yamaa / Benchmark

TEST.TIMELINE

Start Dates Read From Each Row's Own Record

input files
3
subjects
3
expected rows
9
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: build one timeline row per subject, adverse event and concomitant medication, and complete the start date (STDT) of every event and medication row from the record that built it.

Input: one spec.yaml over the subjects (input/dm.csv: domain, subject and reference start date), their adverse events (input/ae.csv: domain, subject, sequence, reported term and start date) and their concomitant medications (input/cm.csv: domain, subject, sequence, medication name and start date).

Variables:

  • SEQ: the sequence number of the record behind the row, and 1 on the subject's own row.
  • TERM: the reported adverse event term or medication name, and REFERENCE START on the subject's own row.
  • STDT: the start date collected on the record behind the row: the adverse event's or the medication's own start date, and the subject's reference start date on the subject's row; blank when that record has no start date.

Note: the start date is stated once for the event and medication rows, naming the start dates of both. Each row reads the date of its own record. The other file is matched on the subject and the domain, so a medication row never takes an adverse event's date, and an event without a start date stays blank even when the subject's medication has one.

Inputs

Under review3 source files

input/ae.csv

Edit3 rows
DOMAINUSUBJIDAESEQAETERMAESTDTC
AE1HEADACHE2024-03-04
AE2NAUSEA2024-03-11
AE1RASH—

input/cm.csv

Edit3 rows
DOMAINUSUBJIDCMSEQCMTRTCMSTDTC
CM1PARACETAMOL2024-03-04
CM1IBUPROFEN2024-02-20
CM2OMEPRAZOLE—

input/dm.csv

Edit3 rows
DOMAINUSUBJIDRFSTDTC
DM2024-03-01
DM2024-03-02
DM2024-02-15

Expected output

Under review9 expected rows

expected/timeline.csv

Edit9 rows
DOMAINUSUBJIDSEQTERMSTDT
DM1REFERENCE START2024-03-01
DM1REFERENCE START2024-03-02
DM1REFERENCE START2024-02-15
AE1HEADACHE2024-03-04
AE2NAUSEA2024-03-11
AE1RASH—
CM1PARACETAMOL2024-03-04
CM1IBUPROFEN2024-02-20
CM2OMEPRAZOLE—
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

Variable NameVariable LabelTypeLengthControlled Terms or FormatOriginCoreConversion DefinitionVariable TypeVariable OrderComments for Define
DOMAINDomain AbbreviationCharDerivedSet per constructed row; see the Row construction sheet.SDTM1
USUBJIDUnique Subject IdentifierCharDerivedSet per constructed row; see the Row construction sheet.SDTM2
SEQSequence NumberNumDerivedSet per constructed row; see the Row construction sheet.SDTM3
TERMReported TermCharDerivedSet per constructed row; see the Row construction sheet.SDTM4
STDTStart DateCharISO 8601DerivedFirst non-missing of AE.AESTDTC and CM.CMSTDTC.SDTM5
TemplateInclude whenDOMAINUSUBJIDSEQTERMSTDT
subjectsCopy DM.DOMAINCopy DM.USUBJIDConstant "1"Constant "REFERENCE START"Copy DM.RFSTDTC
adverse_eventsCopy AE.DOMAINCopy AE.USUBJIDCopy AE.AESEQCopy AE.AETERMNone
medicationsCopy CM.DOMAINCopy CM.USUBJIDCopy CM.CMSEQCopy CM.CMTRTNone
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_spec("spec.yaml")$run()$output

Python

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