yamaa / Benchmark

ADaM.ADAE

Carry Several Supplemental Qualifiers Onto Their Adverse Events

input files
2
subjects
3
expected rows
5
Review ask

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Summary

Lifecycle: draftEditUnder reviewWhat this benchmark means
README.md

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

Goal: carry three record-level supplemental qualifiers of each adverse event onto its analysis row: the location detail (AEXSITE), the suspected cause (AEXCAUS) and the reaction size (AEXSIZE).

Input: one spec.yaml over adverse event records and the supplemental qualifier records of the AE domain (SDTMIG section 8.4), each naming the parent event by its sequence number, the qualifier name and its value.

Variables:

  • AETERM is the reported term of the event, as collected.
  • AEXSITE is the value of the event's AEXSITE qualifier; empty when the event has none.
  • AEXCAUS is the value of the event's AEXCAUS qualifier; empty when the event has none.
  • AEXSIZE is the value of the event's AEXSIZE qualifier as a number; empty when the event has none.

Note: one declaration names the three qualifiers, and each becomes a field of the event's supplemental records. A subject-level qualifier, which names no sequence number, and a qualifier of a sequence number no event carries change nothing. A qualifier record whose name is none of the three would stop the run rather than be dropped.

Inputs

Under review2 source files

input/ae.csv

Edit5 rows
STUDYIDUSUBJIDAESEQAETERM
YAMAA-011HEADACHE
YAMAA-012RASH
YAMAA-011NAUSEA
YAMAA-012RASH
YAMAA-011FATIGUE

input/suppae.csv

Edit9 rows
STUDYIDRDOMAINUSUBJIDIDVARIDVARVALQNAMQLABELQVALQORIG
YAMAA-01AEAESEQ1AEXSITELocation DetailLEFT TEMPLECRF
YAMAA-01AEAESEQ1AEXCAUSSuspected CauseSTRESSCRF
YAMAA-01AEAESEQ2AEXSITELocation DetailRIGHT FOREARMCRF
YAMAA-01AEAESEQ2AEXSIZEReaction Size (mm)12CRF
YAMAA-01AE——AEXSUBJSubject NoteATOPICCRF
YAMAA-01AEAESEQ2AEXSIZEReaction Size (mm)30CRF
YAMAA-01AEAESEQ2AEXSITELocation DetailUPPER BACKCRF
YAMAA-01AEAESEQ9AEXSITELocation DetailORPHANCRF
YAMAA-01AEAESEQ1AEXCAUSSuspected CauseUNKNOWNCRF

Expected output

Under review5 expected rows

expected/adae.csv

Edit5 rows
STUDYIDUSUBJIDAESEQAETERMAEXSITEAEXCAUSAEXSIZE
YAMAA-011HEADACHELEFT TEMPLESTRESS—
YAMAA-012RASHRIGHT FOREARM—12
YAMAA-011NAUSEA———
YAMAA-012RASHUPPER BACK—30
YAMAA-011FATIGUE—UNKNOWN—
Shaded columns are derived— = missing value

Human review and assessment

Your review

2 questions and your comments · View benchmark 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
ADAEAETERMReported Term for the Adverse EventcharacterCopy value from AE.AETERM.Predecessor
ADAEAEXSITELocation DetailcharacterTake AEXSITE from the SUPPAE record whose STUDYID equals AE.STUDYID, USUBJID equals AE.USUBJID and IDVARVAL equals AE.AESEQ, where SUPPAE.RDOMAIN = 'AE' AND SUPPAE.IDVAR = 'AESEQ', and no match yields blank.Derived
ADAEAEXCAUSSuspected CausecharacterTake AEXCAUS from the SUPPAE record whose STUDYID equals AE.STUDYID, USUBJID equals AE.USUBJID and IDVARVAL equals AE.AESEQ, where SUPPAE.RDOMAIN = 'AE' AND SUPPAE.IDVAR = 'AESEQ', and no match yields blank.Derived
ADAEAEXSIZEReaction Size (mm)numericTake AEXSIZE from the SUPPAE record whose STUDYID equals AE.STUDYID, USUBJID equals AE.USUBJID and IDVARVAL equals AE.AESEQ, where SUPPAE.RDOMAIN = 'AE' AND SUPPAE.IDVAR = 'AESEQ', and no match yields blank.Derived
VersionDateAuthorDescriptionReviewerSign-off
1.72026-10-20yamaa docs buildRead 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
1.62026-10-17yamaa docs buildDescribe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight
1.52026-10-17yamaa docs buildName 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
1.42026-10-15yamaa docs buildState datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks
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

Public calls generated from benchmark.yaml; results must match the expected output

R

Edit3 lines
library(yamaa)yamaa_spec("spec.yaml")$run()$output

Python

Edit3 lines
import yamaayamaa.spec("spec.yaml").run().output