Treatment Start and End Datetimes From Dates

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: one row per subject with the datetimes of first (TRTSDTM) and last (TRTEDTM) exposure to treatment, built from the treatment start and end dates (TRTSDT, TRTEDT), and a flag (TRTSTMF) marking that the start's time of day was supplied.

Input: one spec.yaml over subject-level records carrying the study, the subject and the treatment start and end dates, held as dates rather than as collected text. A subject may still be on treatment, with no end date, or never treated, with neither date.

Variables:

TRTSDTM is the first moment of the start date, 00:00:00. A subject with no start date has no start datetime.
TRTSTMF is H when the start datetime exists: its hour, minute and second were all supplied, because a date carries no time of day. It is empty when there is no start datetime.
TRTEDTM is the last moment of the end date, 23:59:59, so a comparison against it includes the whole last day of treatment. A subject with no end date has no end datetime.

Note: a date becomes a datetime only by naming which moment of the day is meant; nothing else about the date changes.

YAML specification

1 spec file

spec.yaml

Edit73 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADSL5keys: [STUDYID, USUBJID]6input:7  SL:8    path: input/sl.csv9    types: {TRTSDT: date, TRTEDT: date}10base: SL1112output:13  path: adsl.csv14  columns: [STUDYID, USUBJID, TRTSDT, TRTEDT, TRTSDTM, TRTSTMF, TRTEDTM]1516columns:17  - name: STUDYID18    type: str19    label: Study Identifier20    derivation: SL.STUDYID2122  - name: USUBJID23    type: str24    label: Unique Subject Identifier25    derivation: SL.USUBJID2627  - name: TRTSDT28    type: date29    label: Date of First Exposure to Treatment30    derivation: SL.TRTSDT3132  - name: TRTEDT33    type: date34    label: Date of Last Exposure to Treatment35    derivation: SL.TRTEDT3637  # A date carries no time of day, so the first moment of the day is38  # supplied; the start keeps the date's collected precision.39  - name: TRTSDTM40    type: datetime41    label: Datetime of First Exposure to Treatment42    derivation:43      impute:44        type: datetime45        source: TRTSDT46        time: first4748  - name: TRTSTMF49    type: str50    label: Time of First Exposure Imputation Flag51    derivation:52      imputation_flag:53        source: TRTSDTM54        part: time5556  # The last moment of the day is supplied to the end date.57  - name: TRTEDTM58    type: datetime59    label: Datetime of Last Exposure to Treatment60    derivation:61      impute:62        type: datetime63        source: TRTEDT64        time: last6566verifications:67  - row_count:68      min: 369      max: 370  - assert:71      id: a-start-date-gives-a-start-datetime72      when: "TRTSDT IS NOT NULL"73      require: "TRTSDTM IS NOT NULL"

Inputs

Under review1 source file

input/sl.csv

Edit3 rows

input/sl.csv
STUDYID	TRTSDT	TRTEDT
YAMAA-01	2025-03-04	2025-06-30
YAMAA-01	2025-03-11	—
YAMAA-01	—	—

Expected output

Under review3 expected rows

expected/adsl.csv

Edit3 rows

expected/adsl.csv
STUDYID	TRTSDT	TRTEDT	TRTSDTM	TRTSTMF	TRTEDTM
YAMAA-01	2025-03-04	2025-06-30	2025-03-04T00:00:00	H	2025-06-30T23:59:59
YAMAA-01	2025-03-11	—	2025-03-11T00:00:00	H	—
YAMAA-01	—	—	—	—	—

Shaded columns are derived— = missing value

Human review and assessment

Dataset Name	Variable Name	Variable Label	Type	Codelist/Controlled Terms	Computational Method	Origin
ADSL	STUDYID	Study Identifier	character		Copy value from SL.STUDYID.	Predecessor
ADSL	USUBJID	Unique Subject Identifier	character		Copy value from SL.USUBJID.	Predecessor
ADSL	TRTSDT	Date of First Exposure to Treatment	numeric	ISO 8601	Copy value from SL.TRTSDT.	Predecessor
ADSL	TRTEDT	Date of Last Exposure to Treatment	numeric	ISO 8601	Copy value from SL.TRTEDT.	Predecessor
ADSL	TRTSDTM	Datetime of First Exposure to Treatment	numeric	ISO 8601	Impute incomplete datetime from TRTSDT, giving each time part the source lacks its earliest value; a source without a complete date gives blank; invalid text is an error.	Derived
ADSL	TRTSTMF	Time of First Exposure Imputation Flag	character		Time imputation flag for TRTSDTM: "H" when the whole time was imputed, "M" when the minutes and seconds were, "S" when only the seconds were; blank when the time was collected to the second.	Derived
ADSL	TRTEDTM	Datetime of Last Exposure to Treatment	numeric	ISO 8601	Impute incomplete datetime from TRTEDT, giving each time part the source lacks its latest value; a source without a complete date gives blank; invalid text is an error.	Derived

Version	Date	Author	Description
1.7	2026-10-20	yamaa docs build	Read 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
1.6	2026-10-17	yamaa docs build	Describe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight
1.5	2026-10-17	yamaa docs build	Name 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
1.4	2026-10-15	yamaa docs build	State datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks
1.3	2026-09-29	yamaa docs build	Show study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.2	2026-09-29	yamaa docs build	Classify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.1	2026-09-29	yamaa docs build	Resolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0		yamaa docs build	Initial generation from spec.yaml

R

Edit3 lines

1library(yamaa)23yamaa_spec("spec.yaml")$run()$output

Python

Edit3 lines

1import yamaa23yamaa.spec("spec.yaml").run().output

input/sl.csv

expected/adsl.csv

Your review

Mapping spec

yamaa code

R

Python