docs: update vignettes for accuracy and current features - #576
Open
billdenney wants to merge 1 commit into
Open
Conversation
From a consistency review of all 19 vignettes against the PKNCA book, with every behavioral claim tested against the current package. Corrections: v03's duration-selection text now describes the actual filter_interval() behavior (selection by collection start time only) and its two illustrating figures draw again (logical-indexing and inverted-comparison bugs fixed); v05's partial-AUC section is rewritten around the aucint.* family, retiring an eight-year-old "future version" promise; v06-tobit's automatic point selection now matches the implementation (lambda-z filter first, then minimize the residual-SD criterion with the n-points penalty, ties to the most points); v20 names the real superposition arguments (method/auc.type — the documented interp.method/extrap.method never existed); v22's stepwise-linear description now moves the window start forward as the code does; v30 no longer tells readers to put text in the logical exclude_half.life/include_half.life columns (which silently excludes nothing); v07-post-processing drops the deprecated not.requested.string. Currency: v01 gains units, lloq/Tobit, route, and as.data.frame/CDISC pointers plus accurate update() semantics; v04 gains sparse AUMC, the five derived parameters, and the df/BLQ-zeroing/linear-only behavior notes; v07-unit-conversion gains allow_partial_missing_units and the PKNCAdata units-table method; v07-post-processing gains get_halflife_points() and the exclusion-reason override note; v08 documents each start_* method, the chain-collapse caveat, and end_conc_drop; v21 finally enumerates its event types (generated from the package so it cannot drift). Every edited vignette was chunk-extracted and executed against the installed package; v03's figures were additionally render-verified. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
From a consistency review of all 19 vignettes against the PKNCA book, with every behavioral claim tested against the current package.
Corrections (vignette text contradicted the implementation): v03's duration-selection rule now describes actual
filter_interval()behavior and its two illustrating figures render again (two plotting-helper bugs); v05's partial-AUC section is rewritten aroundaucint.*, retiring an eight-year-old "future version" promise; v06-tobit's automatic point selection matches the code (λz filter first, residual-SD criterion with the n-points penalty, ties to most points); v20 names the realsuperposition()arguments (method/auc.type— the documentedinterp.method/extrap.methodnever existed and error if used); v22's stepwise-linear window moves forward as the code does; v30 no longer suggests text values for the logicalexclude_half.life/include_half.lifecolumns (silently excludes nothing); v07-post-processing drops deprecatednot.requested.string.Currency (features with book coverage but no vignette prose): v01 gains units,
lloq/Tobit,route, andas.data.frame()/CDISC pointers plus accurateupdate()semantics; v04 gains sparse AUMC + the five derived parameters and the df/BLQ-zeroing/linear-only notes; v07-unit-conversion gainsallow_partial_missing_unitsand thePKNCAdataunits-table method; v07-post-processing gainsget_halflife_points()and the exclusion-reason override note; v08 documents eachstart_*method, the chain-collapse caveat, andend_conc_drop; v21 enumerates its event types, generated from the package internals with astopifnotgate so the list cannot drift.Verification
Every edited vignette purled and executed end-to-end against the installed dev build; v03 figures render-verified (segments + legend correct); all corrected behavioral claims reproduced empirically before writing.
A companion set of drafted issues covers the code-side problems documentation cannot fix (duration doc-vs-code,
start_conc0overwrite, sparse options forwarding, asuperposition()infinite loop, and others).🤖 Generated with Claude Code