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Options for Controlling PKNCA

Bill Denney

Summary

PKNCA has many options that control its function. These options have effects throughout the package. The options are controlled using either the PKNCA.options function or by passing the options argument to any of the functions with that as an argument. All options supported by the current version of PKNCA (0.11.0) are listed below with their descriptions.

Options

adj.r.squared.factor

The adjusted r^2 for the calculation of lambda.z has this factor times the number of data points added to it. It allows for more data points to be preferred in the calculation of half-life.

The default value is: 1e-04

max.missing

The maximum fraction of the data that may be missing (‘NA’) to calculate summary statistics with the business.* functions.

The default value is: 0.5

auc.method

The method used to calculate the AUC and related statistics. Options are: “lin up/log down”, “linear”, “lin-log”

The default value is: lin up/log down

conc.na

How should missing (‘NA’) concentration values be handled? See help for ‘clean.conc.na’ for how to use this option.

The default value is: drop

conc.blq

How should below the limit of quantification (zero, 0) concentration values be handled? See help for ‘clean.conc.blq’ for how to use this option.

$first [1] “keep”

$middle [1] “drop”

$last [1] “keep”

first.tmax

If there is more than one concentration equal to Cmax, which time should be selected for Tmax? If ‘TRUE’, the first will be selected. If ‘FALSE’, the last will be selected.

The default value is: TRUE

allow.tmax.in.half.life

Should the concentration and time at Tmax be allowed in the half-life calculation? ‘TRUE’ is yes and ‘FALSE’ is no.

The default value is: FALSE

keep_interval_cols

What additional columns from the intervals should be kept in the results?

NULL

min.hl.points

What is the minimum number of points required to calculate half-life?

The default value is: 3

min.span.ratio

What is the minimum span ratio required to consider a half-life valid?

The default value is: 2

max.aucinf.pext

What is the maximum percent extrapolation to consider an AUCinf valid?

The default value is: 20

min.hl.r.squared

What is the minimum r-squared value to consider a half-life calculation valid?

The default value is: 0.9

progress

A value to pass to purrr::pmap(.progress = ) to create a progress bar while running

The default value is: TRUE

tau.choices

What values for tau (repeating interdose interval) should be considered when attempting to automatically determine the intervals for multiple dosing? See ‘choose.auc.intervals’ and ‘find.tau’ for more information. ‘NA’ means automatically look at any potential interval.

The default value is: NA

single.dose.aucs

When data is single-dose, what intervals should be used?

start	end	auclast	aucall	aumclast	aumcall	aucint.last	aucint.last.dose	aucint.all	aucint.all.dose	c0	cmax	cmin	tmax	tlast	tfirst	clast.obs	cl.last	cl.all	f	mrt.last	mrt.iv.last	vss.last	vss.iv.last	cav	cav.int.last	cav.int.all	ctrough	cstart	ptr	tlag	deg.fluc	swing	ceoi	aucabove.predose.all	aucabove.trough.all	count_conc	totdose	ae	clr.last	clr.obs	clr.pred	fe	sparse_auclast	sparse_auc_se	sparse_auc_df	time_above	aucivlast	aucivall	aucivint.last	aucivint.all	aucivpbextlast	aucivpbextall	aucivpbextint.last	aucivpbextint.all	half.life	r.squared	adj.r.squared	lambda.z	lambda.z.time.first	lambda.z.n.points	clast.pred	span.ratio	thalf.eff.last	thalf.eff.iv.last	kel.last	kel.iv.last	aucinf.obs	aucinf.pred	aumcinf.obs	aumcinf.pred	aucint.inf.obs	aucint.inf.obs.dose	aucint.inf.pred	aucint.inf.pred.dose	aucivinf.obs	aucivinf.pred	aucivpbextinf.obs	aucivpbextinf.pred	aucpext.obs	aucpext.pred	cl.obs	cl.pred	mrt.obs	mrt.pred	mrt.iv.obs	mrt.iv.pred	mrt.md.obs	mrt.md.pred	vz.obs	vz.pred	vss.obs	vss.pred	vss.iv.obs	vss.iv.pred	vss.md.obs	vss.md.pred	cav.int.inf.obs	cav.int.inf.pred	thalf.eff.obs	thalf.eff.pred	thalf.eff.iv.obs	thalf.eff.iv.pred	kel.obs	kel.pred	kel.iv.obs	kel.iv.pred	auclast.dn	aucall.dn	aucinf.obs.dn	aucinf.pred.dn	aumclast.dn	aumcall.dn	aumcinf.obs.dn	aumcinf.pred.dn	cmax.dn	cmin.dn	clast.obs.dn	clast.pred.dn	cav.dn	ctrough.dn
0	24	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE
0	Inf	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE

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They may not be fully stable and should be used with caution. We make no claims about them.