MCSim under R

This MCSim sandbox aim to help the beginner (especially Windows user) run GNU MCSim (current version 6.1.0) in R.

Prerequisites

• R (https://cran.r-project.org/)
• RStudio (https://www.rstudio.com/)
• Rtools (https://cran.r-project.org/bin/windows/Rtools/)

Instruction

(1) Download all files from this repository or HERE.

(2) Open "MCSim_under_R.Rproj".

(3) Open the R script in examples folder and follow the guidance to do the simple test run.

• Note: Use getwd() in R to make sure your working directory is in MCSim_under_R, such as C:/Users/nanhung/MCSim_under_R. The default install location of Rtools is c:/Rtools.

Workflow

The workflow of MCSim under R can separate into three levels as following diagram,

Functions

Here are the R functions that can help you run MCSim in R environment more easily. All R functions are put in functions.R in MCSim folder.

• makemcsim(model, deSolve): Preprocessing and compiling the model-file to the executable file as makemcsim in GNU MCSim. The model assignment is a string giving the name of the model-file (e.g., "pbpk.model.R"). The deSolve assignment is a logical factor to use deSolve package as an ODE solver.
• mcsim(model, input): Using the compiled program with the input-file to run simulation. See Running Simulations. The input assignment is a string giving the name of the input-file (e.g., "linear.in.R").

Help

• Welcome to submit your problem in issues

• For more detail, please see this tutorial slide

Reference

• GNU MCSim website
• R. Woodrow Setzer. Dynamic Modeling using MCSim and R
• MCSim under R (Windows)
• Using MCSim on Windows with RStudio