Find the first dose ending in the second day band

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: give each subject the sequence of their first dose ending in day band 2 (B2SEQ).

Input: alternative specifications share subjects, dose starts and lengths, and inclusive day bands. The self-join reads the dose file again under a second input identifier.

Variables:

B2SEQ is the earliest dose sequence ending in band 2, and blank when no dose ends there. In the self-join it is the earliest dose whose most recent earlier dose has sequence 1.

Note: an earlier value computed for each dose is available to the selection that dose reads, bare or qualified by its input identifier.

Specification variants

spec_filter_qualified.yaml and spec_filter_bare.yaml compare the dose's computed last day to both band bounds in a correlated filter.
spec_between_qualified.yaml and spec_between_bare.yaml use the same computed last day as the range value.
spec_filter_expression.yaml repeats the last-day arithmetic.
spec_self_join.yaml compares another dose's start to the reading dose's computed last day, while excluding the reading dose and later doses.

YAML specification

1 spec file

spec_self_join.yaml

Edit42 lines

1yamaa: "1.0"2type: spec3domain: BANDDOSE4keys: [USUBJID]5input:6  SUBJECTS: input/subjects.csv7  DOSES: {path: input/doses.csv, types: {SEQ: int, DAY: int, DUR: int}}8  OTHER: {path: input/doses.csv, types: {SEQ: int, DAY: int, DUR: int}}9base: SUBJECTS1011output:12  path: self_join.csv13  columns: [USUBJID, B2SEQ]1415intermediates:16  - id: PRIOR17    dataset: OTHER18    key: [USUBJID]19    filter: "OTHER.SEQ < DOSES.SEQ AND OTHER.DAY <= DOSES.LASTDAY"20    order_by: [OTHER.SEQ]21    keep: last2223  - id: FIRST_B224    dataset: DOSES25    key: [USUBJID]26    filter: "DOSES.PRIORSEQ = 1"27    order_by: [DOSES.DAY]28    keep: first29    derivations:30      LASTDAY: "DAY + DUR - 1"31      PRIORSEQ: {type: int, derivation: PRIOR.SEQ}3233columns:34  - name: USUBJID35    type: str36    label: Unique Subject Identifier37    derivation: SUBJECTS.USUBJID3839  - name: B2SEQ40    type: int41    label: First Qualifying Dose Sequence42    derivation: FIRST_B2.SEQ

Inputs

Under review3 source files

input/bands.csv

Edit6 rows

input/bands.csv
BAND	LO	HI
1	1	28
2	29	56
1	1	28
2	29	56
1	1	28
2	29	56

input/doses.csv

Edit6 rows

input/doses.csv
SEQ	DAY	DUR
1	1	14
2	20	14
3	40	7
1	1	28
2	30	7
1	5	10

input/subjects.csv

Edit3 rows

input/subjects.csv
USUBJID

Expected output

Under review18 expected rows

expected/between_bare.csv

Edit3 rows

expected/between_bare.csv
USUBJID	B2SEQ
	2
	2
	—

expected/between_qualified.csv

Edit3 rows

expected/between_qualified.csv
USUBJID	B2SEQ
	2
	2
	—

expected/filter_bare.csv

Edit3 rows

expected/filter_bare.csv
USUBJID	B2SEQ
	2
	2
	—

expected/filter_expression.csv

Edit3 rows

expected/filter_expression.csv
USUBJID	B2SEQ
	2
	2
	—

expected/filter_qualified.csv

Edit3 rows

expected/filter_qualified.csv
USUBJID	B2SEQ
	2
	2
	—

expected/self_join.csv

Edit3 rows

expected/self_join.csv
USUBJID	B2SEQ
	2
	2
	—

Shaded columns are derived— = missing value

Human review and assessment

Variable Name	Variable Label	Type	Length	Controlled Terms or Format	Origin	Core	Conversion Definition	Variable Type	Variable Order	Comments for Define
USUBJID	Unique Subject Identifier	Char			Collected		Copy value from SUBJECTS.USUBJID.	SDTM	1
B2SEQ	First Qualifying Dose Sequence	Num			Derived		Take SEQ from the first DOSES record matching on USUBJID, where DOSES.PRIORSEQ = 1, ordered by DOSES.DAY, and no match yields blank.	SDTM	2

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

Edit8 lines

1library(yamaa)23yamaa_spec("spec_filter_qualified.yaml")$run()$save()4yamaa_spec("spec_filter_bare.yaml")$run()$save()5yamaa_spec("spec_between_qualified.yaml")$run()$save()6yamaa_spec("spec_between_bare.yaml")$run()$save()7yamaa_spec("spec_filter_expression.yaml")$run()$save()8yamaa_spec("spec_self_join.yaml")$run()$output

Python

Edit8 lines

1import yamaa23yamaa.spec("spec_filter_qualified.yaml").run().save()4yamaa.spec("spec_filter_bare.yaml").run().save()5yamaa.spec("spec_between_qualified.yaml").run().save()6yamaa.spec("spec_between_bare.yaml").run().save()7yamaa.spec("spec_filter_expression.yaml").run().save()8yamaa.spec("spec_self_join.yaml").run().output

Specification variants

input/bands.csv

input/doses.csv

input/subjects.csv

expected/between_bare.csv

expected/between_qualified.csv

expected/filter_bare.csv

expected/filter_expression.csv

expected/filter_qualified.csv

expected/self_join.csv

Your review

Mapping spec

yamaa code

R

Python