Stated Fallbacks

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Summary

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README.md

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

Goal: derive vital-signs analysis values where each fragile read states its fallback beside it: an unmapped or absent test code, a collected result that cannot be read as a whole number, and a subject with more than one dosing record.

Input: one spec.yaml. VS carries the vital-signs records: subject, sequence, test code, the result as entered text, and units. EX carries the dosing records: subject, sequence, treatment, dose, and start date.

Fallbacks:

PARAM codes each test: a collected code with no dictionary entry, and a record with no collected code at all, both take the stated "Other measure" label.
AVAL reads the collected result as a whole number: a result that cannot be read that way, such as "ND" or the fractional "98.6", is left blank by the stated fallback. A record with no collected result is blank because there is nothing to read.
LASTDOSE takes each subject's latest dose: a dosing record with no dose never qualifies, the dosed record with the latest start date wins, and a subject with no dosed record keeps the dose blank.

Note: each fallback is stated beside the read it guards, so the run completes with the stated answers instead of failing; a read whose condition never occurs keeps its ordinary value.

YAML specification

1 spec file

spec.yaml

Edit71 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADVS5keys: [USUBJID, VSSEQ]6input:7  VS: {path: input/vs.csv, types: {VSSTRESN: str}}8  EX: {path: input/ex.csv, types: {EXDOSE: float}, key: [USUBJID]}9base: VS1011output:12  path: advs.csv13  columns: [STUDYID, USUBJID, VSSEQ, PARAM, AVAL, LASTDOSE]1415columns:16  - name: STUDYID17    type: str18    label: Study Identifier19    derivation: VS.STUDYID2021  - name: USUBJID22    type: str23    label: Unique Subject Identifier24    derivation: VS.USUBJID2526  - name: VSSEQ27    type: int28    label: Sequence Number29    derivation: VS.VSSEQ3031  # A collected code with no dictionary entry, and a record with no32  # collected code at all, both take the stated fallback label.33  - name: PARAM34    type: str35    label: Parameter36    derivation:37      mapping:38        source: VS.VSTESTCD39        dict:40          SYSBP: Systolic Blood Pressure41          DIABP: Diastolic Blood Pressure42          PULSE: Pulse Rate43        missing: Other measure44        unmapped: Other measure4546  # The collected result is entered as text. "ND" and the fractional47  # "98.6" cannot be read as whole numbers, so the stated fallback48  # leaves them blank; a record with no collected result is blank49  # because there is nothing to read. This `unconvertible` sits beside50  # `value` and answers only a failed conversion to int.51  - name: AVAL52    type: int53    label: Analysis Value54    derivation:55      value: VS.VSSTRESN56      unconvertible: null5758  # A dosing record with no dose never qualifies; among the dosed59  # records the later start date wins. Multiple matches fail by default;60  # `order_by` + `keep` selects the later start date instead. A subject61  # with no dosed record takes the stated `absent`, keeping the dose62  # blank; `absent` would also answer a variable absent from context.63  - name: LASTDOSE64    type: float65    label: Latest Dose66    derivation:67      source:68        variable: EX.EXDOSE69        filter: "EX.EXDOSE IS NOT NULL"70        order_by: [EX.EXSTDTC]71        keep: last

Inputs

Under review2 source files

input/ex.csv

Edit4 rows

input/ex.csv
STUDYID	EXSEQ	EXTRT	EXDOSE	EXSTDTC
YAMAA-01	1	DRUG A	10	2026-01-05
YAMAA-01	2	DRUG A	20	2026-02-05
YAMAA-01	3	DRUG A	—	2026-03-05
YAMAA-01	1	DRUG A	10	2026-01-10

input/vs.csv

Edit8 rows

input/vs.csv
STUDYID	VSSEQ	VSTESTCD	VSSTRESN	VSSTRESU
YAMAA-01	1	SYSBP	120	mmHg
YAMAA-01	2	DIABP	80	mmHg
YAMAA-01	3	PULSE	72	beats/min
YAMAA-01	1	SYSBP	ND	mmHg
YAMAA-01	2	DIABP	78	mmHg
YAMAA-01	3	TEMP	98.6	F
YAMAA-01	4	—	—	—
YAMAA-01	1	PULSE	68	beats/min

Expected output

Under review8 expected rows

expected/advs.csv

Edit8 rows

expected/advs.csv
STUDYID	VSSEQ	PARAM	AVAL	LASTDOSE
YAMAA-01	1	Systolic Blood Pressure	120	20
YAMAA-01	2	Diastolic Blood Pressure	80	20
YAMAA-01	3	Pulse Rate	72	20
YAMAA-01	1	Systolic Blood Pressure	—	10
YAMAA-01	2	Diastolic Blood Pressure	78	10
YAMAA-01	3	Other measure	—	10
YAMAA-01	4	Other measure	—	10
YAMAA-01	1	Pulse Rate	68	—

Shaded columns are derived— = missing value

Human review and assessment

Dataset Name	Variable Name	Variable Label	Type	Computational Method	Origin
ADVS	STUDYID	Study Identifier	character	Copy value from VS.STUDYID.	Predecessor
ADVS	USUBJID	Unique Subject Identifier	character	Copy value from VS.USUBJID.	Predecessor
ADVS	VSSEQ	Sequence Number	numeric	Copy value from VS.VSSEQ.	Predecessor
ADVS	PARAM	Parameter	character	Recode VS.VSTESTCD: "SYSBP" → "Systolic Blood Pressure", "DIABP" → "Diastolic Blood Pressure", "PULSE" → "Pulse Rate"; missing or unlisted values → "Other measure".	Derived
ADVS	AVAL	Analysis Value	numeric	Copy value from VS.VSSTRESN; a value that cannot be converted → blank.	Derived
ADVS	LASTDOSE	Latest Dose	numeric	Copy value from EX.EXDOSE where EX.EXDOSE IS NOT NULL, keeping the last ordered by EX.EXSTDTC.	Predecessor

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/ex.csv

input/vs.csv

expected/advs.csv

Your review

Mapping spec

yamaa code

R

Python