extractPK_DB: Extract PK from a Simcyp Simulator database file

In shirewoman2/Consultancy: Standardized tools for using R within the Simcyp Consultancy Team

Extract PK from a Simcyp Simulator database file

Description

extractPK_DB pulls PK data from a database file and calculates summary statistics for the data

Usage

extractPK_DB(
  sim_data_file,
  compoundToExtract = "substrate",
  PKparameters = NA,
  which_doses = NA,
  tissue = "plasma",
  existing_exp_details,
  returnAggregateOrIndiv = "aggregate"
)

Arguments

sim_data_file	name of the database file containing the simulator output, in quotes
compoundToExtract	For which compound do you want to extract PK data? Options are: "substrate" (default), "primary metabolite 1", "primary metabolite 2", "secondary metabolite", "inhibitor 1" – this can be an inducer, inhibitor, activator, or suppresesor, but it's labeled as "Inhibitor 1" in the simulator, "inhibitor 2" for the 2nd inhibitor listed in the simulation, "inhibitor 1 metabolite" for the primary metabolite of inhibitor 1
PKparameters	PK parameters you want to extract from the simulator output file. Options are: "all" all possible parameters "AUC tab" only those parameters that would be found on an "AUC" tab of the Excel output (default) "Absorption tab" only those parameters that would be found on the "Absorption" or "Overall Fa Fg" tab "Regional ADAM" regional fraction absorbed and fraction metabolized from intestinal segments; only applies to ADAM models where the tab "Regional ADAM Fractions (Sub)" is included in the Excel file and currently only applies to substrate a vector of any combination of specific, individual parameters, each surrounded by quotes and encapsulated with c(...) An example: c("Cmax_dose1", "AUCtau_last"). To see the full set of possible parameters to extract, enter view(PKParameterDefinitions) into the console. Not case sensitive. If you use "_first" instead of "_dose1", that will also work.
which_doses	optionally specify which doses you would like. If left as NA (default), only the first- and last-dose PK will be included. An example of good input: which_doses = 1 or which_doses = c(1:3, 7) or which_doses = "first" or which_doses = "last"
tissue	For which tissue would you like the PK parameters to be pulled? Options are "plasma" (default), "unbound plasma", "blood", "unbound blood", "peripheral plasma", or "peripheral blood". NOTE: PK for peripheral sampling is not as well tested as for other tissues and is only set up for V21+. Please check your results carefully.
existing_exp_details	If you have already run extractExpDetails_mult or extractExpDetails to get all the details from the "Input Sheet" (e.g., when you ran extractExpDetails you said exp_details = "Input Sheet" or exp_details = "all"), you can save some processing time by supplying that object here, unquoted. If left as NA, this function will run extractExpDetails behind the scenes to figure out some information about your experimental set up.
returnAggregateOrIndiv	return aggregate (default) and/or individual PK parameters? Options are "aggregate", "individual", or "both". For aggregate data, values are pulled from simulator output – not calculated – and the output will be a data.frame with the PK parameters in columns and the statistics reported exactly as in the simulator output file.

Value

a list: "individual" = individual PK data, "aggregate" = aggregate PK data, "TimeInterval" = the time intervals used

Examples

# none yet

shirewoman2/Consultancy documentation built on Feb. 18, 2025, 10 p.m.