In a recent post, I showcased my setup for writing academic papers with R. Today, we expand this setup by Pythonand other languages.

We look at two options: The first one, is to use the reticulate package with R Markdown, and the second option is to move to Quarto.

Quarto is a generalisation of R Markdown by the same core developers.  This framework allows you to weave together R, Python, Julia, and OJS with the code's output and your writing.

Python in R Markdown – using the reticulate package

The reticulate package intermediates between R and Python.

Besides writing hybrid scripts which feature both languages, it allows you to use Python code chunks in R Markdown.

For this to work, you need to load reticulate, and set your Python interpreter in your r setup code chunk.

```{r setup}
library(reticulate)
use_python("path/to/my/python")
```

Now you can use Python in the same way that you would use R code: You just need to change the chunk's tag from r to python. Even chunk options such as echo, or warnings still work as expected.

```{python}
import numpy as np
a = [1, 2, 3]
print(np.sum(a))
```

This is a great option if you want to simply extend your current workflow by the occasional chunk of Python code.

Embrace hybrid documents by changing to Quarto

Quarto can generate anything from a plain .docx, or .pdf, to a full interactive websites. It can compile Markdown files (.qmd), and the engine also renders Jupyter Notebooks into documents. You can find examples and extensive documentation on quarto.org.