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, the current value of the option is returned).
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(),
PKNCA_options_defaults()
Examples
PKNCA.options()
#> $adj.r.squared.factor
#> [1] 1e-04
#>
#> $r.squared.factor
#> [1] NA
#>
#> $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
#>
#> $first.tmin
#> [1] TRUE
#>
#> $allow.tmax.in.half.life
#> [1] FALSE
#>
#> $keep_interval_cols
#> NULL
#>
#> $min.hl.points
#> [1] 3
#>
#> $max.hl.points
#> [1] Inf
#>
#> $min.hl.start.time
#> [1] 0
#>
#> $min.span.ratio
#> [1] 2
#>
#> $max.aucinf.pext
#> [1] 20
#>
#> $min.hl.r.squared
#> [1] 0.9
#>
#> $progress
#> [1] TRUE
#>
#> $tau.choices
#> [1] NA
#>
#> $auto.interval.method
#> [1] "builder"
#>
#> $auto.interval.tolerance
#> [1] 0.05
#>
#> $single.dose.aucs
#> start end auclast auclast_se auclast_df aucall aucall_se aucall_df aumclast
#> 1 0 24 TRUE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 0 Inf FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> aumclast_se aumclast_df aumcall aumcall_se aumcall_df aucint.last aucint.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> aumcint.last aumcint.all aucivint.last aucivint.all aucivpbext.int.last
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aucivpbext.int.all aumcivint.last aumcivint.all c0 cmax cmin tmax tmin
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE
#> tlast tfirst clast.obs cl.last cl.all cl.int.all cl.int.last cl.ivint.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> cl.ivint.last mrt.last mrt.all mrt.int.all mrt.int.last mrt.iv.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.ivint.all mrt.ivint.last vss.last vss.iv.last vss.all vss.int.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.int.last vss.ivint.all vss.ivint.last cav.last cav.int.last cav.int.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> cav.all cav.ivint.last cav.ivint.all ctrough cstart ptr tlag deg.fluc
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> swing ceoi aucabove.predose.all aucabove.trough.all count.conc
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> count.conc.measured totdose volpk ae clr.last clr.int.inf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> clr.int.inf.obs clr.int.all clr.int.last clr.all clr.inf.obs clr.inf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> fe ertlst ermax ertmax erint erlst ratio.cmax ratio.auclast
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> ratio.aucint.last ratio.aucint.all sparse_auclast sparse_auc_se sparse_auc_df
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> sparse_aumclast sparse_aumc_se sparse_aumc_df time.above aucivlast
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aucivlast_se aucivlast_df aucivall aucivall_se aucivall_df aucivpbext.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> aucivpbext.all aumcivlast aumcivlast_se aumcivlast_df aumcivall aumcivall_se
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> aumcivall_df half.life r.squared adj.r.squared lambda.z.corrxy lambda.z
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE TRUE FALSE FALSE FALSE FALSE
#> lambda.z.time.first lambda.z.time.last lambda.z.n.points clast.pred
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> span.ratio tobit.residual adj.tobit.residual lambda.z.n.points.blq
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> thalf.eff.last thalf.eff.int.all thalf.eff.int.last thalf.eff.all
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> thalf.eff.iv.last thalf.eff.ivint.all thalf.eff.ivint.last kel.last
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> kel.iv.last kel.all kel.int.all kel.int.last kel.ivint.all kel.ivint.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> cl.iv.all cl.iv.last cl.sparse.last f.last f.all f.int.last f.int.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.sparse.last mrt.iv.all vz.all vz.int.all vz.int.last vz.iv.all vz.iv.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> vz.ivint.all vz.ivint.last vz.last vss.iv.all vss.sparse.last cav.iv.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> cav.iv.all aucinf.obs aucinf.obs_se aucinf.obs_df aucinf.pred aumcinf.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE TRUE FALSE FALSE FALSE FALSE
#> aumcinf.obs_se aumcinf.obs_df aumcinf.pred aucint.inf.obs aucint.inf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aumcint.inf.obs aumcint.inf.pred aucivint.inf.obs aucivint.inf.pred
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> aucivinf.obs aucivinf.obs_se aucivinf.obs_df aucivinf.pred aucivpbext.inf.obs
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aucivpbext.inf.pred aumcivint.inf.pred aumcivint.inf.obs aumcivinf.obs
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> aumcivinf.obs_se aumcivinf.obs_df aumcivinf.pred thalf.eff.iv.all
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> aucpext.inf.obs aucpext.inf.pred kel.iv.all kel.sparse.last cl.inf.obs
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> cl.inf.pred cl.int.inf.obs cl.int.inf.pred cl.iv.inf.obs cl.iv.inf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> cl.ivint.inf.pred cl.ivint.inf.obs f.inf.obs f.inf.pred f.int.inf.obs
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> f.int.inf.pred mrt.inf.obs mrt.inf.pred mrt.int.inf.obs mrt.int.inf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> mrt.iv.inf.obs mrt.iv.inf.pred mrt.ivint.inf.pred mrt.ivint.inf.obs
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> mrt.md.inf.obs mrt.md.inf.pred mrt.ivmd.inf.obs mrt.ivmd.inf.pred vz.inf.obs
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> vz.inf.pred vz.int.inf.obs vz.int.inf.pred vz.iv.inf.obs vz.iv.inf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> vz.ivint.inf.pred vz.ivint.inf.obs vz.sparse.last vss.inf.obs vss.inf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> vss.iv.inf.obs vss.iv.inf.pred vss.md.inf.obs vss.md.inf.pred
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> vss.ivmd.inf.obs vss.ivmd.inf.pred vss.int.inf.obs vss.int.inf.pred
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> vss.ivint.inf.pred vss.ivint.inf.obs cav.int.inf.obs cav.int.inf.pred
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> cav.ivint.inf.obs cav.ivint.inf.pred ratio.aucinf.obs ratio.aucinf.pred
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> thalf.eff.inf.obs thalf.eff.inf.pred thalf.eff.int.inf.pred
#> 1 FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE
#> thalf.eff.int.inf.obs thalf.eff.iv.inf.obs thalf.eff.iv.inf.pred
#> 1 FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE
#> thalf.eff.ivint.inf.pred thalf.eff.ivint.inf.obs kel.inf.obs kel.inf.pred
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> kel.iv.inf.obs kel.iv.inf.pred kel.int.inf.obs kel.int.inf.pred
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> kel.ivint.inf.pred kel.ivint.inf.obs auclast.dn aucall.dn aucinf.obs.dn
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aucinf.pred.dn aumclast.dn aumcall.dn aumcinf.obs.dn aumcinf.pred.dn cmax.dn
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> cmin.dn clast.obs.dn clast.pred.dn cav.last.dn ctrough.dn adj_tobit_residual
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> aucivpbextall aucivpbextinf.obs aucivpbextinf.pred aucivpbextint.all
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> aucivpbextint.last aucivpbextlast aucpext.obs aucpext.pred cav cav.dn
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> cl.iv.obs cl.iv.pred cl.obs cl.pred clr.obs clr.pred count_conc
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> count_conc_measured f.int.obs f.int.pred f.obs f.pred kel.iv.obs kel.iv.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> kel.obs kel.pred lambda.z.n.points_blq mrt.iv.obs mrt.iv.pred mrt.ivmd.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.ivmd.pred mrt.md.obs mrt.md.pred mrt.obs mrt.pred thalf.eff.iv.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> thalf.eff.iv.pred thalf.eff.obs thalf.eff.pred time_above tobit_residual
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> vss.iv.obs vss.iv.pred vss.ivmd.obs vss.ivmd.pred vss.md.obs vss.md.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.obs vss.pred vz.iv.obs vz.iv.pred vz.obs vz.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#>
#> $allow_partial_missing_units
#> [1] FALSE
#>
#> $hl_method
#> [1] "log-linear"
#>
#> $sparse_lambda_z_se
#> [1] "delta"
#>
#> $tobit_n_points_penalty
#> [1] 0
#>
#> $tobit_optim_control
#> list()
#>
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)