I will try again at another time, but for for the moment, you can either download this branch through

remotes::install_github("nmfs-ost/stockplotr@fix-biomass-plt")

or fork the repository and make adjustments on your own repo then open a PR from that.

Please perform the testing mentioned in the PR description above.

Let me know if you have any questions or are unable to do this at this time 😄

[Ovec8hkin]

@Schiano-NOAA this appears to work fine for the SPR_SERIES module but still appears to plot landings when module="TIME_SERIES". Looking at the output of the filter_data call, it seems like landings biomass is still getting into the plotting data.

[Schiano-NOAA]

@Ovec8hkin thanks for taking a look! Could you provide a reprex to show how you got the same result? Here is the process I followed and the biomass and landings are completely different:

1. Download a Report.sso file (https://www.pcouncil.org/documents/2026/01/yelloweye-rockfish-update-assessment-2025-model-files.zip/)
2. Run the following code

devtools::load_all()
test <- convert_output("~/Report.sso")
plot_biomass(test) # select 4: TIME _SERIES
plot_landings(test)

Biomass:

Landings:

Note: I just rebased this branch because there was an update to the general plotting function. This should not have impacted your results thought with this test. I think one of two things are happening here (1) I am not setting the correct quantity as biomass or (2) you tested this off of the main branch rather than the fix-biomass-plt branch. Either way, can you pull the changes from this repo to your fork, test again, and add a reprex to a comment in this PR?

Thanks!!

Second note: I have noticed that there is an error in the converter for landings somehow and I am fixing it. If you get this error as well, let me know.