Reject Baseline Tied on Date and Time

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Summary

EditUnder reviewWhat this benchmark means

README.md

Public entries: Python and R. Passing coverage requires an installed inventory.

Goal: flag each subject's baseline result (ABLFL) as the result collected last on or before treatment start.

Input: laboratory results carrying subject, sequence number (LBSEQ), collection date (ADT) and time (ATM), result (AVAL), and the subject's treatment start date (TRTSDT).

Variables:

ADT, ATM, AVAL and TRTSDT would be carried through unchanged.
ABLFL would be Y on the result with the latest date on or before treatment start, the latest collection time breaking a same-day tie, and blank on every other result.

Note: two results can share both the latest date and its collection time, and either one gives the subject a different baseline. The run fails and no dataset is accepted.

How to fix

Decide which of the two results is the baseline before choosing how to state it. Two results drawn at the same date and time are usually a sample and its repeat, or one result recorded twice; the source data system should carry the result the study reports, and correcting it there leaves the rule saying what it means.

When both results are reportable and the study names a further tie-break, add it after the collection time:

baseline_flag:
  date: ADT
  reference: TRTSDT
  source: AVAL
  window:
    group_by: [USUBJID]
    order_by: [ADT, ATM, LBSEQ]

Order by the term the study names; the sequence number above stands in for it and is not itself a clinical rule. Do not average the two results into one baseline value, which reports a measurement nobody took.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: derivation
condition: ambiguous_baseline
rule: WINDOW-9

expected/error.yaml

phase: derivation
condition: ambiguous_baseline
spec_paths:
  - columns.ABLFL.derivation.baseline_flag
rule: WINDOW-9
context:
  date: "2025-03-04"
  match_count: 2
  keys:
    - USUBJID: "02"

YAML specification

1 spec file

spec.yaml

Edit59 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADLB5keys: [USUBJID, LBSEQ]6input:7  LB:8    path: input/lb.csv9    types: {LBSEQ: int, ADT: date, AVAL: float, TRTSDT: date}1011output:12  path: adlb.csv13  columns: [USUBJID, LBSEQ, ADT, ATM, AVAL, TRTSDT, ABLFL]1415columns:16  - name: USUBJID17    type: str18    label: Unique Subject Identifier19    derivation: LB.USUBJID2021  - name: LBSEQ22    type: int23    label: Sequence Number24    derivation: LB.LBSEQ2526  - name: ADT27    type: date28    label: Analysis Date29    derivation: LB.ADT3031  - name: ATM32    type: str33    label: Analysis Time34    derivation: LB.ATM3536  - name: AVAL37    type: float38    label: Analysis Value39    derivation: LB.AVAL4041  - name: TRTSDT42    type: date43    label: Date of First Exposure to Treatment44    derivation: LB.TRTSDT4546  # The latest result on or before treatment start, same-day results ordered47  # by collection time. Two results sharing that date and time still tie,48  # and the run stops rather than pick one.49  - name: ABLFL50    type: str51    label: Baseline Record Flag52    derivation:53      baseline_flag:54        date: ADT55        reference: TRTSDT56        source: AVAL57        window:58          group_by: [USUBJID]59          order_by: [ADT, ATM]

Inputs

Under review1 source file

input/lb.csv

Edit4 rows

input/lb.csv
LBSEQ	ADT	ATM	AVAL	TRTSDT
1	2025-03-02	08:00	30	2025-03-03
2	2025-03-02	14:30	34	2025-03-03
1	2025-03-04	09:00	22	2025-03-05
2	2025-03-04	09:00	25	2025-03-05

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Human review and assessment

Dataset Name	Variable Name	Variable Label	Type	Codelist/Controlled Terms	Computational Method	Origin
ADLB	USUBJID	Unique Subject Identifier	character		Copy value from LB.USUBJID.	Predecessor
ADLB	LBSEQ	Sequence Number	numeric		Copy value from LB.LBSEQ.	Predecessor
ADLB	ADT	Analysis Date	numeric	ISO 8601	Copy value from LB.ADT.	Predecessor
ADLB	ATM	Analysis Time	character		Copy value from LB.ATM.	Predecessor
ADLB	AVAL	Analysis Value	numeric		Copy value from LB.AVAL.	Predecessor
ADLB	TRTSDT	Date of First Exposure to Treatment	numeric	ISO 8601	Copy value from LB.TRTSDT.	Predecessor
ADLB	ABLFL	Baseline Record Flag	character		"Y" for the last record with ADT on or before TRTSDT and a non-missing AVAL within each group of USUBJID, ordered by ADT then ATM; blank otherwise.	Derived

Version	Date	Author	Description
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

How to fix

input/lb.csv

Your review

Mapping spec