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 c0 cmax cmin tmax tmin tlast tfirst clast.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE
#> cl.last cl.all cl.int.all cl.int.last mrt.last mrt.all mrt.int.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.int.last mrt.iv.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 cav cav.int.last cav.int.all ctrough cstart ptr tlag
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> deg.fluc swing ceoi aucabove.predose.all aucabove.trough.all count_conc
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> count_conc_measured totdose volpk ae clr.last clr.obs clr.pred fe
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> ertlst ermax ertmax erint erlst ratio.cmax ratio.auclast ratio.aucint.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> ratio.aucint.all sparse_auclast sparse_auc_se sparse_auc_df sparse_aumclast
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> sparse_aumc_se sparse_aumc_df time_above aucivlast aucivlast_se aucivlast_df
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> aucivall aucivall_se aucivall_df 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 aumcivlast_se
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aumcivlast_df aumcivall aumcivall_se aumcivall_df aumcivint.last
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aumcivint.all 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.iv.last kel.last kel.iv.last kel.all kel.int.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> kel.int.last cl.iv.all cl.iv.last cl.ivint.all cl.ivint.last cl.sparse.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> f.last f.int.last f.int.all mrt.sparse.last mrt.iv.all mrt.ivint.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.ivint.last vz.all vz.int.all vz.int.last vz.iv.all vz.iv.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> vz.ivint.all vz.ivint.last vz.last vss.iv.all vss.ivint.all vss.ivint.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.sparse.last aucinf.obs aucinf.obs_se aucinf.obs_df aucinf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE TRUE FALSE FALSE FALSE
#> aumcinf.obs aumcinf.obs_se aumcinf.obs_df aumcinf.pred aucint.inf.obs
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aucint.inf.pred aumcint.inf.obs aumcint.inf.pred aucivinf.obs aucivinf.obs_se
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aucivinf.obs_df aucivinf.pred aucivpbextinf.obs aucivpbextinf.pred
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> aumcivinf.obs aumcivinf.obs_se aumcivinf.obs_df aumcivinf.pred aucpext.obs
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aucpext.pred kel.iv.all kel.ivint.all kel.ivint.last kel.sparse.last cl.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> cl.pred cl.int.inf.obs cl.int.inf.pred cl.iv.obs cl.iv.pred f.obs f.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> f.int.obs f.int.pred mrt.obs mrt.pred mrt.int.inf.obs mrt.int.inf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.iv.obs mrt.iv.pred mrt.md.obs mrt.md.pred mrt.ivmd.obs mrt.ivmd.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> vz.obs vz.pred vz.int.inf.obs vz.int.inf.pred vz.iv.obs vz.iv.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> vz.sparse.last 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.ivmd.obs vss.ivmd.pred vss.int.inf.obs vss.int.inf.pred cav.int.inf.obs
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> cav.int.inf.pred ratio.aucinf.obs ratio.aucinf.pred thalf.eff.obs
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> thalf.eff.pred thalf.eff.iv.obs thalf.eff.iv.pred kel.obs kel.pred kel.iv.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> kel.iv.pred kel.int.inf.obs kel.int.inf.pred auclast.dn aucall.dn
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aucinf.obs.dn aucinf.pred.dn aumclast.dn aumcall.dn aumcinf.obs.dn
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aumcinf.pred.dn cmax.dn cmin.dn clast.obs.dn clast.pred.dn cav.dn ctrough.dn
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> clr.last.dn clr.obs.dn clr.pred.dn
#> 1 FALSE FALSE FALSE
#> 2 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)