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CSA Legacy Python Data Dictionary

This repository expects a historical Excel workbook layout used for the central sleep apnea project. The original workbook is restricted clinical data and is not included.

Input Workbook Contract

ReadExcel.py reads the first worksheet and uses fixed zero-based column positions from the historical workbook. The first row is treated as a header row and skipped.

Zero-based index Historical field Derived dataframe column Notes
4 Age at diagnostic sleep study Age Numeric years.
5 Sex Sex Lowercased and categorical.
6 Race / ethnicity Race Lowercased; historical Utah-specific recode maps not hispanic/latino to white.
8 Body mass index BMI Numeric kg/m2.
9 Smoking status Smoking Lowercased and categorical.
10 General comorbidities Comorb Recoded to combinations of htn, dm, psych, ckd, none.
11 Cardiac comorbidities Heart Recoded to combinations of cad, afib, hfpef, hfref, other, none.
12 CNS comorbidities CNS Recoded to combinations of cva, neurodegenerative, dementia, chiari, other, none.
13 Baseline apnea category BaseDx Recoded to ordered categories: Mainly OSA, Combined OSA/CSA, Predominantly CSA, Pure CSA.
14 Diagnostic AHI AHI Numeric events/hour.
15 Post-titration / etiologic diagnosis PostDx Recoded to TECSA, Cardiac, Neurologic, Medication, Primary; multiple labels may be joined with +.
16 Final treatment FinalTx Recoded to niv-o2, niv, asv, bipap-o2, bipap, cpap, mad, O2, none.
17 Outcome Outcome Historical categorical text used by downstream summaries.
18 Path to ASV ProcToASV Recoded to other, initial treatment, after trial of cpap, after trial of bipap.
19 Time to ASV TimeToASV Recoded to other, within 2 mo, 3-6 mo, 6+ mo.
21 Diagnostic study type StudyType Historical PSG/HSAT-like source field.

Derived Variables

  • AHI_label: OSA severity category derived from AHI.
  • InitTx: inferred initial treatment from FinalTx, ProcToASV, and Outcome.
  • FinalTx_coll: encoded-output helper collapsing final treatment to CPAP/BPAP/ASV/Other.
  • PercOSA: encoded-output helper collapsing BaseDx into mostly OSA vs mostly CSA.

Restricted Data Rules

  • Do not commit the original workbook or any row-level clinical export.
  • Keep local clinical workbooks under data/private/, which is ignored by git.
  • Use the synthetic workbook in tests/fixtures/ only for code smoke tests.