Reject Log Zero

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: carry each collected laboratory result into AVAL and add its natural logarithm as AVALLN, with one record for each subject and parameter.

Input: five laboratory records across five subjects: a detectable viral load (12,000 copies/mL), an undetectable viral load reported as zero - the record the run rejects - a missing result, a low near-limit result (40), and a CD4 count (480), showing one record for each subject and parameter.

Variables:

AVAL would be the analysis value, mapped from the collected numeric result (LBSTRESN).
AVALLN would be the natural logarithm of AVAL, which the analysis models rather than the untransformed result, and blank when AVAL is blank. Zero has no logarithm, and a result below the limit of detection needs a stated substitution before it can be transformed, so the run fails while the values are computed and no artifact is accepted.

How to fix

State the analysis policy for an undetectable value. If it should produce a missing transformed result, guard zero explicitly:

derivation: "LN(NULLIF(AVAL, 0))"

If the study instead substitutes a value related to the assay limit, derive that stated substitute first and apply LN to it. Do not replace zero with an unstated constant.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: derivation
condition: ln_of_nonpositive
rule: FORMULA-15

expected/error.yaml

phase: derivation
condition: ln_of_nonpositive
spec_paths:
  - columns.AVALLN.derivation
rule: FORMULA-15
context:
  expr: "LN(AVAL)"
  keys:
    - STUDYID: PILOT7
      USUBJID: P7-762
      PARAMCD: HIVRNA

YAML specification

1 spec file

spec.yaml

Edit39 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADLB5keys: [STUDYID, USUBJID, PARAMCD]6input:7  LB: input/lb.csv89output:10  path: adlb.csv11  columns: [STUDYID, USUBJID, PARAMCD, AVAL, AVALLN]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: LB.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: LB.USUBJID2324  - name: PARAMCD25    type: str26    label: Parameter Code27    derivation: LB.LBTESTCD2829  - name: AVAL30    type: float31    label: Analysis Value32    derivation: LB.LBSTRESN3334  # LN of zero or a negative value fails the run while values are computed;35  # a missing AVAL gives a missing result instead.36  - name: AVALLN37    type: float38    label: Natural Log of Analysis Value39    derivation: "LN(AVAL)"

Inputs

Under review1 source file

input/lb.csv

Edit5 rows

input/lb.csv
STUDYID	LBTESTCD	LBSTRESN
PILOT7	HIVRNA	12000
PILOT7	HIVRNA	0
PILOT7	HIVRNA	—
PILOT7	HIVRNA	40
PILOT7	CD4	480

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
ADLB	STUDYID	Study Identifier	character	Copy value from LB.STUDYID.	Predecessor
ADLB	USUBJID	Unique Subject Identifier	character	Copy value from LB.USUBJID.	Predecessor
ADLB	PARAMCD	Parameter Code	character	Copy value from LB.LBTESTCD.	Predecessor
ADLB	AVAL	Analysis Value	numeric	Copy value from LB.LBSTRESN.	Predecessor
ADLB	AVALLN	Natural Log of Analysis Value	numeric	Compute LN(AVAL).	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/lb.csv

Your review

Mapping spec