Data train course "Causal Learning" (Nov 2025) Uni Bremen

Practicals for the Data Train Course "Causal learning" 2025 (V Didelez)

Install the following programs before the course:

If you use your own machine, ensure you have R v4.0.0 or higher.

Windows users, please make sure that rtools is installed on your computer! (https://cran.r-project.org/bin/windows/Rtools/)

Package installation

Please use the R package pak to install the packages. It automatically chooses the right platform like, e.g., CRAN, Bioconductor, also for dependency packages.

# Install the following R packages within R/RStudio (please keep the order)

install.packages("pak")
library(pak)

# Install a package from github, which we will need in Part 3
pkg_install("github::ericstrobl/RCIT")

# if you need a github personal access token (PAT) in order to install the package
# scroll down - there is a how to.

To install the course R-package from github, simply type:

pkg_install("github::bips-hb/DataTrainCausalLearning")

# load the package.
library(DataTrainCausalLearning)

# install all other packages that are needed within the course
install_more()

Practicals

To open the practicals in your PDF reader, type

openPDF("Practical_part1_2025.pdf")
openPDF("Practical_part2_2025.pdf")   
openPDF("Practical_part3_2025.pdf")   

Code

To open the code, type

openCode("Causal2_code.html")

Download R-Packages from Github

1. Generate a Personal Access Token (PAT)

• Go to [GitHub → Settings → Developer Settings → Personal Access Tokens → Tokens (classic)].
• Click "Generate new token".
• Give it a name (e.g., R Pak Token).
• Select scopes:
  • For most R packages: repo and read:packages are enough.
• Click Generate token.
• Copy the token immediately — you won’t see it again.

2a. Set the PAT in R temporarily

This works for the current R session:

 Sys.setenv(GITHUB_PAT = "your_personal_access_token_here")

2b. Set the PAT permanently

 install.packages("usethis")  # if not already installed
 usethis::edit_r_environ()

• This opens the .Renviron file.
• Add a line:

GITHUB_PAT=your_personal_access_token_here

• Save the file and restart R.
• Now all GitHub installs will automatically use this PAT.

3. Restart R

Restart R try again to install from github

library(pak)
pak::pkg_install("github::ericstrobl/RCIT")

Download binary R-Packages

Download the ZIP-files and install it directly in RStudio over Tools → Install Packages ... → Install from Package Archive File → upload ZIP file

Download the files from here:
RCIT
DataTrainCausalLearning