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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
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 addedRRRrecord. A missing or zero heart rate adds noRRRrecord; any other value, including a negative one, still derives.AVALU: the collected unit on a kept record, or milliseconds (ms) on an addedRRRrecord. A heart rate record that contributes a result must usebeats/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 acceptedexpected/error.yaml- phase
- verification
- condition
- assert_failed
- rule
- CHECK-12
expected/error.yaml
phase: verification
condition: assert_failed
spec_paths:
- verifications[1].assert
rule: CHECK-12
context:
verification_id: reject-pre-existing-rrr
failure_count: 1
keys:
- STUDYID: YAMAA-01
USUBJID: YAMAA-01-105
PARAMCD: RRR
AVISIT: VISIT 1
Inputs
Under review1 source fileinput/adeg.csv
Edit6 rows| STUDYID | USUBJID | 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 artifactexpected/adeg.csv
Edit9 rows| STUDYID | USUBJID | 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 |
Human review and assessment
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | 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 | Reviewer | Sign-off |
|---|---|---|---|---|---|
| 1.7 | 2026-10-20 | yamaa docs build | Read a specification in the 1.0 surface as its 0.5 counterpart; state that missing values stay missing where a mapping declares no missing handler, and leave out a declared missing answer that restates a handler's default | ||
| 1.6 | 2026-10-17 | yamaa docs build | Describe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight | ||
| 1.5 | 2026-10-17 | yamaa docs build | Name collected precision in words instead of letter codes; state imputation fallbacks, minimum source precision, bounds ignored outside the collected period, and invalid text with no handler as an error; describe date and datetime shifts, imputation flag codes, and partial text giving no date part | ||
| 1.4 | 2026-10-15 | yamaa docs build | State datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks | ||
| 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 |