yamaa / Benchmark

ADaM.ADSL

Inherited Entry Removal

input files
1
subjects
3
expected rows
3
Review ask

As a clinical trial statistician or programmer, answer two short questions in Your review: the task and the inputs and outputs. Agreeing with both approves this benchmark; disagreeing with either needs a comment. Propose a fix with the Edit button on any source file, or add it to your comments.

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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: demonstrate a study level removing one entry from a translation it inherits, keeping the rest, to derive DCSREAS.

Input: two spec files, read root-first:

  • spec_organization.yaml translates each collected discontinuation reason code, AE, LTFU, WBS and PD, into its reason, and reports any other code as OTHER;
  • spec_study.yaml is the entry: it names the organization level as its parent, removes only the translation of PD with clear, and declares the complete output.

Variables:

  • DCSREAS is ADVERSE EVENT, LOST TO FOLLOW-UP or WITHDRAWAL BY SUBJECT from the code; a PD code is OTHER, because progressive disease is not a reason this study recognizes.

Note: clear removes the inherited PD translation before the study layer composes. The other three translations, and OTHER for a code without a translation, still come from the organization level.

Inputs

Under review1 source file

input/ds.csv

Edit3 rows
USUBJIDDSREASCD
AE
PD
LTFU

Expected output

Under review3 expected rows

expected/adsl.csv

Edit3 rows
USUBJIDDCSREAS
ADVERSE EVENT
OTHER
LOST TO FOLLOW-UP
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
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_study.yaml")$run()$output

Python

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