Jupyter R Bridge

Convert between R markdown and Jupyter notebook

Differences

This table lists the difference between exporting Jupyter notebook and knitting R markdown.

Description	Jupyter notebook	R markdown	Knit
Support options command. It is mainly used to suppress warnings and adjust figure size, e.g. {r warning=FALSE}, {r fig.width=5,fig.size=5}.	✗	✓	✓
Preview graphs created by grid library. In R Studio, write grid.newpage() at the beginning of each chunk to fix it.	✓	✗	✓

Install R kernel in Jupyter Lab

Windows 10

1. Create a python virtual environment. Denote the location is $venv.

2. Run pip install jupyterlab in Python environment to install Jupyter Lab. Reference There should be an executive file $venv\Scripts\jupyter-lab.exe.

3. Run the following script in R terminal, where $venv should be absolute path. (i.e. C:\Users\Administrator\PycharmProjects\R\venv) It should only use slash / and avoid backslash \. Reference

   # Python environment. Use slash '/' only.
   setwd('$venv/Scripts')
   install.packages("IRkernel")
   IRkernel::installspec()

4. Create a directory to save your projects. Denote the location is $JupyterLab.

5. Run the following script to start Jupyter lab.

   netstat -ano | findstr :8888
   cd $JupyterLab
   $venv\Scripts\jupyter-lab.exe --port 8888

Ubuntu 20.04

1. Run the following command to install R 4.x.

   sudo apt install --no-install-recommends software-properties-common dirmngr
   wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
   sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
   sudo apt install --no-install-recommends r-base

2. If you have conda, run the following command.

   conda create -n R python=3.11
   pip install jupyterlab
   cd ~/.conda/envs/R/bin/
   R

   Otherwise, please use pip install jupyterlab in Python environment and locate to jupyter-lab executive file. You can use which python to locate Python installation path (denoted as $venv) and browse to $venv/bin/.

3. In R command line, run the following command to install R kernel for Jupyter lab.

   install.packages("IRkernel")
   IRkernel::installspec()
   quit()

4. If you access Ubuntu machine by SSH, run the following command to start Jupyter lab.

   cd ~
   jupyter-lab --port 6007 --no-browser --ip 0.0.0.0

   You can customize the port 6007, but should not modify IP address 0.0.0.0.

   If you use Ubuntu machine and access Jupyter lab locally (without SSH), run the following command to start Jupyter lab.

   cd ~
   jupyter-lab --port 6007

   In this case, you have done all the steps.

5. Start a SSH tunnel:

   Local port forwarding
   Remote server: 0.0.0.0
   Remote port: 6007
   Forwarded port: 6007
   

   SSH server is different according to how you connect to Ubuntu machine.

R Studio notes

1. Export customized key bindings setting by copying the files in %APPDATA%/RStudio/keybindings.

Acknowledge

We use rmd2jupyter to convert *.Rmd to *.ipynb. The script is modified.