Birth Date Completion

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Summary

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README.md

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

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 year for a year alone, month for a year and month, and day for a full date, read from the collected text; blank when the text is blank.
DOB_PREC_DT holds the same word 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

Edit111 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADSL5keys: [STUDYID, USUBJID]6input:7  SOURCE: {path: input/adsl.csv, types: {DTMSTR: datetime, REFDTSTR: date}}89output:10  path: adsl.csv11  columns: [STUDYID, USUBJID, DOBTC, DTM, REFDT, DOB_FIRST,12    DOB_LAST, DOB_PREC_TX, DOB_PREC_DT, DTMDT, DOBDY]1314columns:15  - name: STUDYID16    type: str17    label: Study Identifier18    derivation: SOURCE.STUDYID1920  - name: USUBJID21    type: str22    label: Unique Subject Identifier23    derivation: SOURCE.USUBJID2425  - name: DOBTC26    type: str27    label: Date of Birth (Collected Text)28    derivation: SOURCE.DOBTC2930  # The input has no declared types, so the assessment moment and the31  # reference date arrive as text; the column types convert them.32  - name: DTM33    type: datetime34    label: Datetime of Assessment35    derivation: SOURCE.DTMSTR3637  - name: REFDT38    type: date39    label: Reference Start Date40    derivation: SOURCE.REFDTSTR4142  # Year-only text gets June and the first day; year-month text gets the43  # first day; a full date is returned unchanged. Blank text or text that44  # is not a date gives a missing date. `year` is the default minimum and45  # is what lets a year alone receive both a month and a day.46  - name: DOB_FIRST47    type: date48    label: Date of Birth Completed to First Day49    derivation:50      impute:51        type: date52        source: DOBTC53        month: 654        day: first55        invalid: null5657  # The same completion, to the last day of the month the date lands in58  # (28 or 29 in a February, by year).59  - name: DOB_LAST60    type: date61    label: Date of Birth Completed to Last Day62    derivation:63      impute:64        type: date65        source: DOBTC66        month: 667        day: last68        invalid: null6970  # year, month or day: 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      precision:76        type: date77        source: DOBTC78        invalid: null7980  # The completed date keeps the precision of the text it came from, so81  # this reads the same word as DOB_PREC_TX. A date value is never invalid82  # text, and a missing date gives a missing precision.83  - name: DOB_PREC_DT84    type: str85    label: Date of Birth Precision From Date86    derivation:87      precision:88        type: date89        source: DOB_FIRST9091  - 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        source: DOB_FIRST106        reference: REFDT107108verifications:109  - row_count:110      min: 5111      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	year	year	2025-01-12	1
CATH	1980-02	2024-02-29T23:59:59	1980-02-02	1980-02-01	1980-02-29	month	month	2024-02-29	-1
CATH	1990-06-15	1990-06-15T00:00:00	1990-06-15	1990-06-15	1990-06-15	day	day	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	month	month	2000-02-29	18

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 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; 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; invalid text → blank.	Derived
ADSL	DOB_PREC_TX	Date of Birth Precision From Text	character		Collected date precision of DOBTC: "day" for a complete date, "month" for a year and month, "year" for a year alone, "none" for an entirely imputed date or text with an unknown year; invalid text → blank.	Derived
ADSL	DOB_PREC_DT	Date of Birth Precision From Date	character		Collected date precision of DOB_FIRST: "day" for a complete date, "month" for a year and month, "year" for a year alone, "none" for an entirely imputed date or text with an unknown year; invalid text is an error.	Derived
ADSL	DTMDT	Date of Assessment	numeric	ISO 8601	Take the date part of DTM, blank for a year or a year and month alone.	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
1.7	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/adsl.csv

expected/adsl.csv

Your review

Mapping spec

yamaa code

R

Python