Python and Reticulate

Author

David Gerard

Published

October 23, 2025

Learning Objectives

Set up R Studio environment for Python.
Python REPL.
Python chunks and Python scripts.
Getting Started with Reticulate
Installing Python Packages

Setting Up Python for R Studio

Most Python pros use Jupyter Notebook as their IDE when developing in Python.
But for R programmers who only need to dabble in Python (me, for example), we can use R Studio and the reticulate package.

R
```
install.packages("reticulate")
```
You might need to accept the conda terms of service to use conda. So run the following code to load reticulate.

R
```
Sys.setenv(CONDA_PLUGINS_AUTO_ACCEPT_TOS = "yes")
library(reticulate)
```
You can also put this in your R environment (opened via usethis::edit_r_environ()). Then you don’t need to set the enviornment variable every time you load reticulate.
```
CONDA_PLUGINS_AUTO_ACCEPT_TOS = "yes"
```
To install a version of Python that reticulate will use, run in the terminal:

R
```
reticulate::install_miniconda()
```
To validate that Python was installed and is available, run

R
```
reticulate::py_available()
```
Python programmers typically modularize their projects into environments, which are separate installations of python and packages. That way, if you go back to a project, you go back to the exact same version of python and packages that you know work for that project. This reduces chances for breaking changes to affect old projects.

Use conda_list() to list all of the environments.

reticulate::conda_list()

          name
1         base
2 r-reticulate
3    anaconda3
4      msprime
                                                               python
1                   /home/dgerard/.local/share/r-miniconda/bin/python
2 /home/dgerard/.local/share/r-miniconda/envs/r-reticulate/bin/python
3                                  /home/dgerard/anaconda3/bin/python
4                     /home/dgerard/anaconda3/envs/msprime/bin/python

Use conda_create() to create a new environment. You can choose the version of python that this environment uses.

R
```
reticulate::conda_create(envname = "objects", python_version = "3.13.3")
```
Use use_condaenv() to specify the environment you want to use.

R
```
reticulate::use_condaenv("objects")
```
To install Python packages, use py_install(). You need to specify the environment to which the packages are installed. For example, we can install the numpy, pandas, and matplotlib packages via

R
```
reticulate::py_install(envname = "objects", packages = c("numpy", "pandas", "matplotlib", "seaborn"))
```
Note: We used conda environments here, but there is a competing system of environments called “virtualenv” which some folks use.
If you want to update the python version of a specific environment, I’ve found the easiest way was to just remove it with conda_remove() and recreate it with the specified python version.

Python REPL’s, Chunks, and Scripts

To start an IPython shell — similar to the R command promp — run the following in R:

R
```
reticulate::repl_python()
```
“REPL” stands for “read–eval–print loop”, which is an interactive programming environment (like the R command prompt or the IPython shell).
You can exit the REPL by typing the following:

Python
```
exit
```
You can have Python chunks in R Markdown files by replacing the “r” at the beginning of the chunk by “python”:
```
  ```{python}
  # Code goes here
  ```
```
You can access R objects in Python using the r object. That is, r.x will access, in Python, the x variable defined using R.

R
```
x <- c(1, 4, 6, 2)
```
Python
```
r.x
```
```
[1.0, 4.0, 6.0, 2.0]
```
You can access Python objects in R using the py object. That is, py$x will access, in R, the x variable defined using Pythong.

Python
```
x = [8, 9, 11, 3]
```
R
```
py$x
```
```
[1]  8  9 11  3
```
Sometimes it’s buggy, but you can usually begin a Python REPL by also hitting Control/Command + Enter inside the Python chunk:
Python scripts (where there is only Python code and no plain text) end in “.py”. You can create a Python script in R Studio:
Hitting Control/Command + Enter inside a Python script will also start a Python REPL.