Feature request: SDTM input (EX to PKNCAdose)#517
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Gero1999 wants to merge 9 commits intohumanpred:mainfrom
Open
Feature request: SDTM input (EX to PKNCAdose)#517Gero1999 wants to merge 9 commits intohumanpred:mainfrom
Gero1999 wants to merge 9 commits intohumanpred:mainfrom
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This script simulates a Phase I dose-escalation study with various parameters for drug exposure. It creates a data frame for the SDTM EX domain, detailing subjects, treatments, doses, and timing.
Add tests for ex_to_PKNCAdose function covering various scenarios including handling of oral doses, IV infusions, duration calculations, and optional columns.
Extract std_dtc_to_rdate, parse_iso8601_duration, and route_cdisc_to_pknca as top-level internal helpers. Parse EXELTM from ISO 8601 duration to numeric hours when character. Derive NFRLT = (EXRFTDTC + EXELTM) - min(EXRFTDTC) per dose grouping and use it as time.nominal in PKNCAdose instead of raw EXELTM. Co-authored-by: Ona <no-reply@ona.com>
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Closes #516
This PR introduces
ex_to_PKNCAdoseto convert SDTM EX (Exposure) domain data into a PKNCAdose object, along with shared SDTM helpers and unit tests.Key changes
ex_to_PKNCAdoseEXSTDTC,EXENDTC,EXRFTDTC) with mixed precisionEXDURfromEXENDTC - EXSTDTCwhen not pre-existingEXELTMfromEXSTDTC - EXRFTDTCwhen not pre-existing; parses ISO 8601 duration strings (e.g."PT2H") to numeric hours when characterAFRLT(actual time from reference) as hours from first dose per subjectNFRLT(nominal time from reference) as(EXRFTDTC + EXELTM) - min(EXRFTDTC)per dose grouping (EXTRT + USUBJID), used astime.nominalin the PKNCAdose object"intravascular"/"extravascular"EXDUR,EXELTM,EXRFTDTC,EXROUTE,EXDOSU) are optional — the function adapts to what's availableShared internal helpers (extracted as top-level
@keywords internal)std_dtc_to_rdate— ISO 8601 date-time parsing with mixed precisionparse_iso8601_duration— ISO 8601 duration to numeric hours (supports negative values)route_cdisc_to_pknca— CDISC route mappingNFRLT derivation
When both
EXRFTDTCandEXELTMare present,NFRLTis derived per dose grouping as a continuous nominal time axis. When either is absent,NFRLTis not derived andtime.nominalis omitted from the PKNCAdose object.Tests
std_dtc_to_rdate,parse_iso8601_duration,route_cdisc_to_pkncaex_to_PKNCAdose: basic object creation, oral/IV duration, route mapping, relative time, mixed precision, EXELTM derivation, pre-existing EXDUR/EXELTM, minimal datasetstime.nominalassignment, absent EXRFTDTC fallback, per-treatment-group derivation