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: select each subject's disposition record by ordering on a rank derived per donor record.

Input: one spec.yaml declaring two datasets. DM carries one row per subject. DS carries disposition records with sequence, study day, and a representative numeric value.

Lookups:

  • EOT derives EOT_FALLBACK for each disposition record: the study day plus the sequence number divided by 1000, so the earlier study day ranks first and the sequence breaks a tie within a day. It then filters and orders on that derived rank. A record with no study day has no rank and is ineligible; among the remaining records, keep: first selects the smallest rank. A subject with no ranked record reads missing in all three selected values.

Columns: the chosen donor's decoded term lands in DSDECOD, its representative numeric value lands in DSVALUE, and the computed rank is read through EOT.EOT_FALLBACK into EOT_FALLBACK. The numbers are written with the shortest digits that read back as the same value, so 0.30000000000000004 is not rounded to 0.3.

Inputs

Under review
2 source files

input/dm.csv

Edit
3 rows
input/dm.csv
STUDYIDUSUBJID
YAMAA-01
YAMAA-01
YAMAA-01

input/ds.csv

Edit
5 rows
input/ds.csv
STUDYIDUSUBJIDDSSEQDSSTDYDSDECODDSVALUE
YAMAA-01110COMPLETED0.1
YAMAA-0123EARLY TERMINATION0.30000000000000004
YAMAA-011—WITHDRAWN0.3
YAMAA-0127COMPLETED0.4
YAMAA-011—LOST TO FOLLOW-UP0.5

Expected output

Under review
3 expected rows

expected/adsl.csv

Edit
3 rows
expected/adsl.csv
STUDYIDUSUBJIDDSDECODDSVALUEEOT_FALLBACK
YAMAA-01EARLY TERMINATION0.300000000000000043.002
YAMAA-01COMPLETED0.47.002
YAMAA-01———
Shaded columns are derived— = missing value

Comments and assessment materials

Comments

Signed in with GitHub; saved in repository Discussions

Mapping spec

Generated from the benchmark YAML; do not edit by hand

Dataset NameVariable NameVariable LabelTypeCodelist/Controlled TermsCoreComputational MethodOrigin
ADSLSTUDYIDStudy IdentifiercharacterCopy value from DM.STUDYID.Predecessor
ADSLUSUBJIDUnique Subject IdentifiercharacterCopy value from DM.USUBJID.Predecessor
ADSLDSDECODSelected Disposition TermcharacterTake DSDECOD from the first DS record matching on the shared output keys, where DS.EOT_FALLBACK IS NOT NULL, ordered by DS.EOT_FALLBACK, and no match yields blank.Derived
ADSLDSVALUESelected Numeric ValuenumericTake DSVALUE from the first DS record matching on the shared output keys, where DS.EOT_FALLBACK IS NOT NULL, ordered by DS.EOT_FALLBACK, and no match yields blank.Derived
ADSLEOT_FALLBACKSelected Derived RanknumericTake EOT_FALLBACK from the first DS record matching on the shared output keys, where DS.EOT_FALLBACK IS NOT NULL, ordered by DS.EOT_FALLBACK, where EOT_FALLBACK is derived as compute DSSTDY + DSSEQ / 1000, and no match yields blank.Derived
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)adsl <- yamaa_domain("spec.yaml")$outputadsl

run.py

Edit
4 lines
import yamaaadsl = yamaa.yamaa_domain("spec.yaml").outputadsl