yamaa / Benchmark

ADaM.ADAE

One Fragment on Two Templates

input files
2
subjects
2
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: demonstrate one reusable fragment adding the analysis duration ADURN to both an adverse event and a concomitant medication dataset, with a second fragment adding the severity code ASEVN to adverse events only.

Input: six spec files:

  • spec_ae.yaml and spec_cm.yaml are the templates: each reads its own records and gives the subject, the record's sequence number, AESEQ or CMSEQ, and its analysis start and end dates, ASTDT and AENDT;
  • spec_duration.yaml derives the duration from those two dates and names no template of its own;
  • spec_severity.yaml codes the reported severity of an adverse event;
  • spec_adae.yaml is the adverse event entry: it names spec_ae.yaml as its parent, lists both fragments under include, and declares the complete output;
  • spec_adcm.yaml is the medication entry: it names spec_cm.yaml as its parent and lists the duration fragment alone.

Variables:

  • ADURN is the number of days from ASTDT to AENDT, counting both the first and the last day, so an event that starts and ends on one day lasts 1; it is missing while the end date is not known;
  • ASEVN (adverse events only) is 1 for a mild, 2 for a moderate and 3 for a severe event.

Note: each entry composes its parent first, then the fragments it lists in order, then its own fields, so a fragment adds to whichever template includes it and the entry has the last word. The one duration file serves both datasets: nothing in it names a template.

Inputs

Under review2 source files

input/ae.csv

Edit3 rows
USUBJIDAESEQAESEVAESTDTCAEENDTC
1MILD2026-01-052026-01-07
2SEVERE2026-01-102026-01-10
1MODERATE2026-02-01—

input/cm.csv

Edit2 rows
USUBJIDCMSEQCMSTDTCCMENDTC
12026-01-032026-01-12
12026-02-02—

Expected output

Under review5 expected rows

expected/adae.csv

Edit3 rows
USUBJIDAESEQASTDTAENDTADURNASEVN
12026-01-052026-01-0731
22026-01-102026-01-1013
12026-02-01——2

expected/adcm.csv

Edit2 rows
USUBJIDCMSEQASTDTAENDTADURN
12026-01-032026-01-1210
12026-02-02——
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

Edit4 lines
library(yamaa)yamaa_spec("spec_adcm.yaml")$run()$save()yamaa_spec("spec_adae.yaml")$run()$output

Python

Edit4 lines
import yamaayamaa.spec("spec_adcm.yaml").run().save()yamaa.spec("spec_adae.yaml").run().output