A comprehensive Quarto book documenting the PKNCA R package (≥ 0.13.0) with runnable examples throughout. Every parameter, option, and user-facing function is covered and verified against live PKNCA output; the underlying pk.calc.* calculation functions are indexed in the Developer Reference.
Live book: https://humanpred.github.io/pknca-book/
# Install PKNCA 0.13.0 or later
remotes::install_github("humanpred/pknca")git clone https://github.com/humanpred/pknca-book
cd pknca-book
quarto render
open _book/index.html| Chapter | Topics |
|---|---|
| Workflow | PKNCAconc → PKNCAdose → PKNCAdata → pk.nca; default intervals; all options with defaults; update() |
| Interval selection & parameter catalog | Interval data frame; pknca_interval_table(); presets; interval_add_*(); impute columns; validation; the parameter catalog, rendered live |
| Automatic intervals & dosing regimens | Interval builder vs legacy; find.dose.regimen(); find.tau(); nominal times; regimen changes; classed warnings |
| AUC types & integration methods | auclast/aucall/aucinf; dose-aware partial AUCs; lin up/log down vs linear vs lin-log; AUMC; aumcint; aumciv |
| Half-life & terminal phase | Point selection controls; Tobit regression; exclusion rules; get_halflife_fit()/get_halflife_curve(); lambda.z.corrxy |
| Extravascular (oral/SC) | BLQ handling; imputation; tmin; lag time; f.obs pointer; cl/vz/vss/mrt families |
| Intravascular (IV) | IV bolus; C0 back-extrapolation; auciv*; IV infusion; cl.iv/vz.iv; MRT correction |
| Multiple-dose / steady-state | deg.fluc; swing; PTR; Cav; tau detection; mrt.md/vss.md; accumulation |
| Superposition | Predicting multiple-dose profiles from single-dose data |
| Time to steady state | pk.tss.monoexponential; pk.tss.stepwise.linear; pk.tss |
| Urine excretion | ae; fe; renal clearance in one run; volpk; ermax/ertmax/ertlst; erint/erlst |
| Secondary parameters | interval_id/_ref; interval_add_secondary(); bioavailability (f.); ratio.; renal clearance; composed units |
| Sparse PK sampling | Serial/batch designs; auclast etc. with _se/_df; start_conc0; BLQ rule; summary with SE; sparse_bootstrap() |
| Sparse AUC to infinity & its uncertainty | Yuan vs delta method (sparse_lambda_z_se); IV bolus C0; recommendations; prior work |
| Bioequivalence | be_assess(); ABE/ABEL/RSABE/NTID/HVNTID/descriptive; crossover, replicate, parallel; sparse bootstrap route |
| Data quality checks | pknca_missing_samples(); exclude_nca_tmax_coverage(); LLOQ and input validation |
| Post-processing | exclude(); exclusion rules; normalize(); .dn parameters; summary() options; PKNCA.set.summary |
| Units | pknca_units_table(); automatic units; preferred units; timeu and tau; conversions |
| Date-time data & time references | POSIXct/Date times; time references; date-time intervals; PPSTINT/PPENINT/PPTPTREF/PPRFTDTC |
| Imputation | start_conc0; start_predose; start_predose_conc0; start_cmin; end_conc_drop; chaining order; custom methods |
| Dose-aware interpolation | interp.extrap.conc.dose; dose-aware aucint rules |
| Custom parameters | add.interval.col(); FUN_sparse; pknca_ref(); registering new NCA parameters |
| Utility functions | clean.conc.; interp.extrap.conc(); check.interval.specification(); get.parameter.deps(); route helpers; assert_ |
| Regulatory & CDISC | CDISC output; pknca_cdisc_codes(); PPANMETH; PPGRPID; exclusion tracking; summary() for CSR tables |
| Validation & testing | testthat suite; version pinning; manual AUClast spot-check; PPANMETH |
| Chapter | Topics |
|---|---|
| Architecture | Internal structure of PKNCA |
| Function dependencies | Parameter dependency graph |
See the book's introduction for the full list. Highlights: automatic intervals rebuilt from the dosing regimen (breaking); secondary parameters (bioavailability f.obs etc., ratios, renal clearance) in one run; bioequivalence (be_assess()); sparse NCA with standard parameter names, the delta-method AUC to infinity, and sparse_bootstrap(); dose-aware partial AUCs; data quality checks; date-time data and CDISC time references.
- PKNCA source: https://github.com/humanpred/pknca
- pkgdown reference: https://humanpred.github.io/pknca/reference/index.html
- CRAN: https://cran.r-project.org/package=PKNCA
- Discussion: humanpred/pknca#541