Using python and R together in Rmarkdown

[Hrishikesh_Hardikar]

I am trying to use RMarkdown to have python and R integrated together in one document.
The objects that I created in R are usable in python, and vice versa, when I use the RMarkdown in Rstudio. But when I knit it to PDF, following behaviour is observed:

Python code:

x = ‘hello’

R code:

py$x 

If I run this without knitting, it returns the ‘hello’ in the console. But when I knit it to PDF, I can see the output to be ##NULL

Can anyone please help me with this?

[FactOREO]

Did you try to use quarto instead of RMarkdown for multilanguage projects? Quarto should be somewhat more versatile if you incorporate Python as well as R in your documents.

[andresrcs]

Do you manually set your python environment using reticulate? It would make it easier to help you if you can provide a complete minimal reprex.

[Hrishikesh_Hardikar]

Thanks for your reply.
I’m kinda new to this. Can you please tell me what to you mean by provide ‘complete reprex’?
So I’ll be able to post it.

[andresrcs]

If you've never heard of a reprex before, you might want to start by reading this FAQ:

FAQ: How to do a minimal reproducible example ( reprex ) for beginners

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…

In the context of an Rmd document, you should provide a minimal document that incluyes the necessary code chunks to reproduce your specific issue.

[Hrishikesh_Hardikar]

Thank you for the help.
As I sat down to create a minimal Reprex for you, the problem got solved.

I was unnecessarily putting extra arguments to the r setup.

Here's how r-setup looks like when used stock:

{r setup, include = FALSE} 
knitr::opts_chunk$set(echo = TRUE) 

What I was doing:

{r setup, include = TRUE, echo = TRUE, eval = TRUE} 
knitr::opts_chunk$set(echo = TRUE, cache = TRUE, eval = TRUE) 

It is highly likely that these settings interfered with each other creating erroneous results.
The reason I modified the settings in the first place was that I wasn't able to call R objects in python (exactly the opposite of my current problem), for which some answers online suggested that setting eval = TRUE and cache = TRUE can do the job.

However, now everything seems to work just fine even with the stock settings.

Thank you again!

[andresrcs]

@Hrishikesh_Hardikar

As I sat down to create a minimal Reprex for you, the problem got solved.

This happens very often, that is why asking programming related questions with a reprex is such a good idea.

I'm glad you found a solution to your problem. Now to close the loop, if your question's been answered (even by you!), would you mind choosing a solution? It helps other people see which questions still need help, or find solutions if they have similar problems. Here’s how to do it:

FAQ: How do I mark a solution?

If your question has been answered, don't forget to mark the solution! How do I mark a solution? Find the reply you want to mark as the solution and look for the row of small gray icons at the bottom of that reply. Click the one that looks like a box with a checkmark in it: [image] Hovering over the mark solution button shows the label, "Select if this reply solves the problem". If you don't see the mark solution button, try clicking the three dots button ( ••• ) to expand the full set of options. When a solution is chosen, the icon turns green and the hover label changes to: "Unselect if this reply no longer solves the problem". Success! [solution_reply_author] …