21  QC Completeness

21.1 Why this matters

Completeness checks ensure analyses are based on well-linked data across lab, scanner, and PACS. Missing links can hide failure modes.

21.2 Case Linkage Funnel

# A tibble: 3 × 3
  stage              count rate_vs_lab
  <chr>              <int>       <dbl>
1 Lab cases          47759      1     
2 With scanner match  2670      0.0559
3 With PACS match    24885      0.521 

21.3 Missingness by Field

21.4 Interpretation Guide

• Low linkage from lab to scanner signals unmatched IDs or gaps in scanner logs; prioritize fixing ID parsing in raw files.
• PACS missingness highlights upload failures or filtering that removed too many slides; revisit exclusion logic if high.
• Track missing rates over time (weekly render) to ensure pipeline changes do not silently erode data completeness.