Add add_if_missing parameter to control NA handling in interpretive rules

[msberends]

Summary

Added a new add_if_missing parameter to interpretive_rules() and eucast_rules() functions to provide fine-grained control over whether rules should be applied to missing (NA) values.

Key Changes

• Added add_if_missing parameter (default: TRUE) to interpretive_rules() function signature
• Updated documentation with detailed explanation of the new parameter's behavior
• Modified edit_sir() helper function to accept and handle the add_if_missing parameter
• Refactored the cell modification logic in edit_sir() to use a unified apply_mask approach that respects both overwrite and add_if_missing settings
• Passed the parameter through all internal function calls (4 locations where edit_sir() is invoked)
• Updated version number and NEWS.md with feature documentation

Implementation Details

The new parameter enables users to:

• When add_if_missing = TRUE (default): Apply rules to all cells, including NA values (preserves existing behavior)
• When add_if_missing = FALSE: Apply rules only to cells that already contain an SIR value, leaving NA cells untouched

This is particularly useful when using overwrite = TRUE with custom rules to update reported results without imputing values for drugs that were not tested.

The implementation consolidates the conditional logic for cell selection into a single apply_mask variable, improving code maintainability and reducing duplication in the warning handling section.

https://claude.ai/code/session_01Nucc8nXGLqNUjtuC9GrhTc