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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: derive cumulative dose (DOSECUM) and relative dose
intensity (RDI) by subject and treatment.
Input: a subject-treatment inventory carrying the dose unit
(EXDOSU), with component exposure records carrying the
treatment (EXTRT), the administered dose (EXDOSE), and the
planned dose (EXPLDOS) on each administration record.
Variables:
EXTRTnames the treatment component, andEXDOSUis the unit that component is measured in.DOSECUMis the total administered dose across the component's exposure records.RDIis meant to be that total as a percentage of the planned dose. The planned dose is recorded on each administration record rather than once for the treatment, so dividing the total by it leaves open which record supplies the denominator, and that choice would decide the answer. The run is rejected before any data is read, and no artifact is accepted.
How to fix
First decide what the denominator means. If each exposure row carries its own planned administration, total both actual and planned dose:
derivation:
aggregate: >-
100 * SUM(EX.EXDOSE) / NULLIF(SUM(EX.EXPLDOS), 0)
If the denominator is one treatment-level plan, store it once in the subject
treatment source, bind it to a numeric column, and compute RDI from that
column and DOSECUM. Do not select one exposure row arbitrarily.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- validation
- condition
- aggregate_identifier_not_grouped
- rule
- FORMULA-22
expected/error.yaml
phase: validation
condition: aggregate_identifier_not_grouped
spec_paths:
- columns.RDI.derivation.aggregate.expr
rule: FORMULA-22
context:
dataset: EX
identifier: EX.EXPLDOS
Inputs
Under review2 source filesinput/ex.csv
Edit5 rows| STUDYID | USUBJID | EXTRT | EXSEQ | EXDOSE | EXPLDOS |
|---|---|---|---|---|---|
| YAMAA-01 | Pembrolizumab | 1 | 200 | 200 | |
| YAMAA-01 | Pembrolizumab | 2 | 150 | 200 | |
| YAMAA-01 | Pembrolizumab | 3 | 150 | 150 | |
| YAMAA-01 | Pemetrexed | 4 | 500 | 500 | |
| YAMAA-01 | Pembrolizumab | 1 | 200 | 200 |
input/subject_treatment.csv
Edit3 rows| STUDYID | USUBJID | EXTRT | EXDOSU |
|---|---|---|---|
| YAMAA-01 | Pembrolizumab | mg | |
| YAMAA-01 | Pemetrexed | mg/m2 | |
| YAMAA-01 | Pembrolizumab | mg |
Unexpected Output
Under reviewNo artifact is producedNo fixture files in this directory.
Human review and assessment
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | Computational Method | Origin |
|---|---|---|---|---|---|---|---|
| ADEX | STUDYID | Study Identifier | character | Copy value from TRT.STUDYID. | Predecessor | ||
| ADEX | USUBJID | Unique Subject Identifier | character | Copy value from TRT.USUBJID. | Predecessor | ||
| ADEX | EXTRT | Name of Treatment | character | Copy value from TRT.EXTRT. | Predecessor | ||
| ADEX | EXDOSU | Dose Units | character | Copy value from TRT.EXDOSU. | Predecessor | ||
| ADEX | DOSECUM | Cumulative Dose | numeric | Aggregate SUM(EX.EXDOSE) over records matching on the shared output keys. | Derived | ||
| ADEX | RDI | Relative Dose Intensity | numeric | Aggregate 100 * SUM(EX.EXDOSE) / EX.EXPLDOS over records matching on STUDYID, USUBJID and EXTRT. | 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 |