feat: add CDISC PPTESTCD/PPTEST columns to PKNCAresults#536
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Gero1999 wants to merge 12 commits intohumanpred:mainfrom
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feat: add CDISC PPTESTCD/PPTEST columns to PKNCAresults#536Gero1999 wants to merge 12 commits intohumanpred:mainfrom
Gero1999 wants to merge 12 commits intohumanpred:mainfrom
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New optional arguments for CDISC standard parameter code and name. Accepts a character string for simple mappings or a named list for route-dependent mappings. Defaults to name/desc when not provided.
Map all NCA parameters to CDISC PPTESTCD/PPTEST codes. Route-dependent parameters (CL, VZ, MRT, VSS) use nested lists to distinguish intravascular (IC) and extravascular (EV) CDISC codes.
Add as.data.frame.PKNCAresults() logic to extract PPTESTCD and PPTEST columns from the CDISC metadata stored in each parameter's formalsmap. Handles route-dependent parameters by matching against the dosing route.
Map DN parameters to their CDISC PPTESTCD/PPTEST codes. Uses the same route-dependent nested list pattern for CL, VZ, MRT, and VSS variants.
Add pptestcd_cdisc and pptest_cdisc to expected lists in test-001-add.interval.col.R. Remove test-cdisc.R; CDISC output tests now live in test-class-PKNCAresults.R.
When out_format='cdisc' and any PPTESTCD contains 'INT', add PPSTINT and PPENINT columns with ISO 8601 durations relative to the last dose time. The time unit designator is derived from timeu_pref or timeu.
…esults.R Cover PPTESTCD/PPTEST translation, route-dependent resolution, PPSTINT/PPENINT with various time units, multi-dose relative timing, and format_iso8601_duration edge cases.
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Can you please add tests for the newly missing lines? https://app.codecov.io/gh/humanpred/pknca/pull/536 Also, I have removed document.yaml in |
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Fixes #403
What this does
Adds
out_format = \"cdisc\"toas.data.frame.PKNCAresults(). Translates PPTESTCD to CDISC PP domain codes and adds a PPTEST column.Key design decisions
CDISC metadata stored in
add.interval.col()— newpptestcd_cdisc/pptest_cdiscargs, defaulting to parameter name/description. All parameter files updated.Route-dependent codes — CL, VZ, MRT, VSS use
list(route = list(extravascular = ..., intravascular = ...)). Resolved per row by joining against dose data. Falls back to extravascular. Seeresolve_cdisc_value()andpknca_cdisc_get_route()inclass-PKNCAresults.R.PPSTINT/PPENINT columns — Added when any PPTESTCD contains "INT". ISO 8601 durations relative to last dose time (most recent dose ≤ interval start). Time unit designator from
timeu_prefortimeu. Only populated for INT rows,NAotherwise.DN parameters — Inherit base CDISC code with "D" appended. Route-dependent lists passed through unchanged.
Files changed
R/001-add.interval.col.R— new argsR/class-PKNCAresults.R— translation + PPSTINT/PPENINT logicR/zzz-pk.calc.dn.R— DN CDISC derivationadd.interval.col()callstests/testthat/test-class-PKNCAresults.R— 9 new testsHow to test