yamaa / Benchmark

ADaM.ADSL

Shorthand Spellings

input files
2
subjects
8
expected rows
4
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 reviewWhat this benchmark means
README.md

Goal: show that a lone value may stand where a list is accepted, and a lone condition or label string may stand where its full form is accepted: the short spellings run exactly as their long forms.

Input: one spec.yaml over a demographics file (one record per subject: sex and age) and a weight file (several dated weight records per subject).

Variables:

  • SEX: the subject's recorded sex.
  • AGE: the subject's age in years; blank when not collected.
  • AGE65FL: Y for subjects aged 65 or older; blank otherwise. A lone condition needs no explicit yes or no text: it answers Y when true and stays blank when false or unknown.
  • SUBJLBL: a readable label joining the subject identifier and sex, written as one plain string with placeholders.
  • WTMAX: the largest collected weight across the subject's weight records; the grouping key is written as a single key.
  • LASTWT: the weight from the subject's latest dated record; the latest record wins because a single ordering value sorts earliest-first, and the match key is written as a single key.

Note: each short spelling expands to its full form before the run: a lone key becomes a one-key list, a lone check becomes a one-check list, a lone condition answers Y when true and stays blank otherwise, a lone label string keeps its placeholders, and a lone ordering value sorts earliest-first.

Inputs

Under review2 source files

input/dm.csv

Edit4 rows
USUBJIDSEXAGE
M34
F67
M—
F72

input/wt.csv

Edit7 rows
USUBJIDWTSEQWTDTCWT
12026-01-0570.5
22026-02-0571.0
12026-01-0668.0
22026-02-0667.5
12026-01-0780.0
12026-01-0855.0
22026-02-0856.0

Expected output

Under review4 expected rows

expected/adsl.csv

Edit4 rows
STUDYIDUSUBJIDSEXAGEAGE65FLSUBJLBLWTMAXLASTWT
YAMAA-01M34—Subject YAMAA-01-001 (M)7171
YAMAA-01F67YSubject YAMAA-01-002 (F)6867.5
YAMAA-01M——Subject YAMAA-01-003 (M)8080
YAMAA-01F72YSubject YAMAA-01-004 (F)5656
Shaded columns are derived— = missing value

Comments and assessment materials

Comments

Signed in with GitHub; saved in repository Discussions

Mapping spec

Generated from the benchmark YAML; do not edit by hand

Dataset NameVariable NameVariable LabelTypeCodelist/Controlled TermsCoreComputational MethodOrigin
ADSLSTUDYIDStudy IdentifiercharacterSet constant value "YAMAA-01".Assigned
ADSLUSUBJIDUnique Subject IdentifiercharacterCopy value from DM.USUBJID.Predecessor
ADSLSEXSexcharacterCopy value from DM.SEX.Predecessor
ADSLAGEAgenumericCopy value from DM.AGE.Predecessor
ADSLAGE65FLAge 65 or Older Flagcharacter"Y" when AGE >= 65; blank otherwise.Derived
ADSLSUBJLBLSubject LabelcharacterFill the template "Subject {USUBJID} ({SEX})".Derived
ADSLWTMAXMaximum Collected WeightnumericAggregate MAX(WT.WT) over records matching on USUBJID.Derived
ADSLLASTWTLatest Collected WeightnumericTake WT from the last WT record matching on USUBJID, ordered by WT.WTDTC, and a row with no match is an error.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

Edit4 lines
library(yamaa)adsl <- yamaa_domain("spec.yaml")$outputadsl

run.py

Edit4 lines
import yamaaadsl = yamaa.yamaa_domain("spec.yaml").outputadsl