Non-Finite Values

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?

The other tabs beside Comments are background for assessment, not under review.

Summary

EditUnder reviewWhat this benchmark means

README.md

Goal: show that a non-finite number (positive infinity, negative infinity, or Not-a-Number, NaN) is stored as missing, whichever of three routes brings it into a column: a value written in the specification, a value read from the source, or a value returned by a study calculation.

Input: one spec.yaml over a subject-level dataset whose numeric fields POSITIVE_INFINITY, NEGATIVE_INFINITY, and NOT_A_NUMBER each hold one non-finite value.

Columns: every one of these is stored as missing.

YAML_PINF, YAML_NINF, and YAML_NAN write positive infinity, negative infinity, and NaN directly in spec.yaml.
SOURCE_PINF, SOURCE_NINF, and SOURCE_NAN copy them from POSITIVE_INFINITY, NEGATIVE_INFINITY, and NOT_A_NUMBER.
FUNCTION_PINF, FUNCTION_NINF, and FUNCTION_NAN take them from the study calculation numeric_constant. Its contract allows a missing result; a calculation that may not return one fails the run when it returns a non-finite value.

Note: a quoted spelling such as '.inf' remains text unless converted to a numeric type.

Engines: numeric_constant belongs to the ordinary installed packages in rust/tests/project-programs. The explicit python/environment.yaml and r/environment.yaml carry equivalent versionless definitions and inline tests. Both return the same three non-finite constants.

YAML specification

1 spec file

spec.yaml

Edit94 lines

1schema_version: "1.0"2domain: ADSL3keys: [USUBJID]4input:5  DM:6    path: input/dm.csv7    # Declared float, so the stored text .inf, -.Inf, and .NAN is read as8    # non-finite numbers, and each is stored as missing on the way in.9    types:10      POSITIVE_INFINITY: float11      NEGATIVE_INFINITY: float12      NOT_A_NUMBER: float1314output:15  path: adsl.csv16  columns:17    - USUBJID18    - YAML_PINF19    - YAML_NINF20    - YAML_NAN21    - SOURCE_PINF22    - SOURCE_NINF23    - SOURCE_NAN24    - FUNCTION_PINF25    - FUNCTION_NINF26    - FUNCTION_NAN2728columns:29  - name: USUBJID30    type: str31    label: Unique Subject Identifier32    derivation: DM.USUBJID3334  # Unquoted YAML spellings, one in each accepted letter case, resolve to35  # non-finite floats and are stored as missing.36  - name: YAML_PINF37    type: float38    label: Positive Infinity YAML Literal39    derivation: {literal: .inf}4041  - name: YAML_NINF42    type: float43    label: Negative Infinity YAML Literal44    derivation: {literal: -.Inf}4546  - name: YAML_NAN47    type: float48    label: Not-a-Number YAML Literal49    derivation: {literal: .NAN}5051  - name: SOURCE_PINF52    type: float53    label: Positive Infinity Source Value54    derivation: DM.POSITIVE_INFINITY5556  - name: SOURCE_NINF57    type: float58    label: Negative Infinity Source Value59    derivation: DM.NEGATIVE_INFINITY6061  - name: SOURCE_NAN62    type: float63    label: Not-a-Number Source Value64    derivation: DM.NOT_A_NUMBER6566  # The project calculation returns a real infinity or NaN. Its contract67  # allows a missing result, so each is stored as missing; without that68  # allowance the returned value fails the run.69  - name: FUNCTION_PINF70    type: float71    label: Positive Infinity Function Result72    derivation:73      function:74        name: numeric_constant75        args:76          kind: {literal: positive-infinity}7778  - name: FUNCTION_NINF79    type: float80    label: Negative Infinity Function Result81    derivation:82      function:83        name: numeric_constant84        args:85          kind: {literal: negative-infinity}8687  - name: FUNCTION_NAN88    type: float89    label: Not-a-Number Function Result90    derivation:91      function:92        name: numeric_constant93        args:94          kind: {literal: nan}

Inputs

Under review1 source file

input/dm.csv

Edit1 row

input/dm.csv
USUBJID	POSITIVE_INFINITY	NEGATIVE_INFINITY	NOT_A_NUMBER
	.inf	-.Inf	.NAN

Expected output

Under review1 expected row

expected/adsl.csv

Edit1 row

expected/adsl.csv
USUBJID	YAML_PINF	YAML_NINF	YAML_NAN	SOURCE_PINF	SOURCE_NINF	SOURCE_NAN	FUNCTION_PINF	FUNCTION_NINF	FUNCTION_NAN
	—	—	—	—	—	—	—	—	—

Shaded columns are derived— = missing value

Comments and assessment materials

Dataset Name	Variable Name	Variable Label	Type	Computational Method	Origin
ADSL	USUBJID	Unique Subject Identifier	character	Copy value from DM.USUBJID.	Predecessor
ADSL	YAML_PINF	Positive Infinity YAML Literal	numeric	Set constant value "inf".	Assigned
ADSL	YAML_NINF	Negative Infinity YAML Literal	numeric	Set constant value "-inf".	Assigned
ADSL	YAML_NAN	Not-a-Number YAML Literal	numeric	Set constant value "nan".	Assigned
ADSL	SOURCE_PINF	Positive Infinity Source Value	numeric	Copy value from DM.POSITIVE_INFINITY.	Predecessor
ADSL	SOURCE_NINF	Negative Infinity Source Value	numeric	Copy value from DM.NEGATIVE_INFINITY.	Predecessor
ADSL	SOURCE_NAN	Not-a-Number Source Value	numeric	Copy value from DM.NOT_A_NUMBER.	Predecessor
ADSL	FUNCTION_PINF	Positive Infinity Function Result	numeric	Call project function numeric_constant with kind = positive-infinity.	Derived
ADSL	FUNCTION_NINF	Negative Infinity Function Result	numeric	Call project function numeric_constant with kind = negative-infinity.	Derived
ADSL	FUNCTION_NAN	Not-a-Number Function Result	numeric	Call project function numeric_constant with kind = nan.	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", environment = "r/environment.yaml")$output4adsl

run.py

Edit4 lines

1import yamaa23adsl = yamaa.domain("spec.yaml", environment="python/environment.yaml").output4adsl

input/dm.csv

expected/adsl.csv

Comments

Mapping spec

yamaa code

run.R

run.py