extractExpDetails_VBE: Extract details about the experimental design of a VBE...

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

Extract details about the experimental design of a VBE simulation - UNDER CONSTRUCTION

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_VBE(
  sim_data_files,
  existing_exp_details = NA,
  overwrite = FALSE,
  sheet_names = NA,
  ...
)

Arguments

sim_data_files	a character vector of simulator output files, each in quotes and encapsulated with c(...), NA to extract experimental details for all the Excel files in the current folder, or "recursive" to extract experimental details for all the Excel files in the current folder and all subfolders. Example of acceptable input: sim_data_files = c("sim1.xlsx", "sim2.xlsx"). If some of your Excel files are not regular simulator output, e.g. they are sensitivity analyses or a file where you were doing some calculations, those files will be skipped. A note: There are just a few items that we will attempt to extract from the matching workspace file (actually, no, it won't. This is placeholder text for when we do implement that; at present, it will only look at Excel files); 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".
existing_exp_details	(optional) a data.frame that contains previously extracted experimental details. If this object does exist, it should NOT be in quotes, e.g. existing_exp_details = MyDeets. Because we can see scenarios where you might want to extract some experimental details and then run more simulations for comparisons, this function will add data to that data.frame. It will not overwrite existing data unless overwrite is set to TRUE.
overwrite	TRUE or FALSE (default) on whether to re-extract the experimental details from output files that are already included in existing_exp_details. Since pulling data from Excel files is slow, by default, this will not overwrite existing data and instead will only add data from any Excel files that aren't already included. A situation where you might want to set this to TRUE would be when you have changed input parameters for simulations and re-run them OR when you have extracted only some of the possible experimental details and you now would like more experimental details from each simulator output file.

Value

Returns a named list of simulation experimental details for simulator files

shirewoman2/Consultancy documentation built on June 1, 2025, 6:05 p.m.