extractForestData: Extract pertinent data from Simulator output files for...

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

Extract pertinent data from Simulator output files for creating forest plots

Description

extractForestData automatically extracts data for generating forest plots from Simulator output files and formats them for use with forest_plot or the forest plot shiny app. This will take some time to run since it needs to open multiple Excel files. For detailed instructions and examples, please see the SharePoint file "Simcyp PBPKConsult R Files - Simcyp PBPKConsult R Files/SimcypConsultancy function examples and instructions/Forest plots/Examples-for-making-forest-plots.docx". (Sorry, we are unable to include a link to it here.)

Usage

extractForestData(
  sim_data_files = NA,
  PKparameters = c("AUCinf_ratio_dose1", "AUCt_ratio_dose1", "Cmax_ratio_dose1",
    "AUCtau_ratio_last", "Cmax_ratio_last"),
  compoundToExtract = "substrate",
  tissue = "plasma",
  existing_exp_details = NA,
  sheet = NA,
  checkDataSource = TRUE,
  save_output = NA
)

Arguments

sim_data_files	a character vector of simulator output files, each in quotes and encapsulated with c(...), NA to extract forest-plot data for all the Excel files in the current folder, or "recursive" to extract forest-plot data for all the Excel files in the current folder and all subfolders.
PKparameters	PK parameters to extract from simulator output files; default is all possible AUC and Cmax geometric mean ratios for both dose 1 and the last dose simulated. Input must be among "AUCinf_ratio_dose1", "AUCt_ratio_dose1", "Cmax_ratio_dose1", "AUCtau_ratio_last", or "Cmax_ratio_last". List them in the order you'd like the columns to appear in the output.
compoundToExtract	For which compound do you want to extract PK data? Options are: "substrate" (default), "primary metabolite 1", "primary metabolite 2", or "secondary metabolite"
tissue	For which tissue would you like the PK parameters to be pulled? Options are "plasma" (default), "unbound plasma", "blood", or "unbound blood".
existing_exp_details	If you have already run extractExpDetails_mult in all the files included 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.
sheet	optionally specify the name of the sheet where you'd like to pull the PK data, in quotes; for example, specify the tab where you have a user-defined AUC integration. Note: Unless you want a very specific Excel sheet that's not what the usual sheet name would be for a first or last dose, this function will work best if this is left as NA. Also, since we don't know which dose these data were for, you'll see that the output parameter names do not include the suffixes "_last" or "_dose1".
checkDataSource	TRUE (default) or FALSE: Include in the output a data.frame that lists exactly where the data were pulled from the simulator output file. Useful for QCing.
save_output	optionally save the output by supplying a file name in quotes here, e.g., "My forest graph data.csv". If you leave off ".csv", it will still be saved as a csv file.

Value

a data.frame of data to use for making forest plots

Examples

extractForestData(sim_data_files = NA,
                  save_output = "Forest data.csv")

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