# Alignment Checklist Documentation

## Protocol-to-SAP Alignment Sections
- Study objectives mapping to analysis endpoints
- Treatment group definitions and coding
- Population definitions (ITT, Safety, Efficacy)
- Primary and secondary endpoint specifications
- Statistical methodology consistency
- Missing data handling approach

## SAP-to-Mock Shell Alignment Sections
- Table 14-1.03 Demographics: Title, population, columns, statistics
- Table 14-3.01 Primary Endpoint: Analysis model, population, endpoint, methods
- Table 14-4.01 AE Overview: Population, row categories, display conventions
- Table 14-4.02 AE by SOC/PT: Filtering threshold, sorting, MedDRA coding
- Figure 14-5.01 KM Plot: Endpoint, treatment display, statistical summary

## Mock Shell-to-TLF Output Alignment Sections
- Structure verification (rows, columns, headers)
- Numeric value comparison against ground truth
- Formatting compliance (decimal places, percentages)
- Footnote accuracy and completeness

## Analysis Logic Verification
- ANCOVA model specification: CHG ~ TRTPN + SITEGR1 + BASE
- Type III Sum of Squares with proportional weighting
- Data selection filters: EFFFL, ITTFL, PARAMCD, ANL01FL, AVISITN
- Missing data: LOCF via DTYPE flag
- No multiplicity adjustment for primary endpoint

## Check Summary
- **Protocol-SAP alignment**: 6 sections, all complete
- **SAP-Mock alignment**: 5 mock shells verified
- **Mock-TLF alignment**: 8 TLF outputs cross-referenced
- **Analysis logic**: 4 verification points confirmed
- **Total checks**: 51 (31 passed, 0 failed, 20 pending per consistency validation)
- **Quality report status**: 18/26 checks passed (69%), 3 documented issues
