extractExpDetails: Extract details about the experimental design

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

Extract details about the experimental design

Description

extractExpDetails looks up experimental design details from a Simcyp Simulator output file. For detailed instructions and examples, please see the SharePoint file "Simcyp PBPKConsult R Files - Simcyp PBPKConsult R Files/SimcypConsultancy function examples and instructions/Checking simulation experimental details/Checking-simulation-experimental-details.docx". (Sorry, we are unable to include a link to it here.)

Usage

extractExpDetails(sim_data_file, exp_details = "Summary and Input")

Arguments

sim_data_file

name of the Excel file containing the simulator output, in quotes. A note: There are just a few items that we will attempt to extract from the matching workspace file; for that information, we will look for a workspace file that is named identically to the Excel file except for the file extension. It will ignore the date/time stamp that the autorunner adds as long as that stamp is in a format like this: "myfile - 2023-10-31 07-23-15.xlsx".

exp_details

Experiment details you want to extract from the simulator output file. Options are "Summary and Input" Extract details available from the "Summary tab" and the "Input Sheet" (default) "population tab" Extract details about the population used (data come from the tab with the same name as the population simulated) "Simcyp inputs" Extract all the details that you normally fill out on the "Simcyp inputs (and QC)" tab of a compound data sheet plus trial design information "workspace" Extract a limited set of details directly from the Simcyp Simulator workspace files. The set of possible details may be viewed by entering view(AllWorkspaceDetails) in the console. This only works if the workspace file name perfectly matches the Excel results file name and is located in the same folder. Otherwise, this step in the data extraction will be skipped. "all" Extract all possible parameters NOTES: The default pulls parameters from the "Summary" tab and the "Input Sheet" tab. Note that the "Summary" tab does not include information on any compounds beyond the substrate and inhibitor 1. There are a few places where requesting one item as input will get you multiple items as output: intrinsic clearance, interaction parameters, and transport parameters. For example, if you request intrinsic clearance values (ex: "CLint_sub"), you'll get all the intrinsic clearance values for that compound, and they'll be named according to which parameter it is, which enzyme it's for, etc. Same thing with requesting interaction parameters (ex: "Interaction_inhib" to get all the interaction parameters for inhibitor 1) and transporter parameters (ex: "Transport_sub").

Value

Returns a named list of the experimental details

Examples

extractExpDetails(sim_data_file = "../Example simulator output.xlsx")
extractExpDetails(sim_data_file = "../Example simulator output MD + inhibitor.xlsx")
extractExpDetails(sim_data_file = "../Example simulator output.xlsx",
                  exp_details = "all")

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