yamaa / Benchmark

ADaM.ADSL

End-of-Study Record

input files
2
subjects
3
expected rows
3
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: derive each subject's end-of-study date from their disposition records, checking that no subject has more than one end-of-study record.

Input: one spec.yaml declaring two datasets. DM carries one row per subject. DS carries disposition records: subject, category, decoded term, and start date.

Lookups:

  • DS_EOS names each subject's end-of-study record: a disposition event that is not a screen failure. The subject key is shared with the output, so it is inferred rather than restated. EOSDT is that record's start date; a subject with no such record, such as one who only failed screening, keeps EOSDT blank.

Note: the eligible records are checked for a repeated subject before any row is built, so the lookup needs no rule for choosing among them: a subject with two end-of-study records stops the run rather than taking either one. A screen-failure record is never eligible, so it may sit beside a subject's end-of-study record.

Inputs

Under review2 source files

input/dm.csv

Edit3 rows
STUDYIDUSUBJID
YAMAA-01
YAMAA-01
YAMAA-01

input/ds.csv

Edit4 rows
STUDYIDUSUBJIDDSCATDSDECODDSSTDTC
YAMAA-01DISPOSITION EVENTCOMPLETED2024-01-10
YAMAA-01DISPOSITION EVENTCOMPLETED2024-02-11
YAMAA-01DISPOSITION EVENTSCREEN FAILURE2024-01-02
YAMAA-01DISPOSITION EVENTSCREEN FAILURE2024-03-01

Expected output

Under review3 expected rows

expected/adsl.csv

Edit3 rows
STUDYIDUSUBJIDEOSDT
YAMAA-012024-01-10
YAMAA-012024-02-11
YAMAA-01—
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
ADSLSTUDYIDStudy IdentifiercharacterCopy value from DM.STUDYID.Predecessor
ADSLUSUBJIDUnique Subject IdentifiercharacterCopy value from DM.USUBJID.Predecessor
ADSLEOSDTEnd of Study DatecharacterTake DSSTDTC from the DS record matching on STUDYID and USUBJID, where DS.DSCAT = 'DISPOSITION EVENT' AND DS.DSDECOD <> 'SCREEN FAILURE', 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