Reject Rederived RR

Review ask

As a clinical trial statistician or programmer, challenge anything in this benchmark: describe a problem in Comments, or propose a fix with the Edit button on any source file.

Task: Is this a specification error a study team could realistically make, and should the build stop on it rather than continue?
Inputs: Do they trigger the failure for the reason the summary gives?
Expected failure: Is this the right error, raised at the right point, and would it tell the programmer what to fix?

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Summary

EditUnder reviewWhat this benchmark means

README.md

Goal: keep each collected heart rate (HR) record and add a rederived RR duration (time between successive R waves) record under the code RRR for each subject and analysis visit with a non-missing, non-zero HR result, labeled RR Duration Rederived (ms) and carrying the new result in AVAL and its unit in AVALU.

Input: collected electrocardiogram (ECG) records with heart rate results under the code HR per subject and visit, carrying the record label, result, and result unit; one subject contributes heart rate records at two visits, and other records cover a missing, a zero, and a negative heart rate. One input record already carries the code RRR.

Variables:

AVAL: the collected result on a kept record, or 60000 divided by the heart rate (in beats/min) on an added RRR record. A missing or zero heart rate adds no RRR record; any other value, including a negative one, still derives.
AVALU: the collected unit on a kept record, or milliseconds (ms) on an added RRR record. A heart rate record that contributes a result must use beats/min.

Every RRR record must be produced from a heart rate by the calculation above rather than accepted as collected, so the collected RRR record breaks the stated requirement. The completed dataset is presented to that check and rejected, and no artifact is accepted from this input. The expected file records the completed rows presented to the check.

How to fix

First confirm the RR duration should come from the heart rate rather than from the collected record: the collected RRR record is the defect, not the calculation. Delete the collected RRR input record; keep each contributing HR record with beats/min as the unit. The run then calculates the RR interval itself instead of accepting one as collected.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: verification
condition: assert_failed
requirement: REQ-0384

expected/error.yaml

phase: verification
condition: assert_failed
spec_paths:
  - verifications[2].assert
requirement: REQ-0384
context:
  verification_id: reject-pre-existing-rrr
  failure_count: 1
  keys:
    - STUDYID: YAMAA-01
      USUBJID: YAMAA-01-105
      PARAMCD: RRR
      AVISIT: VISIT 1

YAML specification

1 spec file

spec.yaml

Edit89 lines

1schema_version: "1.0"2domain: ADEG3keys: [STUDYID, USUBJID, PARAMCD, AVISIT]4input:5  ADEG_RAW:6    path: input/adeg.csv7    types: {AVAL: float}89output:10  path: adeg.csv11  columns: [STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, AVAL, AVALU]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: ADEG_RAW.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: ADEG_RAW.USUBJID2324  - name: PARAMCD25    type: str26    label: Parameter Code2728  - name: PARAM29    type: str30    label: Parameter3132  - name: AVISIT33    type: str34    label: Analysis Visit35    derivation: ADEG_RAW.AVISIT3637  - name: AVAL38    type: float39    label: Analysis Value4041  - name: AVALU42    type: str43    label: Analysis Value Unit4445  # Which row template built the row; the last check reads it to tell a46  # calculated RRR record from one that arrived as collected.47  - name: _PROVENANCE48    type: str49    label: Internal Row Provenance5051rows:52  # Every collected record, unchanged, including any collected RRR record.53  - id: collected54    derivations:55      PARAMCD: ADEG_RAW.PARAMCD56      PARAM: ADEG_RAW.PARAM57      AVAL: ADEG_RAW.AVAL58      AVALU: ADEG_RAW.AVALU59      _PROVENANCE: {literal: collected}6061  # One RR record per heart-rate record that can be inverted:62  # 60000 ms per minute divided by beats per minute.63  - id: derived_rrr64    filter: >-65      ADEG_RAW.PARAMCD = 'HR'66      AND ADEG_RAW.AVAL IS NOT NULL67      AND ADEG_RAW.AVAL <> 068    derivations:69      PARAMCD: {literal: RRR}70      PARAM: {literal: RR Duration Rederived (ms)}71      AVAL:72        compute:73          expr: "60000 / NULLIF(ADEG_RAW.AVAL, 0)"74      AVALU: {literal: ms}75      _PROVENANCE: {literal: derived}7677verifications:78  - unique:79      columns: [STUDYID, USUBJID, PARAMCD, AVISIT]80  - assert:81      id: contributing-hr-uses-beats-per-minute82      when: "PARAMCD = 'HR' AND AVAL IS NOT NULL AND AVAL <> 0"83      require: "AVALU = 'beats/min'"84  # An RRR record that did not come from the calculation fails here; the85  # collected RRR input record is the defect this benchmark shows.86  - assert:87      id: reject-pre-existing-rrr88      when: "PARAMCD = 'RRR'"89      require: "_PROVENANCE = 'derived'"

Inputs

Under review1 source file

input/adeg.csv

Edit6 rows

input/adeg.csv
STUDYID	PARAMCD	PARAM	AVISIT	AVAL	AVALU
YAMAA-01	HR	Heart Rate	VISIT 1	60.0	beats/min
YAMAA-01	HR	Heart Rate	VISIT 2	75.0	beats/min
YAMAA-01	HR	Heart Rate	VISIT 1	-50.0	beats/min
YAMAA-01	HR	Heart Rate	VISIT 1	0.0	beats/min
YAMAA-01	HR	Heart Rate	VISIT 1	—	beats/min
YAMAA-01	RRR	Collected RR Duration	VISIT 1	750.0	ms

Unexpected Output

Under review9 rows presented to the failing check - not an accepted artifact

expected/adeg.csv

Edit9 rows

expected/adeg.csv
STUDYID	PARAMCD	PARAM	AVISIT	AVAL	AVALU
YAMAA-01	HR	Heart Rate	VISIT 1	60	beats/min
YAMAA-01	HR	Heart Rate	VISIT 2	75	beats/min
YAMAA-01	HR	Heart Rate	VISIT 1	-50	beats/min
YAMAA-01	HR	Heart Rate	VISIT 1	0	beats/min
YAMAA-01	HR	Heart Rate	VISIT 1	—	beats/min
YAMAA-01	RRR	Collected RR Duration	VISIT 1	750	ms
YAMAA-01	RRR	RR Duration Rederived (ms)	VISIT 1	1000	ms
YAMAA-01	RRR	RR Duration Rederived (ms)	VISIT 2	800	ms
YAMAA-01	RRR	RR Duration Rederived (ms)	VISIT 1	-1200	ms

Shaded columns are derived— = missing value

Comments and assessment materials

Dataset Name	Variable Name	Variable Label	Type	Computational Method	Origin
ADEG	STUDYID	Study Identifier	character	Copy value from ADEG_RAW.STUDYID.	Predecessor
ADEG	USUBJID	Unique Subject Identifier	character	Copy value from ADEG_RAW.USUBJID.	Predecessor
ADEG	PARAMCD	Parameter Code	character	Set per constructed row; see the Row construction sheet.	Derived
ADEG	PARAM	Parameter	character	Set per constructed row; see the Row construction sheet.	Derived
ADEG	AVISIT	Analysis Visit	character	Copy value from ADEG_RAW.AVISIT.	Predecessor
ADEG	AVAL	Analysis Value	numeric	Set per constructed row; see the Row construction sheet.	Derived
ADEG	AVALU	Analysis Value Unit	character	Set per constructed row; see the Row construction sheet.	Derived

Template	Include when	PARAMCD	PARAM	AVAL	AVALU	_PROVENANCE
collected		Copy ADEG_RAW.PARAMCD	Copy ADEG_RAW.PARAM	Copy ADEG_RAW.AVAL	Copy ADEG_RAW.AVALU	Constant "collected"
derived_rrr	ADEG_RAW.PARAMCD = 'HR' AND ADEG_RAW.AVAL IS NOT NULL AND ADEG_RAW.AVAL <> 0	Constant "RRR"	Constant "RR Duration Rederived (ms)"	Compute 60000 / NULLIF(ADEG_RAW.AVAL, 0)	Constant "ms"	Constant "derived"

Version	Date	Author	Description
1.3	2026-09-29	yamaa docs build	Show study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.2	2026-09-29	yamaa docs build	Classify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.1	2026-09-29	yamaa docs build	Resolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0		yamaa docs build	Initial generation from spec.yaml

How to fix

input/adeg.csv

expected/adeg.csv

Comments

Mapping spec