[WIP] Remove mean F calculation for functional groups

[Copilot]

✅ Completed: Remove Mean F Calculation and Process Time-Specific F-at-Age Vectors

Summary

Successfully modified generate_selectivity_curve() to process F-at-age vectors for each year-month combination instead of calculating mean F values across time.

Changes Made

1. Core Implementation (R/generate_selectivity_curve.R)

• ✅ Added year, month, time_step to globalVariables
• ✅ Updated required columns validation to include year and month
• ✅ Removed mean F calculation logic (old lines 143-152)
• ✅ Added time step processing with lapply over year-month combinations
• ✅ Each time step now generates independent selectivity parameters
• ✅ Results include time information in the time column
• ✅ Handles edge cases (zero F values skip with warning)

2. Documentation Updates

• ✅ Updated @param documentation to require year and month columns
• ✅ Updated @return to indicate "one row per parameter per time step"
• ✅ Updated @details to explain time-specific processing
• ✅ Updated man/generate_selectivity_curve.Rd to match
• ✅ Improved cli message formatting with {.val} syntax

3. Test Updates (tests/testthat/test-generate_selectivity_curve.R)

• ✅ Updated row count expectations (2→24 for logistic, 4→48 for double_logistic with 12 months)
• ✅ Changed assertions to use unique() for repeated values
• ✅ Added checks for time column population
• ✅ Simplified validation tests to use single time step
• ✅ Updated error message expectations

Behavioral Changes

Before:

• Calculated mean F value for each functional group (averaged across all time)
• Generated single set of selectivity parameters
• Output: 2 rows (logistic) or 4 rows (double_logistic)
• time column was always NA

After:

• Processes each year-month combination separately
• Generates selectivity parameters for each time step
• Output: (2 rows × n_timesteps) for logistic, (4 rows × n_timesteps) for double_logistic
• time column contains "year-month" identifier (e.g., "2000-1")

Quality Checks

• ✅ Code review: All feedback addressed
• ✅ Security review: No vulnerabilities identified
• ✅ Documentation: Complete and accurate
• ✅ Tests: Updated for new behavior

Breaking Change Notice

This is a breaking change. Users expecting single parameter sets will now receive multiple sets (one per time step). Users should either:

1. Filter results to a specific time step if single values are needed
2. Update their code to handle time-varying parameters

Original prompt

In generate_selectivity_curve.R, don't calculate mean F values for each functional group for the year-month combinations. Extract F at age vector for each year-month combination and generate selectivity parameters. 

Created from VS Code.

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