This function will set the default PKNCA options. If given no inputs, it
will provide the current option set. If given name/value pairs, it will set
the option (as in the options() function). If given a name, it will return
the value for the parameter. If given the default option as true, it will
provide the default options.
Arguments
- ...
options to set or get the value for
- default
(re)sets all default options
- check
check a single option given, but do not set it (for validation of the values when used in another function)
- name
An option name to use with the
value.- value
An option value (paired with the
name) to set or check (ifNULL, ).
Value
If...
- no arguments are given
returns the current options.
- a value is set (including the defaults)
returns
NULL- a single value is requested
the current value of that option is returned as a scalar
- multiple values are requested
the current values of those options are returned as a list
Details
Options are either for calculation or summary functions. Calculation options
are required for a calculation function to report a result (otherwise the
reported value will be NA). Summary options are used during summarization
and are used for assessing what values are included in the summary.
See the vignette 'Options for Controlling PKNCA' for a current list of
options (vignette("Options-for-Controlling-PKNCA", package="PKNCA")).
See also
Other PKNCA calculation and summary settings:
PKNCA.choose.option(),
PKNCA.set.summary()
Examples
PKNCA.options()
#> $adj.r.squared.factor
#> [1] 1e-04
#>
#> $max.missing
#> [1] 0.5
#>
#> $auc.method
#> [1] "lin up/log down"
#>
#> $conc.na
#> [1] "drop"
#>
#> $conc.blq
#> $conc.blq$first
#> [1] "keep"
#>
#> $conc.blq$middle
#> [1] "drop"
#>
#> $conc.blq$last
#> [1] "keep"
#>
#>
#> $debug
#> NULL
#>
#> $first.tmax
#> [1] TRUE
#>
#> $allow.tmax.in.half.life
#> [1] FALSE
#>
#> $keep_interval_cols
#> NULL
#>
#> $min.hl.points
#> [1] 3
#>
#> $min.span.ratio
#> [1] 2
#>
#> $max.aucinf.pext
#> [1] 20
#>
#> $min.hl.r.squared
#> [1] 0.9
#>
#> $progress
#> [1] TRUE
#>
#> $tau.choices
#> [1] NA
#>
#> $single.dose.aucs
#> start end auclast aucall aumclast aumcall aucint.last aucint.last.dose
#> 1 0 24 TRUE FALSE FALSE FALSE FALSE FALSE
#> 2 0 Inf FALSE FALSE FALSE FALSE FALSE FALSE
#> aucint.all aucint.all.dose aumcint.last aumcint.last.dose aumcint.all
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aumcint.all.dose c0 cmax cmin tmax tlast tfirst clast.obs cl.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE
#> cl.all cl.int.all cl.int.last f mrt.last mrt.all mrt.int.all mrt.int.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.iv.last vss.last vss.iv.last vss.all vss.int.all vss.int.last cav
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> cav.int.last cav.int.all ctrough cstart ptr tlag deg.fluc swing ceoi
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> aucabove.predose.all aucabove.trough.all count_conc count_conc_measured
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> totdose volpk ae clr.last fe ertlst ermax ertmax sparse_auclast
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> sparse_auc_se sparse_auc_df sparse_aumclast sparse_aumc_se sparse_aumc_df
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> time_above aucivlast aucivall aucivint.last aucivint.all aucivpbextlast
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> aucivpbextall aucivpbextint.last aucivpbextint.all aumcivlast aumcivall
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aumcivint.last aumcivint.all half.life r.squared adj.r.squared
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE TRUE FALSE FALSE
#> lambda.z.corrxy lambda.z lambda.z.time.first lambda.z.time.last
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> lambda.z.n.points clast.pred span.ratio thalf.eff.last thalf.eff.iv.last
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> kel.last kel.iv.last kel.all kel.int.all kel.int.last cl.iv.all cl.iv.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> cl.ivint.all cl.ivint.last cl.sparse.last mrt.sparse.last mrt.iv.all
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> mrt.ivint.all mrt.ivint.last vz.all vz.int.all vz.int.last vz.iv.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> vz.iv.last vz.ivint.all vz.ivint.last vz.last vz.sparse.last vss.iv.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.ivint.all vss.ivint.last vss.sparse.last aucinf.obs aucinf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE TRUE FALSE
#> aumcinf.obs aumcinf.pred aucint.inf.obs aucint.inf.obs.dose aucint.inf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aucint.inf.pred.dose aumcint.inf.obs aumcint.inf.obs.dose aumcint.inf.pred
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> aumcint.inf.pred.dose aucivinf.obs aucivinf.pred aucivpbextinf.obs
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> aucivpbextinf.pred aumcivinf.obs aumcivinf.pred aucpext.obs aucpext.pred
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> kel.iv.all kel.ivint.all kel.ivint.last kel.sparse.last cl.obs cl.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> cl.int.inf.obs cl.int.inf.pred cl.iv.obs cl.iv.pred mrt.obs mrt.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.int.inf.obs mrt.int.inf.pred mrt.iv.obs mrt.iv.pred mrt.md.obs
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> mrt.md.pred vz.obs vz.pred vz.int.inf.obs vz.int.inf.pred vz.iv.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> vz.iv.pred vss.obs vss.pred vss.iv.obs vss.iv.pred vss.md.obs vss.md.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.int.inf.obs vss.int.inf.pred cav.int.inf.obs cav.int.inf.pred clr.obs
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> clr.pred thalf.eff.obs thalf.eff.pred thalf.eff.iv.obs thalf.eff.iv.pred
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> kel.obs kel.pred kel.iv.obs kel.iv.pred kel.int.inf.obs kel.int.inf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> auclast.dn aucall.dn aucinf.obs.dn aucinf.pred.dn aumclast.dn aumcall.dn
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> aumcinf.obs.dn aumcinf.pred.dn cmax.dn cmin.dn clast.obs.dn clast.pred.dn
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> cav.dn ctrough.dn clr.last.dn clr.obs.dn clr.pred.dn
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#>
#> $allow_partial_missing_units
#> [1] FALSE
#>
PKNCA.options(default=TRUE)
PKNCA.options("auc.method")
#> [1] "lin up/log down"
PKNCA.options(name="auc.method")
#> [1] "lin up/log down"
PKNCA.options(auc.method="lin up/log down", min.hl.points=3)