Restructured src to more logical heirachy

analysis/CLAUDE.md

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+# Analysis Package
+
+Four-step pathway analysis pipeline refactored from original 267-line `generate_graph()` function.
+
+## Module: pathway_analyzer.py
+
+**Main entry points:**
+- `generate_icicle_chart(df, filters)` — Directory charts (Trust → Directory → Drug → Pathway)
+- `generate_icicle_chart_indication(df, indication_df, filters)` — Indication charts using Search_Term hierarchy
+
+**Pipeline steps:**
+1. `prepare_data()` — Filter by date/trusts/drugs/directories. **MUST use `df.copy()`** to prevent mutation.
+2. `calculate_statistics()` — Compute frequency, cost, duration stats
+3. `build_hierarchy()` — Create Trust → Directory/Indication → Drug → Pathway structure
+4. `prepare_chart_data()` — Format data for Plotly icicle chart
+
+**Note on modified UPIDs:**
+For drug-aware indication matching, UPIDs are formatted as `{original}|{search_term}`. The hierarchy-building functions treat UPID as opaque — pipe delimiters work transparently without code changes.
+
+## Module: statistics.py
+
+Statistical calculation helper functions (frequency, cost, duration, per-patient metrics).
+
+Called by `calculate_statistics()` during pipeline execution.