Summary

Rstudio allows to develop and run python scripts. This text shows how to prepare Rstudio to run python scripts. Preparation includes configuring python. This text does not cover installation of python. The following guide applies to local Ubuntu machine. The text shows 2 ways: using Linux terminal and using Rstudio methods.

Terminal method

At first, you work in terminal of your machine. In terminal go to your project directory. Install virtual environment. Create new python environment for your project. Activate your new environment. Install libraries.

cd <your-project-directory>
pip3 install virtualenv
virtualenv <my-env>
source <my-env>/bin/activate
pip install <lib-1> <lib-2> <lib-3>

Here:

Then you install and configure reticulate library in Rstudio. Configure Rstudio to point to the python in your virtual environment. Restart R session.

install.packages("reticulate")
library("reticulate")
Sys.setenv(RETICULATE_PYTHON = "<my-env>/bin/python")

The latter exists in all sessions. You do not need to do this command every time.

Rstudio method

Here you set everything up using Rstudio only. Install reticulate package. Navigate to your project folder. Create new virtual environment and specify packages you would like to have in it. Add path to python in your virtual environment.

install.packages("reticulate")
library("reticulate")
virtualenv_create(envname  = "<my-env>",
                  packages = c("<lib-1>", "<lib-2>", "<lib-3>"))
Sys.setenv(RETICULATE_PYTHON = "<my-env>/bin/python")

Activate your new virtual environment. Check that your python configuration is now pointing to your virtual environment.

use_virtualenv("<my-env>")
py_config()

Check that your desired packages are present in your virtual environment.

grep(pattern = "<lib-1>|<lib-2>|<lib-3>",
     x       = as.character(py_list_packages(envname = "<my-env>")$package))