Birth Date Completion

Review ask

As a clinical trial statistician or programmer, challenge anything in this benchmark: describe a problem in Comments, or propose a fix with the Edit button on any source file.

Task: Would a real study need this derivation, specified this way? Does it follow CDISC ADaM: variable names, controlled terms, record structure? Flag any rule that is ambiguous or that a sponsor would handle differently.
Inputs: Do they look like data collected in a real trial, and do they include the situations you would expect to meet in one?
Expected output: Would independent QC programming reproduce every value from these inputs and rules?

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Summary

EditUnder reviewWhat this benchmark means

README.md

Goal: complete a collected birth date to the first and last day of its month and read how much was collected.

Input: subject-level records carrying a birth date as text DOBTC (a year, a year and month, or a full date), an assessment moment DTM, and a reference start date REFDT. All three reach the output as collected, blank when nothing was collected.

Variables:

DOB_FIRST holds the birth date with a missing month set to June and a missing day set to the first of the month; a full date stands as collected, and blank stays blank.
DOB_LAST holds the birth date completed the same way, but with a missing day set to the last of the month, so February lands on the 28th or 29th by year; a full date stands as collected, and blank stays blank.
DOB_PREC_TX holds Y for a year alone, M for a year and month, and D for a full date, read from the collected text; blank when the text is blank.
DOB_PREC_DT holds the same code read from the completed first-day date; blank when there is no completed date.
DTMDT holds the calendar day of the assessment moment; blank when the moment is blank.
DOBDY holds the study day of the completed first-day date against the reference start, with the reference itself as day one and no zero; blank when either date is blank.

Note: a year alone may receive both a month and a day here, while a complete date is never moved. Precision follows the collected text through completion, and the study day counts a collected day exactly as a supplied one would count.

YAML specification

1 spec file

spec.yaml

Edit113 lines

1schema_version: "1.0"2domain: ADSL3keys: [STUDYID, USUBJID]4input:5  SOURCE: {path: input/adsl.csv, types: {DTMSTR: datetime, REFDTSTR: date}}67output:8  path: adsl.csv9  columns: [STUDYID, USUBJID, DOBTC, DTM, REFDT, DOB_FIRST,10    DOB_LAST, DOB_PREC_TX, DOB_PREC_DT, DTMDT, DOBDY]1112columns:13  - name: STUDYID14    type: str15    label: Study Identifier16    derivation: SOURCE.STUDYID1718  - name: USUBJID19    type: str20    label: Unique Subject Identifier21    derivation: SOURCE.USUBJID2223  - name: DOBTC24    type: str25    label: Date of Birth (Collected Text)26    derivation: SOURCE.DOBTC2728  # The input has no declared types, so the assessment moment and the29  # reference date arrive as text; the column types convert them.30  - name: DTM31    type: datetime32    label: Datetime of Assessment33    derivation: SOURCE.DTMSTR3435  - name: REFDT36    type: date37    label: Reference Start Date38    derivation: SOURCE.REFDTSTR3940  # Year-only text gets June and the first day; year-month text gets the41  # first day; a full date is returned unchanged. Blank text or text that42  # is not a date gives a missing date. `year` is the default minimum and43  # is what lets a year alone receive both a month and a day.44  - name: DOB_FIRST45    type: date46    label: Date of Birth Completed to First Day47    derivation:48      date_impute:49        source: DOBTC50        month: 651        day: first52        minimum_source_precision: year53        missing: null54        invalid: null5556  # The same completion, to the last day of the month the date lands in57  # (28 or 29 in a February, by year).58  - name: DOB_LAST59    type: date60    label: Date of Birth Completed to Last Day61    derivation:62      date_impute:63        source: DOBTC64        month: 665        day: last66        minimum_source_precision: year67        missing: null68        invalid: null6970  # Y, M or D: how much of a date the collected text carries.71  - name: DOB_PREC_TX72    type: str73    label: Date of Birth Precision From Text74    derivation:75      date_precision:76        source: DOBTC77        missing: null78        invalid: null7980  # The completed date keeps the precision of the text it came from, so81  # this reads the same code as DOB_PREC_TX. A date value is never invalid82  # text, so only the missing case needs an answer.83  - name: DOB_PREC_DT84    type: str85    label: Date of Birth Precision From Date86    derivation:87      date_precision:88        source: DOB_FIRST89        missing: null9091  - name: DTMDT92    type: date93    label: Date of Assessment94    derivation:95      to_date:96        source: DTM9798  # CDISC study day: REFDT is day 1, the day before it is -1 (no day 0).99  # Missing when either date is missing.100  - name: DOBDY101    type: int102    label: Study Day of Birth Completion103    derivation:104      study_day:105        date: DOB_FIRST106        reference: REFDT107108verifications:109  - unique:110      columns: [STUDYID, USUBJID]111  - row_count:112      min: 5113      max: 5

Inputs

Under review1 source file

input/adsl.csv

Edit5 rows

input/adsl.csv
STUDYID	DOBTC	DTMSTR	REFDTSTR
CATH	1975	2025-01-12T14:00	1975-06-01
CATH	1980-02	2024-02-29T23:59:59	1980-02-02
CATH	1990-06-15	1990-06-15T00:00:00	1990-06-15
CATH	—	—	2025-01-01
CATH	2000-02	2000-02-29T12:00	2000-01-15

Expected output

Under review5 expected rows

expected/adsl.csv

Edit5 rows

expected/adsl.csv
STUDYID	DOBTC	DTM	REFDT	DOB_FIRST	DOB_LAST	DOB_PREC_TX	DOB_PREC_DT	DTMDT	DOBDY
CATH	1975	2025-01-12T14:00:00	1975-06-01	1975-06-01	1975-06-30	Y	Y	2025-01-12	1
CATH	1980-02	2024-02-29T23:59:59	1980-02-02	1980-02-01	1980-02-29	M	M	2024-02-29	-1
CATH	1990-06-15	1990-06-15T00:00:00	1990-06-15	1990-06-15	1990-06-15	D	D	1990-06-15	1
CATH	—	—	2025-01-01	—	—	—	—	—	—
CATH	2000-02	2000-02-29T12:00:00	2000-01-15	2000-02-01	2000-02-29	M	M	2000-02-29	18

Shaded columns are derived— = missing value

Comments and assessment materials

Dataset Name	Variable Name	Variable Label	Type	Codelist/Controlled Terms	Computational Method	Origin
ADSL	STUDYID	Study Identifier	character		Copy value from SOURCE.STUDYID.	Predecessor
ADSL	USUBJID	Unique Subject Identifier	character		Copy value from SOURCE.USUBJID.	Predecessor
ADSL	DOBTC	Date of Birth (Collected Text)	character		Copy value from SOURCE.DOBTC.	Predecessor
ADSL	DTM	Datetime of Assessment	numeric	ISO 8601	Copy value from SOURCE.DTMSTR.	Predecessor
ADSL	REFDT	Reference Start Date	numeric	ISO 8601	Copy value from SOURCE.REFDTSTR.	Predecessor
ADSL	DOB_FIRST	Date of Birth Completed to First Day	numeric	ISO 8601	Impute incomplete date from DOBTC, defaulting month=6, day=first; a missing source → blank; invalid text → blank.	Derived
ADSL	DOB_LAST	Date of Birth Completed to Last Day	numeric	ISO 8601	Impute incomplete date from DOBTC, defaulting month=6, day=last; a missing source → blank; invalid text → blank.	Derived
ADSL	DOB_PREC_TX	Date of Birth Precision From Text	character		Collected date precision of DOBTC: D for a complete date, M for year and month, Y for a year alone; a missing source → blank; invalid text → blank.	Derived
ADSL	DOB_PREC_DT	Date of Birth Precision From Date	character		Collected date precision of DOB_FIRST: D for a complete date, M for year and month, Y for a year alone; a missing source → blank.	Derived
ADSL	DTMDT	Date of Assessment	numeric	ISO 8601	Take the date part of DTM.	Derived
ADSL	DOBDY	Study Day of Birth Completion	numeric		CDISC study day of DOB_FIRST against REFDT as day 1; there is no day zero.	Derived

Version	Date	Author	Description
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

run.R

Edit4 lines

1library(yamaa)23adsl <- yamaa_domain("spec.yaml")$output4adsl

run.py

Edit4 lines

1import yamaa23adsl = yamaa.yamaa_domain("spec.yaml").output4adsl

input/adsl.csv

expected/adsl.csv

Comments

Mapping spec

yamaa code

run.R

run.py