yamaa / Benchmark

SDTM.LB

Numbered Results Each Keep Their Own Values

input files
1
subjects
2
expected rows
4
Review ask

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Summary

Lifecycle: draftEditUnder reviewWhat this benchmark means
README.md

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

Goal: show that numbering each subject's results by study day (LBSEQ) makes every collected laboratory result its own record, whose values all come from that one result: the result as collected (LBORRES), the numeric result (LBSTRESN), whether the test was done (LBSTAT), and whether the result is above the upper limit of normal (LBNRIND).

Input: one spec.yaml over collected glucose results (input/lb_raw.csv), each carrying the test code (LBTESTCD), the study day (LBDY), the result as text (RESULT) or, when there is none, a character result (RESULTC), the numeric result (STRESN) and the upper limit of normal (HIGH). The project.yaml lists the function file functions/project_value.yaml, whose routine returns the numeric result it is given.

Variables:

  • LBSEQ numbers each subject's results from 1 by study day; results of one day keep their collected order.
  • LBORRES is the result as collected, or the character result when the result is blank.
  • LBSTRESN is the numeric result, as the project's routine returns it, and blank when none was collected.
  • LBSTAT is NOT DONE when no numeric result was collected, and blank otherwise.
  • LBNRIND is HIGH above the upper limit and NORMAL otherwise, and blank when no numeric result was collected.

Note: a subject's two results of one day stay two records, and each record's values come from its own result, never from the other result of that day.

Inputs

Under review1 source file

input/lb_raw.csv

Edit4 rows
USUBJIDLBDYLBTESTCDRESULTRESULTCSTRESNHIGH
1GLUC5.2—5.26.1
8GLUC6.8—6.86.1
8GLUC—HEMOLYZED—6.1
1GLUC4.9—4.96.1

Expected output

Under review4 expected rows

expected/lb.csv

Edit4 rows
USUBJIDLBSEQLBTESTCDLBDYLBORRESLBSTRESNLBSTATLBNRIND
1GLUC15.25.2—NORMAL
2GLUC86.86.8—HIGH
3GLUC8HEMOLYZED—NOT DONE—
1GLUC14.94.9—NORMAL
Shaded columns are derived— = missing value

Human review and assessment

Your review

2 questions and your comments · View benchmark discussions

Mapping spec

Generated from the benchmark YAML; do not edit by hand

Variable NameVariable LabelTypeLengthControlled Terms or FormatOriginCoreConversion DefinitionVariable TypeVariable OrderComments for Define
USUBJIDUnique Subject IdentifierCharCollectedCopy value from LB_RAW.USUBJID.SDTM1
LBSEQSequence NumberNumDerivedRow number within each group of USUBJID, ordered by LB_RAW.LBDY.SDTM2
LBTESTCDLab Test or Examination Short NameCharCollectedCopy value from LB_RAW.LBTESTCD.SDTM3
LBDYStudy Day of Specimen CollectionNumCollectedCopy value from LB_RAW.LBDY.SDTM4
LBORRESResult or Finding in Original UnitsCharDerivedFirst non-missing of LB_RAW.RESULT and LB_RAW.RESULTC.SDTM5
LBSTRESNNumeric Result/Finding in Standard UnitsNumDerivedCall project function project_value with x = LB_RAW.STRESN.SDTM6
LBSTATCompletion StatusCharDerived"NOT DONE" when LB_RAW.STRESN IS NULL; blank otherwise; blank when the condition is unknown.SDTM7
LBNRINDReference Range IndicatorCharDerivedIf LB_RAW.STRESN IS NULL then "None"; otherwise "HIGH" when LB_RAW.STRESN > LB_RAW.HIGH; "NORMAL" otherwise; blank when the condition is unknown.SDTM8
VersionDateAuthorDescriptionReviewerSign-off
1.72026-10-20yamaa docs buildRead 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
1.62026-10-17yamaa docs buildDescribe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight
1.52026-10-17yamaa docs buildName 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
1.42026-10-15yamaa docs buildState datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks
1.32026-09-29yamaa docs buildShow study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.22026-09-29yamaa docs buildClassify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.12026-09-29yamaa docs buildResolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0yamaa docs buildInitial generation from spec.yaml

yamaa code

Public calls generated from benchmark.yaml; results must match the expected output

R

Edit3 lines
library(yamaa)yamaa_project("project.yaml")$spec("LB")$run()$output

Python

Edit3 lines
import yamaayamaa.project("project.yaml").spec("LB").run().output