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 review
What this benchmark means
README.md

Goal: derive each subject's death study day and cause of death by joining their adverse events, and code the cause against a medical dictionary.

Input: one spec.yaml declaring three datasets. DM carries one row per subject. AE carries the adverse-event records: subject, event term, outcome, and study day. MEDDRA carries the dictionary: each lowest-level term beside its preferred term.

Lookups:

  • DEATHEV names each subject's fatal adverse event. Only fatal records are eligible, and the latest study day wins; the subject key is shared with the output, so it is inferred rather than restated. A subject with two fatal records takes the later one's day and term, and a subject with no fatal record keeps DTHDY and DTHCAUS blank.
  • The named intermediate codes the cause into DTHPTERM: the subject's cause is matched against the dictionary's lowest-level term and the preferred term comes back. A missing cause matches nothing, so the coded cause stays blank too, as it does for a cause the dictionary does not list.

Note: a join never changes the row count: every subject keeps exactly one row, and every read of the same lookup sees the one selected record. When no record is selected, each read answers with a blank rather than failing.

Inputs

Under review
3 source files

input/ae.csv

Edit
5 rows
input/ae.csv
USUBJIDAEDECODAEOUTAEDY
HEADACHENOT RECOVERED50
CARDIAC FAILUREFATAL100
MYOCARDIAL INFARCTIONFATAL150
STROKEFATAL80
NAUSEARECOVERED20

input/dm.csv

Edit
4 rows
input/dm.csv
USUBJID

input/meddict.csv

Edit
3 rows
input/meddict.csv
LLTNAMEPTNAME
MYOCARDIAL INFARCTIONAcute myocardial infarction
CARDIAC FAILURECardiac failure
STROKECerebrovascular accident

Expected output

Under review
4 expected rows

expected/adsl.csv

Edit
4 rows
expected/adsl.csv
USUBJIDDTHDYDTHCAUSDTHPTERM
150MYOCARDIAL INFARCTIONAcute myocardial infarction
80STROKECerebrovascular accident
———
———
Shaded columns are derived— = missing value

Comments and assessment materials

Comments

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Mapping spec

Generated from the benchmark YAML; do not edit by hand

Dataset NameVariable NameVariable LabelTypeCodelist/Controlled TermsCoreComputational MethodOrigin
ADSLUSUBJIDUnique Subject IdentifiercharacterCopy value from DM.USUBJID.Predecessor
ADSLDTHDYStudy Day of DeathnumericTake AEDY from the last AE record matching on the shared output keys, where AE.AEOUT = 'FATAL', ordered by AE.AEDY, and no match yields blank.Derived
ADSLDTHCAUSCause of DeathcharacterTake AEDECOD from the last AE record matching on the shared output keys, where AE.AEOUT = 'FATAL', ordered by AE.AEDY, and no match yields blank.Derived
ADSLDTHPTERMCause of Death Preferred TermcharacterTake PTNAME from the MEDDRA record whose LLTNAME equals DTHCAUS, and no match yields blank.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

Edit
4 lines
library(yamaa)adsl <- yamaa_domain("spec.yaml")$outputadsl

run.py

Edit
4 lines
import yamaaadsl = yamaa.yamaa_domain("spec.yaml").outputadsl