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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: rank each subject's adverse events by severity, worst first.
Input: spec.yaml builds one record per row of input/ae.csv,
which carries the subject, the event sequence number, the coded term,
the reported severity, and the onset date.
Variables:
AEDECODholds the coded adverse event term, copied from the source record.AESEVholds the reported severity (MILD, MODERATE, or SEVERE), copied from the source record.AESTDTCholds the event onset date, copied from the source record.SEV_RANKis the event's severity rank within its subject: the worst severity ranks first, and the later onset date breaks a severity tie. Events tied on both share a rank, and the next rank is skipped.SEV_SEQcounts the same ordering without gaps: events tied on every ordering rule take consecutive numbers in the order they appear in the source data.
Note: the ranking runs over each subject's records after every record's severity is scored MILD = 1, MODERATE = 2, SEVERE = 3, so the window reads the scored severity together with the stored subject and onset date; when two records tie on every ordering rule, the earlier source record comes first.
Inputs
Under review1 source fileinput/ae.csv
Edit9 rows| STUDYID | USUBJID | AESEQ | AEDECOD | AESEV | AESTDTC |
|---|---|---|---|---|---|
| YAMAA-01 | 1 | HEADACHE | MILD | 2024-01-02 | |
| YAMAA-01 | 2 | NAUSEA | SEVERE | 2024-01-05 | |
| YAMAA-01 | 3 | FATIGUE | MODERATE | 2024-01-03 | |
| YAMAA-01 | 1 | HEADACHE | SEVERE | 2024-02-01 | |
| YAMAA-01 | 2 | NAUSEA | SEVERE | 2024-02-01 | |
| YAMAA-01 | 3 | FATIGUE | MILD | 2024-02-02 | |
| YAMAA-01 | 1 | HEADACHE | MODERATE | 2024-03-01 | |
| YAMAA-01 | 2 | NAUSEA | MODERATE | 2024-03-05 | |
| YAMAA-01 | 3 | DIZZINESS | SEVERE | 2024-03-01 |
Expected output
Under review9 expected rowsexpected/adae.csv
Edit9 rows| STUDYID | USUBJID | AESEQ | AEDECOD | AESEV | AESTDTC | SEV_RANK | SEV_SEQ |
|---|---|---|---|---|---|---|---|
| YAMAA-01 | 1 | HEADACHE | MILD | 2024-01-02 | 3 | 3 | |
| YAMAA-01 | 2 | NAUSEA | SEVERE | 2024-01-05 | 1 | 1 | |
| YAMAA-01 | 3 | FATIGUE | MODERATE | 2024-01-03 | 2 | 2 | |
| YAMAA-01 | 1 | HEADACHE | SEVERE | 2024-02-01 | 1 | 1 | |
| YAMAA-01 | 2 | NAUSEA | SEVERE | 2024-02-01 | 1 | 2 | |
| YAMAA-01 | 3 | FATIGUE | MILD | 2024-02-02 | 3 | 3 | |
| YAMAA-01 | 1 | HEADACHE | MODERATE | 2024-03-01 | 3 | 3 | |
| YAMAA-01 | 2 | NAUSEA | MODERATE | 2024-03-05 | 2 | 2 | |
| YAMAA-01 | 3 | DIZZINESS | SEVERE | 2024-03-01 | 1 | 1 |
Shaded columns are derived— = missing value
Human review and assessment
Not under review
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | Computational Method | Origin |
|---|---|---|---|---|---|---|---|
| ADAE | STUDYID | Study Identifier | character | Copy value from AE.STUDYID. | Predecessor | ||
| ADAE | USUBJID | Unique Subject Identifier | character | Copy value from AE.USUBJID. | Predecessor | ||
| ADAE | AESEQ | Sequence Number | numeric | Copy value from AE.AESEQ. | Predecessor | ||
| ADAE | AEDECOD | Dictionary-Derived Term | character | Copy value from AE.AEDECOD. | Predecessor | ||
| ADAE | AESEV | Severity/Intensity | character | Copy value from AE.AESEV. | Predecessor | ||
| ADAE | AESTDTC | Start Date/Time of Adverse Event | character | Copy value from AE.AESTDTC. | Predecessor | ||
| ADAE | SEV_RANK | Severity Rank | numeric | Take SEV_RANK from the AE record matching on STUDYID, USUBJID and AESEQ, where SEV_RANK is derived as rank rows from 1 within each group of AE.USUBJID, ordered by SEVN descending then AE.AESTDTC descending; ties share a number and the next distinct value skips the gap, and a row with no match is an error. | Derived | ||
| ADAE | SEV_SEQ | Severity Sequence | numeric | Take SEV_SEQ from the AE record matching on STUDYID, USUBJID and AESEQ, where SEV_SEQ is derived as row number within each group of AE.USUBJID, ordered by AE.SEVN descending then AE.AESTDTC descending, and a row with no match is an error. | 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 |