PumasTutorials.jl holds PDFs, webpages, and interactive Jupyter notebooks showing how to do pharmaceutical modeling and simulation with Pumas.jl.

To run the tutorials interactively via Jupyter notebooks, install the package and open the tutorials like:

using Pkg; Pkg.add("PumasTutorials") # Run the first time to add the package
using PumasTutorials
PumasTutorials.open_notebooks()

• Introduction
  • Introduction to Pumas
  • Generating and Simulating Populations
  • Introduction to Noncompartmental Analysis (NCA)
• Workshop Materials
  • Workshop Exercises
  • Workshop Exercise Solutions
• Models
  • Discrete Response Models
  • Indirect Response Models

First of all, make sure that your current directory is PumasTutorials. All of the files are generated from the Weave.jl files in the tutorials folder. To run the generation process, do for example:

using Pkg, PumasTutorials
cd(joinpath(dirname(pathof(PumasTutorials)), ".."))
Pkg.pkg"activate ."
Pkg.pkg"instantiate"
PumasTutorials.weave_file("introduction","introduction.jmd")

To generate all of the notebooks, do:

PumasTutorials.weave_all()

If you add new tutorials which require new packages, simply updating your local environment will change the project and manifest files. When this occurs, the updated environment files should be included in the PR.