yamaa As a clinical trial statistician or programmer, challenge anything in this benchmark: describe a problem in Comments, or propose a fix with the Edit button on any source file.
- Task: Is this a specification error a study team could realistically make, and should the build stop on it rather than continue?
- Inputs: Do they trigger the failure for the reason the summary gives?
- Expected failure: Is this the right error, raised at the right point, and would it tell the programmer what to fix?
The other tabs beside Comments are background for assessment, not under review.
Summary
EditUnder reviewWhat this benchmark meansREADME.mdGoal: carry each collected laboratory result into AVAL and
add its natural logarithm as AVALLN, with one record for each
subject and parameter.
Input: five laboratory records across five subjects: a detectable viral load (12,000 copies/mL), an undetectable viral load reported as zero - the record the run rejects - a missing result, a low near-limit result (40), and a CD4 count (480), showing one record for each subject and parameter.
Variables:
AVALwould be the analysis value, mapped from the collected numeric result (LBSTRESN).AVALLNwould be the natural logarithm ofAVAL, which the analysis models rather than the untransformed result, and blank whenAVALis blank. Zero has no logarithm, and a result below the limit of detection needs a stated substitution before it can be transformed, so the run fails while the values are computed and no artifact is accepted.
How to fix
State the analysis policy for an undetectable value. If it should produce a missing transformed result, guard zero explicitly:
derivation:
compute:
expr: "LN(NULLIF(AVAL, 0))"
If the study instead substitutes a value related to the assay limit, derive
that stated substitute first and apply LN to it. Do not replace zero with an
unstated constant.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- derivation
- condition
- ln_of_nonpositive
- requirement
- REQ-0432
expected/error.yaml
phase: derivation
condition: ln_of_nonpositive
spec_paths:
- columns.AVALLN.derivation.compute
requirement: REQ-0432
context:
expr: "LN(AVAL)"
keys:
- STUDYID: PILOT7
USUBJID: P7-762
PARAMCD: HIVRNA
Inputs
Under review1 source fileinput/lb.csv
Edit5 rows| STUDYID | USUBJID | LBTESTCD | LBSTRESN |
|---|---|---|---|
| PILOT7 | HIVRNA | 12000 | |
| PILOT7 | HIVRNA | 0 | |
| PILOT7 | HIVRNA | — | |
| PILOT7 | HIVRNA | 40 | |
| PILOT7 | CD4 | 480 |
Unexpected Output
Under reviewNo artifact is producedNo fixture files in this directory.
Comments and assessment materials
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | Computational Method | Origin |
|---|---|---|---|---|---|---|---|
| ADLB | STUDYID | Study Identifier | character | Copy value from LB.STUDYID. | Predecessor | ||
| ADLB | USUBJID | Unique Subject Identifier | character | Copy value from LB.USUBJID. | Predecessor | ||
| ADLB | PARAMCD | Parameter Code | character | Copy value from LB.LBTESTCD. | Predecessor | ||
| ADLB | AVAL | Analysis Value | numeric | Copy value from LB.LBSTRESN. | Predecessor | ||
| ADLB | AVALLN | Natural Log of Analysis Value | numeric | Compute LN(AVAL). | Derived |
| Version | Date | Author | Description | Reviewer | Sign-off |
|---|---|---|---|---|---|
| 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 |
Comments
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