How ebenco36/amr_cascade_platfrom works
AMR Cascade Platform is a research-analysis framework for denominator-aware analysis of antimicrobial susceptibility testing observations. Its main workflow ingests and harmonizes site data, builds eligible episode–drug opportunities, estimates and validates directional cascade patterns, then exports analyses and publication outputs. The README also documents supplementary prediction, prevalence-shift analysis, temporal and sensitivity analyses, and an ESKAPE extension. Edges use README statements for documented workflow relationships; sampled source shows ingestion and storage behavior, while several downstream implementations were not sampled.
Main entry points: report_export_workflow.py Report generation · gold_build_manager.py Gold datasets · cascade_analysis_workflow.py Cascade analysis · main.py Command interface
Components 20
Data preparation
- Raw ingestion
src/amr_cascade_platform/data/ingestion/raw_ingestion_manager.py - Silver cleaning
src/amr_cascade_platform/data/cleaning/site_cleaning_manager.py - Site harmonization
src/amr_cascade_platform/data/harmonization/harmonization_manager.py - Gold datasets
src/amr_cascade_platform/data/gold/gold_build_manager.py - Eligibility rules
src/amr_cascade_platform/domain/services/eligibility_service.py - Feature building
src/amr_cascade_platform/features/workflows/feature_build_workflow.py
Cascade analysis
- Cascade analysis
src/amr_cascade_platform/cascade/workflows/cascade_analysis_workflow.py - Pattern validation
src/amr_cascade_platform/cascade/analyzers/cascade_validation_analyzer.py - Sensitivity analysis
src/amr_cascade_platform/cascade/workflows/implied_sensitivity_workflow.py - ESKAPE extension
src/amr_cascade_platform/cascade/workflows/eskape_family_validation.py
Prediction and surveillance
- Supplementary prediction
src/amr_cascade_platform/modeling/workflows/modeling_workflow.py - Prevalence shifts
src/amr_cascade_platform/surveillance/workflows/prevalence_shift_workflow.py
Reporting and exports
- Report generation
src/amr_cascade_platform/reporting/workflows/report_export_workflow.py - Figure exports
src/amr_cascade_platform/visualization/report/figure_manager.py - Scientific audit
src/amr_cascade_platform/reporting/workflows/scientific_audit_workflow.py
Runtime foundation
- Command interface
src/amr_cascade_platform/cli/main.py - Configuration
src/amr_cascade_platform/core/config/config_loader.py - Path management
src/amr_cascade_platform/core/paths/path_manager.py - Dataset storage
src/amr_cascade_platform/infrastructure/storage/dataset_store.py
Other components
- Researcher
Connections 22
- Researcher → Command interface: runs commands
src/amr_cascade_platform/cli/main.py - Command interface → Configuration: loads settings
src/amr_cascade_platform/cli/main.py - Command interface → Raw ingestion: dispatches ingestion
- Raw ingestion → Dataset storage: writes datasets
- Raw ingestion → Silver cleaning: precedes
README.md - Silver cleaning → Site harmonization: precedes
README.md - Site harmonization → Gold datasets: builds from harmonized data
src/amr_cascade_platform/data/gold/gold_build_manager.py - Gold datasets → Eligibility rules: applies eligibility
src/amr_cascade_platform/data/gold/gold_build_manager.py - Gold datasets → Cascade analysis: supplies opportunities
README.md - Gold datasets → Feature building: supports feature building
README.md - Cascade analysis → Pattern validation: validates patterns
README.md - Cascade analysis → Sensitivity analysis: tests sensitivity
README.md - Cascade analysis → ESKAPE extension: extends analysis
README.md - Feature building → Supplementary prediction: supplies prediction inputs
README.md - Gold datasets → Prevalence shifts: supports shift analysis
README.md - Cascade analysis → Report generation: provides analysis outputs
README.md - Supplementary prediction → Report generation: provides model outputs
README.md - Prevalence shifts → Report generation: provides analysis outputs
README.md - Report generation → Figure exports: exports figures
src/amr_cascade_platform/visualization/report/figure_manager.py - Report generation → Scientific audit: supports readiness audit
README.md - Command interface → Supplementary prediction: dispatches training
src/amr_cascade_platform/cli/main.py - Command interface → Report generation: dispatches reporting
src/amr_cascade_platform/cli/main.py