extractExpDetails_XML: Extract experimental details for multiple Simcyp Simulator...

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

Extract experimental details for multiple Simcyp Simulator workspace files at once

Description

extractExpDetails_XML takes a character vector of Simcyp Simulator or Simcyp Discovery workspaces – or all the workspace files in the current directory if no files are specified – and collects experimental details for the simulations into a single table. It optionally saves that table to a csv or Excel file.

Usage

extractExpDetails_XML(
  sim_workspace_files = NA,
  compoundsToExtract = "all",
  exp_details = "all",
  save_output = NA
)

Arguments

sim_workspace_files	a character vector of simulator files, each in quotes and encapsulated with c(...), NA to extract experimental details for all the Simulator or Discovery workspace files in the current folder, or "recursive" to extract experimental details for all the Simulator or Discovery workspace files in the current folder and all subfolders. Example of acceptable input: c("sim1.wksz", "sim2.wksz").
compoundsToExtract	For which compound do you want to extract concentration-time data? Options are: "all" (default) for all the possible compounds in the simulation (substrate, metabolites, inhibitors, and ADC-related compounds) "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, "conjugated protein" for DAR1-DARmax for an antibody-drug conjugate; observed data with DV listed as "Conjugated Protein Plasma Total" will match these simulated data, "total protein" for DAR0-DARmax for an ADC; observed data with DV listed as "Total Protein Conjugate Plasma Total" will match these simulated data, or "released payload" for the released drug from an ADC, which shows up as primary metabolite 1 in Simulator output files Input to this argument should be all desired compounds as a character vector, e.g., c("substrate", "primary metabolite 1"). Note: If your compound is a therapeutic protein or ADC, we haven't tested this very thoroughly, so please be extra careful to check that you're getting the correct data.
exp_details	experimental details you want to extract from the simulator workspace files; currently "all" is the only acceptable input and anything else will be ignored. These are much more limited than the options for the function extractExpDetails and currently only include a handful of items such as calculated Peff,human, predicted Vss, the XML overlay file used for observed data, and the XML file used for a fixed-trial design.
save_output	optionally save the output by supplying a csv or Excel file name in quotes here, e.g., "Simulation details.csv" or "Simulation details.xlsx". Do not include any slashes, dollar signs, or periods in the file name. If you leave off the file extension, it will be saved as a csv file.

Value

Returns a data.frame of the experimental details

Examples

# None yet

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