22_transforms_reference.md

Transforms Reference

Dataset Transform Registry

Defined in src/amr/data/transforms/__init__.py.

Current Modules

• repro_antimicrobials
• repro_antivirals
• repro_clinical_breakpoints
• repro_dosage
• repro_microorganisms
• repro_microorganisms_groups
• repro_example_isolates_unclean
• repro_intrinsic_resistant
• repro_poorman
• fix_whonet
• fix_salmonella

Transform Rules

• Deterministic ordering
• Conservative normalization by default (trim/canonicalize where safe)
• Dataset-specific adjustments documented in module docstrings

Change Protocol

When modifying a transform:

1. Update module logic.
2. Update this reference.
3. Add/adjust unit tests and parity expectations.