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 (0.9.1) 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’ and ‘linear’.

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

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

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 auclast.dn aucall.dn aumclast.dn aumcall.dn cmax cmin tmax tlast tfirst clast.obs cl.last cl.all f mrt.last mrt.iv.last vss.last vss.iv.last cav ctrough ptr tlag deg.fluc swing ceoi ae clr.last clr.obs clr.pred fe half.life r.squared adj.r.squared lambda.z lambda.z.time.first lambda.z.n.points clast.pred span.ratio cmax.dn cmin.dn clast.obs.dn clast.pred.dn cav.dn ctrough.dn 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 aucinf.obs.dn aucinf.pred.dn aumcinf.obs.dn aumcinf.pred.dn 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 vd.obs vd.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
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
0 Inf FALSE FALSE FALSE 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 TRUE 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 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