Reject a standard deviation of text results

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: keep each replicate systolic blood pressure reading with its result as text (AVALC), and add AVALSD, the standard deviation of the subject's replicate readings.

Input: vital signs with one record per replicate reading, the result collected as text (VSORRES) and as a number in standard units (VSSTRESN).

Variables:

AVALSD would be the sample standard deviation of the subject's replicate readings, the same on each of them. The request computes it from the text results, and a standard deviation needs numbers, so the run is rejected before any data is read.

How to fix

Compute the deviation from the numeric result, carried in its own column:

- name: AVAL
  type: float
  derivation: VS.VSSTRESN

- name: AVALSD
  type: float
  derivation:
    aggregate:
      group_by: [STUDYID, USUBJID, PARAMCD]
      expr: "STDDEV(AVAL)"

Converting the text results instead would read every collected spelling as a number; use the standard numeric result the study already provides.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: incompatible_input_type
rule: FORMULA-23

expected/error.yaml

phase: validation
condition: incompatible_input_type
spec_paths:
  - columns.AVALSD.derivation.aggregate.expr
rule: FORMULA-23
context:
  expr: STDDEV(AVALC)
  reducer: STDDEV
  source: AVALC
  expected: numeric
  actual: str

YAML specification

1 spec file

spec.yaml

Edit48 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADVS5keys: [STUDYID, USUBJID, PARAMCD, VSSEQ]6input:7  VS: {path: input/vs.csv, types: {VSSEQ: int, VSSTRESN: float, VSREPNUM: int}}89output:10  path: advs.csv11  columns: [STUDYID, USUBJID, PARAMCD, VSSEQ, AVALC, AVALSD]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: VS.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: VS.USUBJID2324  - name: PARAMCD25    type: str26    label: Parameter Code27    derivation: VS.VSTESTCD2829  - name: VSSEQ30    type: int31    label: Sequence Number32    derivation: VS.VSSEQ3334  - name: AVALC35    type: str36    label: Analysis Value (C)37    derivation: VS.VSORRES3839  # One standard deviation per subject and parameter, repeated on each of its40  # replicate rows. AVALC holds the results as text, and a standard deviation41  # needs numbers, so the run is rejected before any data is read.42  - name: AVALSD43    type: float44    label: Standard Deviation of Replicate Results45    derivation:46      aggregate:47        group_by: [STUDYID, USUBJID, PARAMCD]48        expr: "STDDEV(AVALC)"

Inputs

Under review1 source file

input/vs.csv

Edit5 rows

input/vs.csv
STUDYID	VSSEQ	VSTESTCD	VSORRES	VSSTRESN	VSREPNUM
YAMAA-01	1	SYSBP	128	128	1
YAMAA-01	2	SYSBP	132	132	2
YAMAA-01	3	SYSBP	125	125	3
YAMAA-01	1	SYSBP	141	141	1
YAMAA-01	2	SYSBP	138	138	2

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

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	PARAMCD	Parameter Code	character	Copy value from VS.VSTESTCD.	Predecessor
ADVS	VSSEQ	Sequence Number	numeric	Copy value from VS.VSSEQ.	Predecessor
ADVS	AVALC	Analysis Value (C)	character	Copy value from VS.VSORRES.	Predecessor
ADVS	AVALSD	Standard Deviation of Replicate Results	numeric	Aggregate STDDEV(AVALC) over records grouped by STUDYID, USUBJID, PARAMCD, matching on the shared output keys.	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

How to fix

input/vs.csv

Your review

Mapping spec