[billdenney]

Summary

Updates the book for PKNCA 0.13.0 (the current development version). Against current PKNCA, 9 chapters no longer rendered, and a review of the development NEWS found most new features undocumented and 15 places where the book taught the old behavior.

• New chapters
  • Automatic Intervals and Dosing Regimens
  • Secondary Parameters
  • Sparse AUC to Infinity and Its Uncertainty
  • Bioequivalence
  • Data Quality Checks
  • Date-Time Data and Time References
• Rewritten: Sparse PK Sampling, now with the standard parameter names and their _se/_df companions, the start_conc0 requirement, the BLQ rule, summary with SE, and sparse_bootstrap().
• Breaking changes taught correctly
  • the rebuilt automatic intervals (single dose → dose to Inf with start_predose_conc0; auto.interval.method = "legacy")
  • f → f.obs
  • dose-aware aucint, with the .dose variants retired
  • renal clearance in one run
• Interval tools: pknca_interval_table(), presets, the parameter table, interval_add_*(), and impute columns of any name.
• Options: all 27 options with verified defaults.
• Other chapter updates: half-life point-selection controls and fit plotting; CDISC output with SDTM time references and PPGRPID; the add.interval.col() API; and the developer chapters.
• Book-wide: all "(≥ 0.12.2)" tags become "(≥ 0.13.0)" (0.12.2 was never released); the What's new section, README, CLAUDE.md, CONTRIBUTING, and the chapter order are updated; the CI package list gains units, lme4, lmerTest, and emmeans.
• Known package issues: examples affected by open PKNCA issues show a warning callout (the bioequivalence design classification, the clr.*.dn registration, half-life flags after imputation). Remove the callouts when those are fixed.

Testing

• quarto render of the whole book against PKNCA main (0.12.1.9002): no errors, no broken internal links; the remaining warnings are deliberate and explained in the text.
• Three review passes against the package source and the rendered output; all findings fixed in the last commit.

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