yamaa / Benchmark

ADaM.ADSL

Place Each Dose in Its Period to Find the First Dose of Period 2

input files
4
subjects
3
expected rows
6
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.

We suggest spending no more than 5 minutes on a review. The other tabs beside Your review are background for assessment, not under review.

Summary

Lifecycle: draftEditUnder reviewWhat this benchmark means
README.md

Public entries: Python and R. Passing coverage requires an installed inventory.

Goal: give each subject the date of their first dose in treatment period 2 (TR02SDT).

Input: the subjects, their dosing records with a start date and the visit each dose was given at, the visits with their start dates, and each subject's treatment periods, each from a first to a last day.

Variables:

  • TR02SDT is the start date of the subject's earliest dose whose period is period 2, and blank for a subject with no dose in period 2.

Note: each dose is placed in the period whose first and last days, both inclusive, hold that dose's own date, so a dose on the first day of a period belongs to that period.

Specification variants

  • spec_date.yaml places each dose by its own start date.
  • spec_visit.yaml places each dose by the start date of the visit it was given at, looked up for that dose; doses fall on their visit's date, so both build the same dataset.

Inputs

Under review4 source files

input/dm.csv

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

input/ex.csv

Edit8 rows
STUDYIDUSUBJIDEXSEQVISITNUMEXSTDT
YAMAA-01112025-01-01
YAMAA-01222025-01-15
YAMAA-01332025-02-01
YAMAA-01442025-02-15
YAMAA-01112025-01-05
YAMAA-01232025-02-06
YAMAA-01112025-01-10
YAMAA-01222025-01-24

input/periods.csv

Edit5 rows
STUDYIDUSUBJIDAPERIODAPERSDTAPEREDT
YAMAA-0112025-01-012025-01-31
YAMAA-0122025-02-012025-02-28
YAMAA-0112025-01-052025-02-05
YAMAA-0122025-02-062025-03-07
YAMAA-0112025-01-102025-02-09

input/sv.csv

Edit8 rows
STUDYIDUSUBJIDVISITNUMSVSTDT
YAMAA-0112025-01-01
YAMAA-0122025-01-15
YAMAA-0132025-02-01
YAMAA-0142025-02-15
YAMAA-0112025-01-05
YAMAA-0132025-02-06
YAMAA-0112025-01-10
YAMAA-0122025-01-24

Expected output

Under review6 expected rows

expected/adsl.csv

Edit3 rows
STUDYIDUSUBJIDTR02SDT
YAMAA-012025-02-01
YAMAA-012025-02-06
YAMAA-01—

expected/adsl_visit.csv

Edit3 rows
STUDYIDUSUBJIDTR02SDT
YAMAA-012025-02-01
YAMAA-012025-02-06
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
ADSLTR02SDTDate of First Exposure in Period 02numericISO 8601Take EXSTDT from the first EX record matching on STUDYID and USUBJID, where EX.DOSEPER = 2, ordered by EX.EXSTDT, 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

Edit4 lines
library(yamaa)yamaa_spec("spec_visit.yaml")$run()$save()yamaa_spec("spec_date.yaml")$run()$output

Python

Edit4 lines
import yamaayamaa.spec("spec_visit.yaml").run().save()yamaa.spec("spec_date.yaml").run().output