Build an interval specification from a description of the analysis
Source:R/interval-table.R
pknca_interval_table.RdChooses the NCA parameters to calculate for an interval, and the imputation
to calculate them from, given when the interval runs and how the drug was
given. The result is a data.frame suitable for the intervals argument of
PKNCAdata().
Usage
pknca_interval_table(
start,
end,
dosing = "single",
route = "extravascular",
sample_type = "spot",
sparse = FALSE,
tier = "common",
include = NULL,
exclude = NULL,
impute = NULL,
preset = NULL,
clast_type = "obs",
...
)Arguments
- start, end
The start and end time of the interval. Both may be vectors, giving one set of rows per interval.
- dosing
Was the drug given once (
"single"), repeatedly without assuming steady state ("multiple"), or repeatedly at steady state ("steady_state")? Asking for"steady_state"also gives the parameters that apply to any repeated dose. Seepknca_dosing().- route
How the drug was given; see
pknca_routes().- sample_type
Were concentrations measured in samples taken at a point in time (
"spot", the usual case for blood, plasma, and serum) or in a collection over an interval ("interval", the usual case for urine and feces)? Seepknca_sample_types().- sparse
Is this a sparse sampling design?
- tier
"common"(the default) gives the parameters usually reported for the context;"all"gives every parameter it can calculate.- include, exclude
NCA parameters or concepts (see
pknca_concepts()) to add to or remove from what the context gives. A parameter named in both is an error.- impute
The imputation to use, as for
PKNCAdata(). The default ofNULLchooses one from the context;NAuses none.- preset
A named set of arguments to start from; see
pknca_presets(). Arguments given explicitly override the preset.- clast_type
Should the extrapolation to infinity use the observed (
"obs") or predicted ("pred") last concentration?- ...
Columns to add to every row, typically the groups the interval applies to.
Value
A data.frame with one or more rows per interval: start, end, a
logical column per parameter, an impute column when any imputation
applies, and any columns given in .... An interval is split into more
than one row when some of its parameters must not be calculated from the
imputed data.
Details
The interval is assumed to start at a dose, which is what makes an
imputation at the start meaningful. Pass impute = NA for an interval
that starts partway through a profile.
Which AUC the interval is built on follows from dosing: a single dose
uses AUClast and the extrapolation to infinity, and a repeated dose uses
the AUCint family, which interpolates at both interval boundaries. The
clearance, volume, and mean residence time that follow from that AUC are
chosen to match.
See also
pknca_parameter_table() for how each parameter is classified,
PKNCAdata(), and the vignette "Selection of Calculation Intervals"
Other Interval specifications:
add.interval.col(),
check.interval.specification(),
choose.auc.intervals(),
get.interval.cols(),
get.parameter.deps(),
interval_add_impute(),
interval_add_param(),
interval_add_secondary(),
pknca_check_parameter_classification(),
pknca_concepts(),
pknca_parameter_table(),
pknca_presets(),
pknca_ref()
Examples
# A single oral dose
pknca_interval_table(0, 24, dosing = "single", route = "extravascular")
#> start end auclast aucall aumclast aumcall aucint.last aucint.last.dose
#> 1 0 24 TRUE FALSE FALSE FALSE FALSE FALSE
#> aucint.all aucint.all.dose aumcint.last aumcint.last.dose aumcint.all
#> 1 FALSE FALSE FALSE FALSE FALSE
#> aumcint.all.dose c0 cmax cmin tmax tmin tlast tfirst clast.obs cl.last
#> 1 FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE
#> cl.all cl.int.all cl.int.last mrt.last mrt.all mrt.int.all mrt.int.last
#> 1 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
#> cav.int.last cav.int.all ctrough cstart ptr tlag deg.fluc swing ceoi
#> 1 FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE
#> aucabove.predose.all aucabove.trough.all count_conc count_conc_measured
#> 1 FALSE FALSE TRUE FALSE
#> totdose volpk ae clr.last clr.obs clr.pred fe ertlst ermax ertmax erint
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> erlst ratio.cmax ratio.auclast ratio.aucint.last ratio.aucint.all
#> 1 FALSE FALSE FALSE FALSE FALSE
#> sparse_auclast sparse_auc_se sparse_auc_df sparse_aumclast sparse_aumc_se
#> 1 FALSE FALSE FALSE FALSE FALSE
#> sparse_aumc_df time_above aucivlast aucivall aucivint.last aucivint.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> aucivpbextlast aucivpbextall aucivpbextint.last aucivpbextint.all aumcivlast
#> 1 FALSE FALSE FALSE FALSE FALSE
#> aumcivall aumcivint.last aumcivint.all half.life r.squared adj.r.squared
#> 1 FALSE FALSE FALSE TRUE FALSE FALSE
#> lambda.z.corrxy lambda.z lambda.z.time.first lambda.z.time.last
#> 1 FALSE FALSE FALSE FALSE
#> lambda.z.n.points clast.pred span.ratio tobit_residual adj_tobit_residual
#> 1 FALSE FALSE FALSE FALSE FALSE
#> lambda.z.n.points_blq thalf.eff.last thalf.eff.iv.last kel.last kel.iv.last
#> 1 FALSE FALSE FALSE FALSE FALSE
#> kel.all kel.int.all kel.int.last cl.iv.all cl.iv.last cl.ivint.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> cl.ivint.last cl.sparse.last f.last f.int.last f.int.all mrt.sparse.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.iv.all mrt.ivint.all mrt.ivint.last vz.all vz.int.all vz.int.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> vz.iv.all vz.iv.last vz.ivint.all vz.ivint.last vz.last vss.iv.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.ivint.all vss.ivint.last vss.sparse.last aucinf.obs aucinf.pred
#> 1 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
#> aucint.inf.pred.dose aumcint.inf.obs aumcint.inf.obs.dose aumcint.inf.pred
#> 1 FALSE FALSE FALSE FALSE
#> aumcint.inf.pred.dose aucivinf.obs aucivinf.pred aucivpbextinf.obs
#> 1 FALSE FALSE FALSE FALSE
#> aucivpbextinf.pred aumcivinf.obs aumcivinf.pred aucpext.obs aucpext.pred
#> 1 FALSE FALSE FALSE TRUE FALSE
#> kel.iv.all kel.ivint.all kel.ivint.last kel.sparse.last cl.obs cl.pred
#> 1 FALSE FALSE FALSE FALSE TRUE FALSE
#> cl.int.inf.obs cl.int.inf.pred cl.iv.obs cl.iv.pred f.obs f.pred f.int.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> f.int.pred mrt.obs mrt.pred mrt.int.inf.obs mrt.int.inf.pred mrt.iv.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.iv.pred mrt.md.obs mrt.md.pred mrt.ivmd.obs mrt.ivmd.pred vz.obs vz.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> vz.int.inf.obs vz.int.inf.pred vz.iv.obs vz.iv.pred vz.sparse.last vss.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.pred vss.iv.obs vss.iv.pred vss.md.obs vss.md.pred vss.ivmd.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.ivmd.pred vss.int.inf.obs vss.int.inf.pred cav.int.inf.obs
#> 1 FALSE FALSE FALSE FALSE
#> cav.int.inf.pred ratio.aucinf.obs ratio.aucinf.pred thalf.eff.obs
#> 1 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
#> kel.iv.pred kel.int.inf.obs kel.int.inf.pred auclast.dn aucall.dn
#> 1 FALSE FALSE FALSE FALSE FALSE
#> aucinf.obs.dn aucinf.pred.dn aumclast.dn aumcall.dn aumcinf.obs.dn
#> 1 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
#> clr.last.dn clr.obs.dn clr.pred.dn impute
#> 1 FALSE FALSE FALSE start_predose_conc0
# At steady state, with the fluctuation parameters added
pknca_interval_table(
144, 168,
dosing = "steady_state", route = "extravascular",
include = "fluctuation"
)
#> start end auclast aucall aumclast aumcall aucint.last aucint.last.dose
#> 1 144 168 FALSE FALSE FALSE FALSE TRUE FALSE
#> aucint.all aucint.all.dose aumcint.last aumcint.last.dose aumcint.all
#> 1 FALSE FALSE FALSE FALSE FALSE
#> aumcint.all.dose c0 cmax cmin tmax tmin tlast tfirst clast.obs cl.last
#> 1 FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE
#> cl.all cl.int.all cl.int.last mrt.last mrt.all mrt.int.all mrt.int.last
#> 1 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
#> cav.int.last cav.int.all ctrough cstart ptr tlag deg.fluc swing ceoi
#> 1 FALSE FALSE TRUE FALSE TRUE TRUE TRUE TRUE FALSE
#> aucabove.predose.all aucabove.trough.all count_conc count_conc_measured
#> 1 FALSE FALSE TRUE FALSE
#> totdose volpk ae clr.last clr.obs clr.pred fe ertlst ermax ertmax erint
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> erlst ratio.cmax ratio.auclast ratio.aucint.last ratio.aucint.all
#> 1 FALSE FALSE FALSE FALSE FALSE
#> sparse_auclast sparse_auc_se sparse_auc_df sparse_aumclast sparse_aumc_se
#> 1 FALSE FALSE FALSE FALSE FALSE
#> sparse_aumc_df time_above aucivlast aucivall aucivint.last aucivint.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> aucivpbextlast aucivpbextall aucivpbextint.last aucivpbextint.all aumcivlast
#> 1 FALSE FALSE FALSE FALSE FALSE
#> aumcivall aumcivint.last aumcivint.all half.life r.squared adj.r.squared
#> 1 FALSE FALSE FALSE TRUE FALSE FALSE
#> lambda.z.corrxy lambda.z lambda.z.time.first lambda.z.time.last
#> 1 FALSE FALSE FALSE FALSE
#> lambda.z.n.points clast.pred span.ratio tobit_residual adj_tobit_residual
#> 1 FALSE FALSE FALSE FALSE FALSE
#> lambda.z.n.points_blq thalf.eff.last thalf.eff.iv.last kel.last kel.iv.last
#> 1 FALSE FALSE FALSE FALSE FALSE
#> kel.all kel.int.all kel.int.last cl.iv.all cl.iv.last cl.ivint.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> cl.ivint.last cl.sparse.last f.last f.int.last f.int.all mrt.sparse.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.iv.all mrt.ivint.all mrt.ivint.last vz.all vz.int.all vz.int.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> vz.iv.all vz.iv.last vz.ivint.all vz.ivint.last vz.last vss.iv.all
#> 1 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
#> aumcinf.obs aumcinf.pred aucint.inf.obs aucint.inf.obs.dose aucint.inf.pred
#> 1 FALSE FALSE TRUE FALSE FALSE
#> aucint.inf.pred.dose aumcint.inf.obs aumcint.inf.obs.dose aumcint.inf.pred
#> 1 FALSE FALSE FALSE FALSE
#> aumcint.inf.pred.dose aucivinf.obs aucivinf.pred aucivpbextinf.obs
#> 1 FALSE FALSE FALSE FALSE
#> aucivpbextinf.pred aumcivinf.obs aumcivinf.pred aucpext.obs aucpext.pred
#> 1 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
#> cl.int.inf.obs cl.int.inf.pred cl.iv.obs cl.iv.pred f.obs f.pred f.int.obs
#> 1 TRUE FALSE FALSE FALSE FALSE FALSE FALSE
#> f.int.pred mrt.obs mrt.pred mrt.int.inf.obs mrt.int.inf.pred mrt.iv.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.iv.pred mrt.md.obs mrt.md.pred mrt.ivmd.obs mrt.ivmd.pred vz.obs vz.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> vz.int.inf.obs vz.int.inf.pred vz.iv.obs vz.iv.pred vz.sparse.last vss.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.pred vss.iv.obs vss.iv.pred vss.md.obs vss.md.pred vss.ivmd.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.ivmd.pred vss.int.inf.obs vss.int.inf.pred cav.int.inf.obs
#> 1 FALSE FALSE FALSE FALSE
#> cav.int.inf.pred ratio.aucinf.obs ratio.aucinf.pred thalf.eff.obs
#> 1 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
#> kel.iv.pred kel.int.inf.obs kel.int.inf.pred auclast.dn aucall.dn
#> 1 FALSE FALSE FALSE FALSE FALSE
#> aucinf.obs.dn aucinf.pred.dn aumclast.dn aumcall.dn aumcinf.obs.dn
#> 1 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
#> clr.last.dn clr.obs.dn clr.pred.dn impute
#> 1 FALSE FALSE FALSE start_predose
# A urine collection
pknca_interval_table(0, 24, dosing = "single", route = "extravascular",
sample_type = "interval")
#> start end auclast aucall aumclast aumcall aucint.last aucint.last.dose
#> 1 0 24 FALSE FALSE FALSE FALSE FALSE FALSE
#> aucint.all aucint.all.dose aumcint.last aumcint.last.dose aumcint.all
#> 1 FALSE FALSE FALSE FALSE FALSE
#> aumcint.all.dose c0 cmax cmin tmax tmin tlast tfirst clast.obs cl.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> cl.all cl.int.all cl.int.last mrt.last mrt.all mrt.int.all mrt.int.last
#> 1 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
#> cav.int.last cav.int.all ctrough cstart ptr tlag deg.fluc swing ceoi
#> 1 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
#> totdose volpk ae clr.last clr.obs clr.pred fe ertlst ermax ertmax erint
#> 1 FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
#> erlst ratio.cmax ratio.auclast ratio.aucint.last ratio.aucint.all
#> 1 FALSE FALSE FALSE FALSE FALSE
#> sparse_auclast sparse_auc_se sparse_auc_df sparse_aumclast sparse_aumc_se
#> 1 FALSE FALSE FALSE FALSE FALSE
#> sparse_aumc_df time_above aucivlast aucivall aucivint.last aucivint.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> aucivpbextlast aucivpbextall aucivpbextint.last aucivpbextint.all aumcivlast
#> 1 FALSE FALSE FALSE FALSE FALSE
#> aumcivall aumcivint.last aumcivint.all half.life r.squared adj.r.squared
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> lambda.z.corrxy lambda.z lambda.z.time.first lambda.z.time.last
#> 1 FALSE FALSE FALSE FALSE
#> lambda.z.n.points clast.pred span.ratio tobit_residual adj_tobit_residual
#> 1 FALSE FALSE FALSE FALSE FALSE
#> lambda.z.n.points_blq thalf.eff.last thalf.eff.iv.last kel.last kel.iv.last
#> 1 FALSE FALSE FALSE FALSE FALSE
#> kel.all kel.int.all kel.int.last cl.iv.all cl.iv.last cl.ivint.all
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> cl.ivint.last cl.sparse.last f.last f.int.last f.int.all mrt.sparse.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.iv.all mrt.ivint.all mrt.ivint.last vz.all vz.int.all vz.int.last
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> vz.iv.all vz.iv.last vz.ivint.all vz.ivint.last vz.last vss.iv.all
#> 1 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
#> aumcinf.obs aumcinf.pred aucint.inf.obs aucint.inf.obs.dose aucint.inf.pred
#> 1 FALSE FALSE FALSE FALSE FALSE
#> aucint.inf.pred.dose aumcint.inf.obs aumcint.inf.obs.dose aumcint.inf.pred
#> 1 FALSE FALSE FALSE FALSE
#> aumcint.inf.pred.dose aucivinf.obs aucivinf.pred aucivpbextinf.obs
#> 1 FALSE FALSE FALSE FALSE
#> aucivpbextinf.pred aumcivinf.obs aumcivinf.pred aucpext.obs aucpext.pred
#> 1 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
#> cl.int.inf.obs cl.int.inf.pred cl.iv.obs cl.iv.pred f.obs f.pred f.int.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> f.int.pred mrt.obs mrt.pred mrt.int.inf.obs mrt.int.inf.pred mrt.iv.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> mrt.iv.pred mrt.md.obs mrt.md.pred mrt.ivmd.obs mrt.ivmd.pred vz.obs vz.pred
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> vz.int.inf.obs vz.int.inf.pred vz.iv.obs vz.iv.pred vz.sparse.last vss.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.pred vss.iv.obs vss.iv.pred vss.md.obs vss.md.pred vss.ivmd.obs
#> 1 FALSE FALSE FALSE FALSE FALSE FALSE
#> vss.ivmd.pred vss.int.inf.obs vss.int.inf.pred cav.int.inf.obs
#> 1 FALSE FALSE FALSE FALSE
#> cav.int.inf.pred ratio.aucinf.obs ratio.aucinf.pred thalf.eff.obs
#> 1 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
#> kel.iv.pred kel.int.inf.obs kel.int.inf.pred auclast.dn aucall.dn
#> 1 FALSE FALSE FALSE FALSE FALSE
#> aucinf.obs.dn aucinf.pred.dn aumclast.dn aumcall.dn aumcinf.obs.dn
#> 1 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
#> clr.last.dn clr.obs.dn clr.pred.dn
#> 1 FALSE FALSE FALSE