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Before you can use Python together with R you first need to have it installed on your computer:

1 Run a Python Script by Running a Terminal Command in R

If we have a Python script Python Script.py as follows:

import distro
import os
import platform
import sys
import datetime
import pwd

print('This is a Python script')
print(f'This script was run on {datetime.datetime.now():%Y-%m-%d}')
print(f'This is a {platform.system()} machine')
print(f'Its name is {platform.node()}')
print(f'Its OS is {distro.linux_distribution()[0]}')
print(f'Its OS version is {distro.linux_distribution()[1]}')
print(f'Its Python version is {platform.python_version()}')
print(f'Python is being run from {sys.executable}')
print(f'The user is {pwd.getpwuid(os.getuid())[0]}')

…and an R script R Script.R as follows:

print('This is an R Script')

system('python3 "Python Script.py"')

…then running the R script will produce:

[1] "This is an R Script"
This is a Python script
This script was run on 2021-07-25
This is a Linux machine
Its name is rowanscomputer
Its OS is Ubuntu
Its OS version is 20.04
Its Python version is 3.8.10
Python is being run from /usr/bin/python3
The user is rowan

In other words, the R script has run a terminal command which has run a Python script.

1.1 Incorporate a Configuration File

If we have the same Python script as in the above example but inside a folder called “Location of Python Script” and, additionally, we have a config file called config.ini with the following inside it:

[location]
python_folder=Location of Python Script

…and an R script as follows:

# Import libraries
library(ini)

# Read ini
config <- read.ini('config.ini')
print(config$location$python_folder)

# Run Python file
cmd = paste("python3 '", file.path(config$location$python_folder, 'Python Script.py'), "'", sep='')
print(cmd)
system(cmd)

…then running the R script will produce:

[1] "Location of Python Script"
[1] "python3 'Location of Python Script/Python Script.py'"
This is a Python script
This script was run on 2021-07-25
This is a Linux machine
Its name is rowanscomputer
Its OS is Ubuntu
Its OS version is 20.04
Its Python version is 3.8.10
Python is being run from /usr/bin/python3
The user is rowan

This is a more robust way of running an external script because if you change its location (eg if it’s on a remote server or the script is being run on someone else’s computer) you only need to update the configuration file.

2 Import a Python Script or Function in R

If you want to run Python code and use its output in R, you can use the reticulate library (a reference to reticulated pythons). Once you’ve installed it, use its source_python() function to run code stored in an external Python script and return its values. If we use the same Python Script.py as in the above examples along with a file Python Function.py containing a function definition like so:

def my_function(x):
    return x + 5

…then if we run the following in R:

library(reticulate)

print('This is an R Script')

# Evaluate the chosen script
source_python('Python Script.py')

# Evaluate the chosen script
source_python('Python Function.py')
# Create parameter to pass to Python function
x = 10
# Call my_function()
y = my_function(x)
print(y)

…it will produce:

[1] "This is an R Script"
This is a Python script
This script was run on 2021-07-25
This is a Linux machine
Its name is rowanscomputer
Its OS is Ubuntu
Its OS version is 20.04
Its Python version is 3.8.10
Python is being run from /usr/bin/python3
The user is rowan
[1] 15

In other words, we’re using a Python function right inside R as if it were an R function!

3 Python Versioning

3.1 Check What Version of Python Your RStudio is Using

Use the reticulate package’s py_config() function to see what Python and Numpy versions it uses and where those are installed:

library(reticulate)
print(reticulate::py_config())
## python:         /usr/bin/python3
## libpython:      /usr/lib/python3.8/config-3.8-x86_64-linux-gnu/libpython3.8.so
## pythonhome:     //usr://usr
## version:        3.8.10 (default, Jun  2 2021, 10:49:15)  [GCC 9.4.0]
## numpy:          /home/rowan/.local/lib/python3.8/site-packages/numpy
## numpy_version:  1.19.1
## 
## python versions found: 
##  /usr/bin/python3
##  /usr/bin/python

3.2 Change the Python Version

  • In order to change what version of Python you are using you first need to have it installed on your computer:
    • Go to the Python website to download the one(s) you want. You can have multiple versions of Python installed on the same computer at once.
    • Check that the version you want is installed by opening the terminal and running which python<x.y> where <x.y> are the relevant version numbers - eg which python3.9 - to see if the location of that Python version is returned. If nothing is returned that’s bad because it means that that version is not installed.
    • Running python<x.y> or just python<x> - eg python3.9 or just python3 - should open that version of Python in your terminal
  • To change the version of Python used by the terminal in RStudio you can add an alias to your Bash profile. This works because the RStudio terminal is simply a Bash terminal, so we can re-map the python command to a specific version of Python across all Bash terminals:
    • Open the hidden file .bash_profile that should be in your home directory (you will need to make hidden files visible in order to do this, or run open ~/.bash_profile in your terminal)
    • Run which python<x.y> to get the location of your Python version x.y
    • Add the text alias python=<location> to your .bash_profile file where <location> is the location of your Python as returned by which in the previous step
    • Save and close .bash_profile, then close and re-open RStudio
  • When running an R or R Markdown script in RStudio the version of Python is set when the ‘reticulate’ library is first loaded, so include the line Sys.setenv(RETICULATE_PYTHON = <location>) BEFORE library(reticulate) to set it manually, as shown below. Again, you need to close and re-open RStudio and re-run your script for it to have an effect:
    • macOS
    # path <- "/Library/Frameworks/Python.framework/Versions/3.8/bin/python3.8"
path <- "/Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9"
Sys.setenv(RETICULATE_PYTHON = path)
library(reticulate)
print(reticulate::py_config())
    ## python:         /Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9
## libpython:      /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/config-3.9-darwin/libpython3.9.d
                   ylib
## pythonhome:     /Library/Frameworks/Python.framework/Versions/3.9:/Library/Frameworks/Python.framework/Versions/
                   3.9
## version:        3.9.5 (v3.9.5:0a7dcbdb13, May  3 2021, 13:17:02)  [Clang 6.0 (clang-600.0.57)]
## numpy:          /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy
## numpy_version:  1.21.0
## 
## NOTE: Python version was forced by RETICULATE_PYTHON
    • Ubuntu
    # path <- "/usr/bin/python3.8"
path <- "/usr/bin/python3.9"
Sys.setenv(RETICULATE_PYTHON = path)
library(reticulate)
print(reticulate::py_config())
    ## python:         /usr/bin/python3.9
## libpython:      /usr/lib/python3.9/config-3.9-x86_64-linux-gnu/libpython3.9.so
## pythonhome:     //usr://usr
## version:        3.9.5 (default, May 19 2021, 11:32:47)  [GCC 9.3.0]
## numpy:          /home/rowan/.local/lib/python3.9/site-packages/numpy
## numpy_version:  1.20.1
## 
## NOTE: Python version was forced by RETICULATE_PYTHON

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