Reject the base-10 logarithm of a zero titer

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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 neutralizing antibody titer into AVAL on the base-10 logarithmic scale, with one record for each subject, parameter and visit.

Input: immunogenicity results with one neutralizing antibody titer per subject and visit and the assay's lower limit of quantitation, one titer reported as zero because no dilution neutralized the virus.

Variables:

PARAMCD: NABLOG10, the base-10 logarithm of the neutralizing antibody titer.
AVAL would be the base-10 logarithm of the titer, and blank when the titer is blank. A titer of zero has no logarithm, so the run fails while the values are computed and no artifact is accepted.

How to fix

Decide what a titer below the lower limit of quantitation means for the analysis. A log-scale analysis usually leaves such titers out; choose the records with a filter that keeps the quantified and the blank titers:

filter: "IS.ISSTRESN IS NULL OR IS.ISSTRESN >= IS.ISLLOQ"

If the study instead imputes such titers, for example as half the lower limit, derive that stated value first and take its logarithm. 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.AVAL.derivation
rule: FORMULA-15
context:
  expr: "LOG10(TITER)"
  function: LOG10
  keys:
    - STUDYID: YAMAA-01
      USUBJID: YAMAA-01-202
      PARAMCD: NABLOG10
      AVISIT: DAY 29

YAML specification

1 spec file

spec.yaml

Edit47 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADIS5keys: [STUDYID, USUBJID, PARAMCD, AVISIT]6input:7  IS:8    path: input/is.csv9    types: {ISSTRESN: int, ISLLOQ: int}1011output:12  path: adis.csv13  columns: [STUDYID, USUBJID, PARAMCD, AVISIT, AVAL]1415columns:16  - name: STUDYID17    type: str18    label: Study Identifier19    derivation: IS.STUDYID2021  - name: USUBJID22    type: str23    label: Unique Subject Identifier24    derivation: IS.USUBJID2526  - name: PARAMCD27    type: str28    label: Parameter Code29    derivation: "'NABLOG10'"3031  - name: AVISIT32    type: str33    label: Analysis Visit34    derivation: IS.VISIT3536  # The collected titer, a reciprocal dilution.37  - name: TITER38    type: int39    label: Neutralizing Antibody Titer40    derivation: IS.ISSTRESN4142  # LOG10 of a zero titer fails the run while values are computed; a43  # missing titer gives a missing result instead.44  - name: AVAL45    type: float46    label: Analysis Value47    derivation: "LOG10(TITER)"

Inputs

Under review1 source file

input/is.csv

Edit4 rows

input/is.csv
STUDYID	ISTESTCD	VISIT	ISSTRESN	ISLLOQ
YAMAA-01	NABTITER	DAY 29	320	10
YAMAA-01	NABTITER	DAY 29	0	10
YAMAA-01	NABTITER	DAY 29	—	10
YAMAA-01	NABTITER	DAY 29	40	10

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
ADIS	STUDYID	Study Identifier	character	Copy value from IS.STUDYID.	Predecessor
ADIS	USUBJID	Unique Subject Identifier	character	Copy value from IS.USUBJID.	Predecessor
ADIS	PARAMCD	Parameter Code	character	Set constant value "NABLOG10".	Assigned
ADIS	AVISIT	Analysis Visit	character	Copy value from IS.VISIT.	Predecessor
ADIS	AVAL	Analysis Value	numeric	Compute LOG10(TITER).	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/is.csv

Your review

Mapping spec