Review ask

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.

  1. Task: Would a real study need this derivation, specified this way? Does it follow CDISC ADaM: variable names, controlled terms, record structure? Flag any rule that is ambiguous or that a sponsor would handle differently.
  2. Inputs: Do they look like data collected in a real trial, and do they include the situations you would expect to meet in one?
  3. Expected output: Would independent QC programming reproduce every value from these inputs and rules?

The other tabs beside Comments are background for assessment, not under review.

Summary

Lifecycle: draftEditUnder review
What this benchmark means
README.md

Goal: show that a single row template can replace a column's stated default for its own rows while every other template keeps it: weight records gain a body-mass-index record computed from baseline height, and all other records carry the standardized result unchanged.

Input: one spec.yaml with two row templates over a vital-signs extract (input/vs.csv: height, weight, and temperature records with standardized numeric results) and a subject-level file (input/adsl.csv) carrying each subject's baseline height in centimetres.

Variables:

  • AVAL: the analysis value. For body-mass-index rows, weight in kilograms divided by squared baseline height in metres; for every other row, the standardized result exactly as collected. A body-mass-index row with no usable baseline height keeps AVAL blank, as does a row whose collected result is blank.
  • PARAMCD: which record a row carries: the collected test code (HEIGHT, WEIGHT, TEMP), or BMI for the derived body-mass-index rows.
  • PARAM: the matching test name, or Body Mass Index (kg/m^2) for the derived rows.

Note: a column's stated default applies to every row template. A template that restates the column replaces the default for its own rows only, and the replacement reads that template's names exactly as if it had been written inside the template. The collected template therefore carries weight records through unchanged: the replacement never leaks onto them, while the body-mass-index template divides each weight by its own subject's baseline height.

Inputs

Under review
2 source files

input/adsl.csv

Edit
2 rows
input/adsl.csv
STUDYIDUSUBJIDHEIGHTBL
YAMAA-01172
YAMAA-01—

input/vs.csv

Edit
7 rows
input/vs.csv
STUDYIDUSUBJIDVISITVSTESTCDVSTESTVSSTRESNVSSTRESU
YAMAA-01BASELINEHEIGHTHeight (cm)172cm
YAMAA-01BASELINEWEIGHTWeight (kg)70kg
YAMAA-01WEEK 4WEIGHTWeight (kg)71kg
YAMAA-01BASELINETEMPTemperature (C)36.6C
YAMAA-01BASELINEHEIGHTHeight (cm)165cm
YAMAA-01BASELINEWEIGHTWeight (kg)80kg
YAMAA-01WEEK 4WEIGHTWeight (kg)—kg

Expected output

Under review
11 expected rows

expected/advs.csv

Edit
11 rows
expected/advs.csv
STUDYIDUSUBJIDAVISITPARAMCDPARAMAVAL
YAMAA-01BASELINEHEIGHTHeight (cm)172
YAMAA-01BASELINEWEIGHTWeight (kg)70
YAMAA-01WEEK 4WEIGHTWeight (kg)71
YAMAA-01BASELINETEMPTemperature (C)36.6
YAMAA-01BASELINEHEIGHTHeight (cm)165
YAMAA-01BASELINEWEIGHTWeight (kg)80
YAMAA-01WEEK 4WEIGHTWeight (kg)—
YAMAA-01BASELINEBMIBody Mass Index (kg/m^2)23.66143861546782
YAMAA-01WEEK 4BMIBody Mass Index (kg/m^2)23.999459167117358
YAMAA-01BASELINEBMIBody Mass Index (kg/m^2)—
YAMAA-01WEEK 4BMIBody Mass Index (kg/m^2)—
Shaded columns are derived— = missing value

Comments and assessment materials

Comments

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Mapping spec

Generated from the benchmark YAML; do not edit by hand

Dataset NameVariable NameVariable LabelTypeCodelist/Controlled TermsCoreComputational MethodOrigin
ADVSSTUDYIDStudy IdentifiercharacterCopy value from VS.STUDYID.Predecessor
ADVSUSUBJIDUnique Subject IdentifiercharacterCopy value from VS.USUBJID.Predecessor
ADVSAVISITAnalysis Visit NamecharacterCopy value from VS.VISIT.Predecessor
ADVSPARAMCDParameter CodecharacterSet per constructed row; see the Row construction sheet.Derived
ADVSPARAMParametercharacterSet per constructed row; see the Row construction sheet.Derived
ADVSAVALAnalysis ValuenumericCopy value from VS.VSSTRESN.Predecessor
TemplateInclude whenPARAMCDPARAMHEIGHTBLAVAL
collectedCopy VS.VSTESTCDCopy VS.VSTESTConstant "None"None
derived_bmiVS.VSTESTCD = 'WEIGHT'Constant "BMI"Constant "Body Mass Index (kg/m^2)"Copy ADSL.HEIGHTBLCompute VS.VSSTRESN / NULLIF(HEIGHTBL * HEIGHTBL / 10000, 0)
VersionDateAuthorDescriptionReviewerSign-off
1.32026-09-29yamaa docs buildShow study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.22026-09-29yamaa docs buildClassify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.12026-09-29yamaa docs buildResolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0yamaa docs buildInitial generation from spec.yaml

yamaa code

Runs the yamaa specification; its result must match the expected output

run.R

Edit
4 lines
library(yamaa)advs <- yamaa_domain("spec.yaml")$outputadvs

run.py

Edit
4 lines
import yamaaadvs = yamaa.yamaa_domain("spec.yaml").outputadvs