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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: derive AOUTCOME, the lesion count each subject is analysed with,
copying a missing count from the most similar subject of the same study,
and record that donor in DONORID and its distance in DONORDST.
Input: spec.yaml reads one subjects file: study, subject, baseline age,
baseline score and the observed lesion count, missing for some subjects.
Variables:
AGE,BSCOREandOUTCOMEare the subject's baseline age, baseline score and observed lesion count, as collected.SDAGEandSDBSCOREare the sample standard deviations of age and of baseline score over every subject of the study with a value.DONORIDis the donor of a subject whose count is missing: the subject of the same study with an observed count whose age and score lie nearest, each difference divided by its study standard deviation. It is missing for a subject with an observed count, and when the study has no donor.DONORDSTis that donor's distance, the square root of the sum of the two squared scaled differences.AOUTCOMEis the observed count, or else the donor's count; it is missing when the subject has neither.
Note: subject 104 of study S1 is nearest subject 103 (age 55 against 54, score 11 against 12), so it is analysed with 103's count of 3. Subject 105 has no age, so it has no distance and is never a donor. In study S2, subjects 201 and 202 are equally near 203; the lower subject number, 201, is the donor. Study S3 has no subject with an observed count, so its subjects keep a missing count. The standard deviations are columns of the dataset, which the donor selection reads for the subject being imputed.
Inputs
Under review1 source fileinput/subjects.csv
Edit10 rows| STUDYID | USUBJID | AGE | BSCORE | OUTCOME |
|---|---|---|---|---|
| S1 | 52 | 10 | 2 | |
| S1 | 61 | 14 | 5 | |
| S1 | 55 | 11 | 3 | |
| S1 | 54 | 12 | — | |
| S1 | — | 11 | 9 | |
| S2 | 40 | 8 | 1 | |
| S2 | 44 | 10 | 4 | |
| S2 | 42 | 9 | — | |
| S3 | 50 | 10 | — | |
| S3 | 56 | 12 | — |
Expected output
Under review10 expected rowsexpected/lesion.csv
Edit10 rows| STUDYID | USUBJID | AGE | BSCORE | OUTCOME | SDAGE | SDBSCORE | DONORID | DONORDST | AOUTCOME |
|---|---|---|---|---|---|---|---|---|---|
| S1 | 52 | 10 | 2 | 3.872983346207417 | 1.51657508881031 | — | — | 2 | |
| S1 | 61 | 14 | 5 | 3.872983346207417 | 1.51657508881031 | — | — | 5 | |
| S1 | 55 | 11 | 3 | 3.872983346207417 | 1.51657508881031 | — | — | 3 | |
| S1 | 54 | 12 | — | 3.872983346207417 | 1.51657508881031 | 103 | 0.7081308320941258 | 3 | |
| S1 | — | 11 | 9 | 3.872983346207417 | 1.51657508881031 | — | — | 9 | |
| S2 | 40 | 8 | 1 | 2 | 1 | — | — | 1 | |
| S2 | 44 | 10 | 4 | 2 | 1 | — | — | 4 | |
| S2 | 42 | 9 | — | 2 | 1 | 201 | 1.4142135623730951 | 1 | |
| S3 | 50 | 10 | — | 4.242640687119285 | 1.4142135623730951 | — | — | — | |
| S3 | 56 | 12 | — | 4.242640687119285 | 1.4142135623730951 | — | — | — |
Human review and assessment
| Variable Name | Variable Label | Type | Length | Controlled Terms or Format | Origin | Core | Conversion Definition | Variable Type | Variable Order | Comments for Define |
|---|---|---|---|---|---|---|---|---|---|---|
| STUDYID | Study Identifier | Char | Collected | Copy value from SUBJ.STUDYID. | SDTM | 1 | ||||
| USUBJID | Unique Subject Identifier | Char | Collected | Copy value from SUBJ.USUBJID. | SDTM | 2 | ||||
| AGE | Age at Baseline | Num | Collected | Copy value from SUBJ.AGE. | SDTM | 3 | ||||
| BSCORE | Baseline Score | Num | Collected | Copy value from SUBJ.BSCORE. | SDTM | 4 | ||||
| OUTCOME | Observed Lesion Count | Num | Collected | Copy value from SUBJ.OUTCOME. | SDTM | 5 | ||||
| SDAGE | Study Standard Deviation of Age | Num | Derived | Aggregate STDDEV(AGE) over records grouped by STUDYID, matching on the shared output keys. | SDTM | 6 | ||||
| SDBSCORE | Study Standard Deviation of Baseline Score | Num | Derived | Aggregate STDDEV(BSCORE) over records grouped by STUDYID, matching on the shared output keys. | SDTM | 7 | ||||
| DONORID | Donor Subject Identifier | Char | Derived | Take USUBJID from the first SUBJ record matching on STUDYID, where SUBJ.OUTCOME IS NOT NULL AND SUBJ.DIST IS NOT NULL AND LESION.OUTCOME IS NULL, ordered by SUBJ.DIST then SUBJ.USUBJID, and no match yields blank. | SDTM | 8 | ||||
| DONORDST | Scaled Distance to the Donor | Num | Derived | Take DIST from the first SUBJ record matching on STUDYID, where SUBJ.OUTCOME IS NOT NULL AND SUBJ.DIST IS NOT NULL AND LESION.OUTCOME IS NULL, ordered by SUBJ.DIST then SUBJ.USUBJID, where DIST is derived as compute SQRT(ZAGE * ZAGE + ZBSCORE * ZBSCORE), and no match yields blank. | SDTM | 9 | ||||
| AOUTCOME | Analysis Lesion Count | Num | Derived | First non-missing of: OUTCOME; OUTCOME from the first SUBJ record matching on STUDYID, where SUBJ.OUTCOME IS NOT NULL AND SUBJ.DIST IS NOT NULL AND LESION.OUTCOME IS NULL, ordered by SUBJ.DIST then SUBJ.USUBJID, and no match yields blank. | SDTM | 10 |
| 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 |