yamaa / Benchmark

ADaM.ADEX

Each Dose Level a Subject Received, Against the Planned Dose

input files
2
subjects
2
expected rows
3
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: show that a record's identity may be computed from that one record, through the project's own routine and through the subject's planned dose: one record per subject and dose level received (DOSE), stating whether the level is above the subject's planned dose (ABOVEFL) and what that planned dose is (PLANDOSE).

Input: one spec.yaml over exposure records (input/ex.csv: one per administration, with the study day and the dose given) and each subject's planned dose (input/plan.csv). The project.yaml lists the function file functions/project_value.yaml, whose routine returns the dose it is given.

Variables:

  • DOSE is a dose level the subject received, as the project's routine returns it.
  • ABOVEFL is Y when that dose is above the subject's planned dose and N otherwise.
  • PLANDOSE is the subject's planned dose.

Note: each administration contributes its own dose and flag, so a level the subject received several times gives one record, while a different level gives another, each in the order of its first administration.

Inputs

Under review2 source files

input/ex.csv

Edit4 rows
USUBJIDEXSTDYEXDOSE
150
850
15100
150

input/plan.csv

Edit2 rows
USUBJIDPLANDOSE
50
100

Expected output

Under review3 expected rows

expected/adex.csv

Edit3 rows
USUBJIDDOSEABOVEFLPLANDOSE
50N50
100Y50
50N100
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
ADEXUSUBJIDUnique Subject IdentifiercharacterCopy value from EX.USUBJID.Predecessor
ADEXDOSEDosenumericCall project function project_value with x = EX.EXDOSE.Derived
ADEXABOVEFLDose Above Planned Flagcharacter"Y" when EX.EXDOSE > PLANDOSE, with PLANDOSE taken from the PLAN record matching on USUBJID, and a row with no match is an error; "N" otherwise; blank when the condition is unknown.Derived
ADEXPLANDOSEPlanned DosenumericTake PLANDOSE from the PLAN record matching on USUBJID, and a row with no match is an error.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

Edit3 lines
library(yamaa)yamaa_project("project.yaml")$spec("ADEX")$run()$output

Python

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