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fix: correct factual errors found in comprehensive review - #5
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Category 1 of 6 from the 2026-08-08 review: ~90 correctness fixes across 20 chapters, each verified against the installed PKNCA (0.12.1.9000). Highlights: tmin is a time not a concentration; aucpext flagging is manual via exclude_nca_max.aucinf.pext() (pk.nca does not auto-flag); Tobit half-life now shown running through the pk.nca() pipeline with lloq passthrough; Indometh described as biexponential; C0 logslope uses the first two post-dose samples; aucivpbext is back-extrapolation; clr.last/clr.obs inequality righted; nonexistent APIs removed (list-of-conc PKNCAdata, value.ok registry field, sort.interval.cols); sparse AUC uses linear trapezoidal weights; broken validation commands replaced with tested ones; urine 0.12.2 parameter demos now execute with live output; dose-aware interpolation now demonstrates out.after and extrapolation with lambda.z. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Category 2 of 6: de-duplicate and reorganize. Post-processing's imputation section is now a pointer to the Imputation chapter; architecture's conflicting exposure.ratio walkthrough is a minimal demo.ratio illustration pointing at the Writing Custom Parameters chapter; extravascular's integration-methods/units/summary sections shrink to brief pointers at their dedicated chapters and its duplicate Vss and bioavailability treatments merge; intravascular's duplicated MRT-correction text collapses to one home. Sibling EV/IV headings and shared landmark tables now match verbatim, forward references from EV to IV are self-contained, and IV gains tmin plus BLQ/integration pointers. auc-methods groups aucabove/time_above/totdose under Other interval parameters and moves boundary interpolation next to partial AUC. The steady-state trio cross-references each other, and the chapter order groups multiple-dose, superposition, and tss together; Developer Reference now leads with Architecture. workflow's redundant re-running section folds into the options section. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Category 3 of 6: motivating sentences before bare code chunks; jargon expanded at first use (BLQ, MRT, IIV, CDISC/SDTM/PP, tobit's phi and sigma); dead code removed (t_seq, start_time, duplicate constructors, unused extractions); comments retitled to match what their chunks show; never-run option demos in the extravascular chapter now execute and show real effects (or state honestly that Theoph shows none); hidden setup chunks made visible per the self-contained-page convention (superposition data prep, postprocessing o_nca construction); interval chapter adopts the d_*/o_* naming convention and drops a vestigial suppressMessages; visNetwork legend now uses registered visGroups so swatch colors match the nodes; seams from the earlier restructuring smoothed. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Category 4 of 6: US spelling throughout (PKNCA declares en-US; ggplot2 colour= API arguments left as-is); every chapter footer now uses the "pkgdown reference:" label (index was the lone holdout, also aligned to plain link text); version tags normalized to the (>= X.Y.Z) form and added to the tobit option rows and normalize_by_col; manual section numbers dropped and headings sentence-cased in intervals, regulatory, validation, halflife, and the remaining Title Case strays; "e.g." without comma standardized (majority form); timepoint, secondary peak, and the exact "lin up/log down" option string unified; dplyr:: prefixes dropped where dplyr is attached (conflicts_prefer calls keep their required qualification); index/workflow mermaid node wording aligned. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Category 5 of 6: regulatory gains a CDISC output format section (out_format = "cdisc", live-verified incl. PPSTINT/PPENINT semantics); units gains an allowing-partial-units section with a real error/warning demonstration and the correct (>= 0.12.0) attribution; superposition gains a multiple-doses-within-an-interval example (dose.times, with per-administration dose.amount semantics discovered by testing); function-deps gains the 203-row parameter-to-function mapping table and get.parameter.deps(); extravascular notes flip-flop kinetics. Chapter footers audited book-wide against current content: missing entries added with verified pkgdown URLs, orphaned entries removed. README and CLAUDE.md coverage claims reworded to what is now true; CONTRIBUTING's tobit gotcha updated for the working lloq passthrough (the sparse sparse_auc_se gotcha re-verified and kept). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Category 6 of 6: the book previously linked pkgdown reference pages everywhere and package vignettes nowhere. Adds ~45 "see also" links across all chapters connecting each topic to its corresponding PKNCA vignette (including section-level anchors for manual λz point selection, per-interval imputation, the dose-aware methods appendix, per-analyte unit tables, sparse grouping, and custom-parameter summary registration), replaces the console-only vignette() citation with a hyperlink, and adds a Vignettes entry to the navbar pointing at the pkgdown articles index. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Second review pass over the updated book (six chapter batches plus a mechanical conventions/coverage/link sweep) surfaced items the first round missed or introduced; all are fixed and the code changes tested: cav.int demo no longer divides by Inf (was rendering four zeros); include_half.life documented as bypassing curve stripping (fits exactly the marked points); get.parameter.deps corrected to a dependents lookup in utilities (matching the other two chapters); intervals' validator and default-interval behavior descriptions aligned to the implementation; exclusion demos now display flagged rows at thresholds that actually flag; Tobit window-selection criterion documented; normalize_by_col and What's-new bullets corrected in the index; urine fe interpretation matches its own output; phantom timeu argument removed; four broken footer URLs repointed at real topic pages; footers completed against demonstrated functions; EV/IV cross-links, tags, and leftover dead code cleaned; tidyr added to CI packages; conventions recorded in CLAUDE.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Category 1 of 6 from the 2026-08-08 review: ~90 correctness fixes across
20 chapters, each verified against the installed PKNCA (0.12.1.9000).
Highlights: tmin is a time not a concentration; aucpext flagging is
manual via exclude_nca_max.aucinf.pext() (pk.nca does not auto-flag);
Tobit half-life now shown running through the pk.nca() pipeline with
lloq passthrough; Indometh described as biexponential; C0 logslope uses
the first two post-dose samples; aucivpbext is back-extrapolation;
clr.last/clr.obs inequality righted; nonexistent APIs removed
(list-of-conc PKNCAdata, value.ok registry field, sort.interval.cols);
sparse AUC uses linear trapezoidal weights; broken validation commands
replaced with tested ones; urine 0.12.2 parameter demos now execute
with live output; dose-aware interpolation now demonstrates out.after
and extrapolation with lambda.z.
Co-Authored-By: Claude Fable 5 noreply@anthropic.com