docs: Tobit half-life now runs end-to-end through pk.nca() - #4
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Upstream humanpred/pknca issue 553 (closed 2026-06-11) added an lloq argument to PKNCAconc() (numeric scalar or column name) and wired it through to pk.calc.half.life(), so hl_method = "tobit" set via PKNCAdata(options = ...) no longer needs the direct pk.calc.half.life() workaround. Verified against the installed PKNCA 0.12.1.9000 (GitHub eff79252, packaged 2026-07-24): the pipeline result matches the direct Tobit call exactly and errors only when lloq is absent from PKNCAconc. - user/halflife.qmd: replace the pipeline-workaround note with a runnable end-to-end example, tagged (>= 0.12.2) - CONTRIBUTING.md: update the Tobit known-gotcha to the remaining pitfall (lloq must be set on PKNCAconc) Co-Authored-By: Claude Fable 5 <[email protected]>
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Summary
Upstream humanpred/pknca issue 553
(closed 2026-06-11) wired the LLOQ from
PKNCAconc()through to the Tobithalf-life method, so
hl_method = "tobit"now works through the fullpk.nca()pipeline and the book's direct-call workaround note is obsolete.Verified empirically against PKNCA 0.12.1.9000 (GitHub eff79252, packaged
2026-07-24, R 4.6.1):
PKNCAconc(..., lloq = 0.1)+PKNCAdata(options = list(hl_method = "tobit"))pk.nca()runs cleanly and returns λz = 0.2659 / half-life = 2.607 h —identical to the direct
pk.calc.half.life(..., hl_method = "tobit")calland distinct from the log-linear control (2.393 h), with the two BLQ points
reported in
lambda.z.n.points_blq.lloqworks as a numeric scalar and as a column name.lloqstill errors ("lloq must be provided when hl_method is'tobit'"), so the LLOQ on the concentration object is required.
Changes
workaround note with a runnable end-to-end pipeline example in a new
section, "Tobit through the
pk.nca()pipeline (≥ 0.12.2)".pitfall: supply the LLOQ via
PKNCAconc(lloq = ).quarto renderpasses with no warnings or errors; the rendered chapter showsthe pipeline and direct-call results matching.
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