Standardized Processing and Visualization of PK-Sim PBPK Outputs in R

Repository Contents and Usage Instructions

This record contains all files necessary to reproduce the concentration–time figures presented in the accompanying project report on reference PBPK simulations generated using PK-Sim. Specifically, it includes the standardised R plotting script (plot_pk_sim_final_readable.R) and the CSV output files exported from PK-Sim, representing concentration–time profiles for all sixteen PBPK simulations. Each CSV file corresponds to one simulation condition, covering four small-molecule compounds (midazolam, mefenamic acid, ethinylestradiol, and S-verapamil), two species (human and rat), and two routes of administration (intravenous bolus and oral), all at a dose of 1 mg/kg over a 24-hour simulation window.

How to reproduce the figures

The CSV files in this record are intended to be used together with the standardised R plotting script also available in this same Zenodo record.

To reproduce all figures, set up the following folder structure on your local machine:

1. Create a project folder, for example named PKSIM_PLOTS
2. Inside PKSIM_PLOTS, create two subfolders: csv_exports and plots_out
3. Place all CSV files from this record into the csv_exports folder.
4. Place the R script in the PKSIM_PLOTS folder alongside the two subfolders.
5. Run the R script. It will automatically detect and process all CSV files present csv_exports and save the resulting figures to plots_out.

No manual file selection is required. The script is fully automated and applies identical formatting, axis scaling, tissue selection, and colour assignments across all panels, ensuring that all figures are directly comparable.