fix: rename PK summary exclusion variables to CDISC names (#1394) - #1418
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fix: rename PK summary exclusion variables to CDISC names (#1394)#1418wangzhengdna-lang wants to merge 1 commit into
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…e#1394) Rename PKSUM1F/PKSUM1FN/PKSUM1RS to PKSUMXF/PKSUMXFN/PKSUMXRS across code, tests, and variable metadata; exclusion semantics unchanged ("Y"/1 = excluded, empty/NA = included). - Helper .derive_pksum1rs() renamed to .derive_pksumxrs() - metadata_nca_variables.csv: removed legacy PKSUM1F/PKSUM1FN rows in favor of the pre-existing CDISC-named PKSUMXF/PKSUMXFN rows (added in pharmaverse#1306); PKSUM1RS renamed to PKSUMXRS with label/role aligned to the CDISC family ("PK Summary Exclusion Reason", Topic) - New names added to inst/WORDLIST (digit-free tokens are spell-checked) - Regenerated metadata_nca_variables.rda and add_exclusion_reasons.Rd - Bump version to 0.1.0.9189
wangzhengdna-lang
requested review from
Gero1999,
Shaakon35 and
h5hoang
as code owners
August 5, 2026 05:30
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Issue
Closes #1394
Description
Renames the PK summary exclusion variables to CDISC-compliant names across code, tests, and variable metadata. Exclusion semantics are unchanged (
"Y"/1= excluded, empty/NA= included).PKSUM1FPKSUMXFPKSUM1FNPKSUMXFNPKSUM1RSPKSUMXRSAdditional details:
.derive_pksum1rs()renamed to.derive_pksumxrs()for consistencyR/zzz.RglobalVariablesupdated, alphabetical order preserveddata-raw/metadata_nca_variables.csv+ regenerateddata/metadata_nca_variables.rdaman/add_exclusion_reasons.Rdregenerated viadevtools::document()inst/WORDLIST(digit-free tokens are spell-checked, unlike the old ones)Metadata deduplication (deviation from a plain rename, flagging for review): the CSV already contained CDISC-named
PKSUMXF/PKSUMXFNrows (added in #1306: "PK Summary Exclusion Flag"/"(N)", role Topic). The legacyPKSUM1F/PKSUM1FNrows were therefore removed instead of renamed, keeping the pre-existing CDISC rows.PKSUM1RShad no CDISC counterpart, so it was renamed toPKSUMXRSwith label/role aligned to the same family ("PK Summary Exclusion Reason", Topic).Definition of Done
PKSUM1F/PKSUM1FN/PKSUM1RSremain in the codebasedevtools::document()run to regenerateman/andNAMESPACENEWS.mdupdated with the change (and the PR number)lintrand all unit tests passHow to test
Rename + metadata change; all behavior covered by existing unit tests (updated expectations):
test-export_cdisc.R(185 PASS),test-PKNCA.R(126 PASS),test-tlg_module.R(21 PASS). Full suite: 2005 PASS / 0 FAIL, lint 0 violations, spellcheck clean.Contributor checklist
.scsschange was done, rundata-raw/compile_css.Rdata-raw/test_suggests_hidden.RNotes to reviewer
The metadata deduplication described above is the only judgment call beyond a mechanical rename — the alternative (renaming the legacy rows) would have produced duplicate
PKSUMXF/PKSUMXFNentries with conflicting labels/roles.