yamaa / Benchmark

ADaM.ADAE

Missing Term Yields Unknown Skin Flag

input files
1
subjects
1
expected rows
2
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 reviewWhat this benchmark means
README.md

Goal: flag adverse events whose term mentions dermatitis or erythema, writing the structured str_contains result straight into SKIN_FLAG. Here every collected term is missing, so the search has nothing to test.

Input: one record per adverse event carrying AESEQ (sequence number) and AEDECOD (dictionary-derived term); both records have no term.

Variables:

  • SKIN_FLAG: UNKNOWN on every row. With no term present, the missing value is used instead of running the search, so the boolean result never appears and the run succeeds.

Inputs

Under review1 source file

input/ae.csv

Edit2 rows
STUDYIDUSUBJIDAESEQAEDECOD
YAMAA-011—
YAMAA-012—

Expected output

Under review2 expected rows

expected/adae.csv

Edit2 rows
STUDYIDUSUBJIDAESEQSKIN_FLAG
YAMAA-011UNKNOWN
YAMAA-012UNKNOWN
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
ADAESTUDYIDStudy IdentifiercharacterCopy value from AE.STUDYID.Predecessor
ADAEUSUBJIDUnique Subject IdentifiercharacterCopy value from AE.USUBJID.Predecessor
ADAEAESEQSequence NumbernumericCopy value from AE.AESEQ.Predecessor
ADAESKIN_FLAGSkin Event FlagcharacterTrue when AE.AEDECOD matches DERMATITIS|ERYTHEMA anywhere, false when it does not; a missing source → "UNKNOWN".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

Edit4 lines
library(yamaa)adae <- yamaa_domain("spec.yaml")$outputadae

run.py

Edit4 lines
import yamaaadae = yamaa.yamaa_domain("spec.yaml").outputadae