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()
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
#>
#> $first.tmin
#> [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 c0 cmax cmin tmax tmin tlast tfirst
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE
#> clast.obs cl.last cl.all f mrt.last mrt.iv.last vss.last vss.iv.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> cav cav.int.last cav.int.all ctrough cstart ptr tlag deg.fluc swing
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> ceoi aucabove.predose.all aucabove.trough.all count_conc count_conc_measured
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> totdose volpk ae clr.last clr.obs clr.pred fe ertlst ermax ertmax
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> sparse_auclast sparse_auc_se sparse_auc_df sparse_aumclast sparse_aumc_se
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> sparse_aumc_df time_above aucivlast aucivall aucivint.last aucivint.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> aucivpbextlast aucivpbextall aucivpbextint.last aucivpbextint.all half.life
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE TRUE
#> r.squared adj.r.squared lambda.z.corrxy lambda.z lambda.z.time.first
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> lambda.z.time.last lambda.z.n.points clast.pred span.ratio tobit_residual
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> adj_tobit_residual lambda.z.n.points_blq thalf.eff.last thalf.eff.iv.last
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> kel.last kel.iv.last cl.sparse.last mrt.sparse.last vss.sparse.last
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> aucinf.obs aucinf.pred aumcinf.obs aumcinf.pred aucint.inf.obs
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 TRUE FALSE FALSE FALSE FALSE
#> aucint.inf.obs.dose aucint.inf.pred aucint.inf.pred.dose aucivinf.obs
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> aucivinf.pred aucivpbextinf.obs aucivpbextinf.pred aucpext.obs aucpext.pred
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> kel.sparse.last cl.obs cl.pred mrt.obs mrt.pred mrt.iv.obs mrt.iv.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.md.obs mrt.md.pred vz.obs vz.pred vz.sparse.last vss.obs vss.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.iv.obs vss.iv.pred vss.md.obs vss.md.pred cav.int.inf.obs
#> 1 FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE
#> cav.int.inf.pred thalf.eff.obs thalf.eff.pred thalf.eff.iv.obs
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> thalf.eff.iv.pred kel.obs kel.pred kel.iv.obs kel.iv.pred auclast.dn
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE FALSE FALSE
#> aucall.dn aucinf.obs.dn aucinf.pred.dn aumclast.dn aumcall.dn aumcinf.obs.dn
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> 2 FALSE 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"
#>
#> $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)