Add columns for calculations within PKNCA intervals

Usage

add.interval.col(
  name,
  FUN,
  values = c(FALSE, TRUE),
  unit_type,
  pretty_name,
  depends = NULL,
  desc = "",
  sparse = FALSE,
  formalsmap = list(),
  datatype = c("interval", "individual", "population"),
  pptestcd_cdisc = NULL,
  pptest_cdisc = NULL
)

Arguments

name: The column name as a non-empty character string (length 1, may not be NA or "").
FUN: The function to run (as a character string) or NA if the parameter is automatically calculated when calculating another parameter.
values: Valid values for the column: either a function used to coerce/validate values (e.g. as.numeric) or a vector of allowed values (e.g. c(FALSE, TRUE)).
unit_type: The type of units to use for assigning and converting units. Must be one of the pre-defined unit types (see Details). This argument is required and has no default; omitting it raises an error.
pretty_name: The name of the parameter to use for printing in summary tables with units. (If an analysis does not include units, then the normal name is used.)
depends: Character vector of columns that must be run before this column.
desc: A human-readable description of the parameter (<=40 characters to comply with SDTM)
sparse: Is the calculation for sparse PK?
formalsmap: A named list mapping parameter names in the function call to NCA parameter names. See the details for information on use of formalsmap.
datatype: The data type used for the calculation. The default is "interval", which is currently the only supported value. The "individual" and "population" data types are reserved for future use and will currently raise an error if selected.
pptestcd_cdisc: The CDISC PPTESTCD code for this parameter. Can be a character string for simple mappings, or a named list for route-dependent mappings with a route element whose value is itself a named list keyed by route (e.g. list(route = list(extravascular = "CLF/FO", intravascular = "CLO"))). Defaults to name if not provided.
pptest_cdisc: The CDISC PPTEST name for this parameter. Can be a character string or a named list (same structure as pptestcd_cdisc). Defaults to desc if not provided.

Value

NULL (Calling this function has a side effect of changing the available intervals for calculations)

Details

The formalsmap argument enables mapping some alternate formal argument names to parameters. It is used to generalize functions that may use multiple similar arguments (such as the variants of mean residence time). The names of the list should correspond to function formal parameter names and the values should be one of the following:

For the current interval:
character strings of NCA parameter name

The value of the parameter calculated for the current interval.

"conc"

Concentration measurements for the current interval.

"time"

Times associated with concentration measurements for the current interval (values start at 0 at the beginning of the current interval).

"volume"

Volume associated with concentration measurements for the current interval (typically applies for excretion parameters like urine).

"duration.conc"

Durations associated with concentration measurements for the current interval.

"dose"

Dose amounts assocuated with the current interval.

"time.dose"

Time of dose start associated with the current interval (values start at 0 at the beginning of the current interval).

"duration.dose"

Duration of dose (typically infusion duration) for doses in the current interval.

"route"

Route of dosing for the current interval.

"start"

Time of interval start.

"end"

Time of interval end.

"options"

PKNCA.options governing calculations.
For the current group:
"conc.group"

Concentration measurements for the current group.

"time.group"

Times associated with concentration measurements for the current group (values start at 0 at the beginning of the current interval).

"volume.group"

Volume associated with concentration measurements for the current interval (typically applies for excretion parameters like urine).

"duration.conc.group"

Durations assocuated with concentration measurements for the current group.

"dose.group"

Dose amounts assocuated with the current group.

"time.dose.group"

Time of dose start associated with the current group (values start at 0 at the beginning of the current interval).

"duration.dose.group"

Duration of dose (typically infusion duration) for doses in the current group.

"route.group"

Route of dosing for the current group.

Examples

if (FALSE) { # \dontrun{
add.interval.col("cmax",
                 FUN="pk.calc.cmax",
                 values=c(FALSE, TRUE),
                 unit_type="conc",
                 pretty_name="Cmax",
                 desc="Maximum observed concentration")
add.interval.col("cmax.dn",
                 FUN="pk.calc.dn",
                 values=c(FALSE, TRUE),
                 unit_type="conc_dosenorm",
                 pretty_name="Cmax (dose-normalized)",
                 desc="Maximum observed concentration, dose normalized",
                 formalsmap=list(parameter="cmax"),
                 depends="cmax")
} # }