PKNCA Documentation Book

A comprehensive Quarto book documenting the PKNCA R package (≥ 0.12.2) with runnable examples throughout. Every function, option, and parameter is verified against live PKNCA output.

Live book: https://teunp.github.io/PKNCA.doc/
Intended home (pending org setup): https://humanpred.github.io/pknca-book/

Build locally

# Install PKNCA 0.12.2
remotes::install_github("humanpred/pknca")

git clone https://github.com/TeunP/PKNCA.doc
cd PKNCA.doc
quarto render
open _book/index.html

Contents

User Guide (19 chapters)

Chapter	Topics
Workflow	PKNCAconc → PKNCAdose → PKNCAdata → pk.nca; all 21 options with defaults
Interval selection & parameter catalogue	Interval data frame structure; group matching; all 143 calculable parameters
AUC types & integration methods	auclast/aucall/aucinf; partial AUC; lin up/log down vs linear vs lin-log; aucabove; time_above; AUMC; cav.int
Half-life & terminal phase	Curve stripping; adj.r.squared.factor; quality filters; Tobit regression; lambda.z.corrxy
Extravascular (oral/SC)	BLQ handling; imputation strategies; tmin; lag time; multiple peaks
Intravascular (IV)	IV bolus NCA; C0 back-extrapolation; IV infusion with ceoi; MRT correction
Multiple-dose / steady-state	deg.fluc; swing; PTR; Cav; tau detection
Urine excretion	ae; fe; clr.; volpk; ermax/ertmax/ertlst; clr..dn
Sparse PK sampling	sparse_auclast + SE + df; sparse AUMC; mrt/cl/kel.sparse.last
Superposition	Predicting multiple-dose profiles from single-dose data
Time to steady state	pk.tss.monoexponential; pk.tss.stepwise.linear; pk.tss
Post-processing	exclude(); normalize(); 17 .dn parameters; PKNCA.set.summary; get_halflife_points
Units	pknca_units_table() S3 generic; PKNCAdata method; preferred units; conversions
Imputation	start_conc0; start_predose; start_cmin; custom imputation methods
Dose-aware interpolation	interp.extrap.conc.dose; .dose AUCint variants
Custom parameters	add.interval.col; registering new NCA parameters
Utility functions	geomean; geocv; clean.conc.*; assert_conc_time
Regulatory & CDISC	PP domain column mapping; exclude → PPEXCLFL; summary() for CSR tables
Validation & testing	testthat suite; version pinning; manual AUClast spot-check

Developer Reference (2 chapters)

Chapter	Topics
Function dependencies	Parameter dependency graph
Architecture	Internal structure of PKNCA

What's new in PKNCA 0.12.2

• Tobit regression for half-life — handles BLQ terminal-phase observations via censored likelihood
• normalize() / normalize_by_col() — normalize results by any column (body weight, BSA, etc.)
• tmin — time of minimum concentration; first.tmin option
• Sparse AUMC (sparse_aumclast, SE, df) and derived parameters (mrt.sparse.last, cl.sparse.last, kel.sparse.last)
• New urine parameters: volpk, ermax, ertmax, ertlst, clr.last.dn, clr.obs.dn, clr.pred.dn
• lambda.z.corrxy — correlation between time and log-concentration for the λz regression window
• pknca_units_table() now an S3 generic with a PKNCAdata method
• allow_partial_missing_units option

Related

• 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
• Setup guide for org repo + hub site: BUILDING_SETUP.md