[chantelwetzel-noaa]

This pull request refactors and improves the codebase for expansion factor calculations and related plotting in several R functions. The main focus is on cleaning up NA and Inf handling, improving plot output and labeling, and making the code and user messaging more robust and clear. Below are the most important changes grouped by theme:

Refactoring NA/Inf Handling and User Messaging:

• Simplified and clarified how NA values are tracked and reported in getExpansion_1(), removing handling of Inf values and focusing only on NA cases; updated user messages to reflect this, and now track NA replacements in a new replace_na column instead of the old replace_na_inf.
• Removed verbose NA/Inf reporting and associated plot generation from EF1_Denominator(), streamlining output and focusing on relevant data. [1] [2] [3]

Plotting Improvements:

• Updated plotting logic in getExpansion_1() to generate clearer boxplots for expansion factors by year and state, separated for lengths and ages, and removed obsolete NA/Inf barplots.
• Overhauled the plots in EF1_Numerator(): replaced a boxplot of sample weights per trip with new barplots showing the proportion and count of samples with NA values in Trip_Sampled_Lbs by gear, year, and state; improved axis labeling, sizing, and facetting for better readability. [1] [2]

Minor Code and Documentation Updates:

• Updated a comment in getExpansion_1() to clarify the challenges of expanding WA data due to missing trip weights.
• Added .positai and .claude to .Rbuildignore to exclude these directories from package builds.

[Copilot]

🟡 Changes recommended

Default verbose execution fails on an undefined counter, and the new plots can misrepresent missing-weight proportions and age-expansion distributions.

3 open issues

• Fix undefined n_na reference in expansion threshold · New
• Dodge state bars to prevent stacking separate proportions · New
• Exclude unaged fish from age expansion boxplot · New

What changed in this PR

This PR refines first-stage expansion diagnostics in the PacFIN processing code, focusing on missing-value reporting and clearer plots.

Changes:

• Simplifies NA reporting and renames the replacement flag to replace_na.
• Separates length and age expansion plots and adds numerator missing-weight proportions and counts by gear.
• Removes redundant denominator diagnostics and excludes local tool directories from builds or version control.

File	Description
R/​getExpansion_1.R	Updates NA reporting and separates length and age boxplots.
R/​EF1_Numerator.R	Adds missing-weight proportion and count plots with gear facets.
R/​EF1_Denominator.R	Removes redundant diagnostics and names plotWL() arguments.
.Rbuildignore	Excludes .positai and .claude from package builds.
.gitignore	Ignores .positai.

_{Review effort: Balanced}

[Copilot]

🟡 Changes recommended

The age-specific missing-value count uses the length expansion factor, and minor labeling, wording, and messaging issues remain.

1 open issue

• Fix malformed y-axis label for NA sample proportion plot · New

2 previously missed issues

In code that hasn't changed since last review

Count missing age expansions using Expansion_Factor_1_A

R/​getExpansion_1.R:173

This age-specific count tests Expansion_Factor_1_L, so it counts missing length expansions rather than missing age expansions. If this count is retained for reporting, it should use Expansion_Factor_1_A; otherwise it is misleading dead code.

This issue also appears on line 174 of the same file.

Correct spelling of challenging

R/​getExpansion_1.R:157

challanging is a spelling error in this newly updated comment; please use challenging.

3 resolved since last review

• Fix undefined n_na reference in expansion threshold
• Exclude unaged fish from age expansion boxplot
• Dodge state bars to prevent stacking separate proportions

_{Review effort: Lite}