rmarkdown VS codebraid

I am surprised they didn't mention RMarkdown (https://rmarkdown.rstudio.com/), which was developed in parallel to Jupyter Notebooks, with lots of convergent evolution.

RMarkdown is essentially Markdown with executable code blocks. While it comes from an R background, code blocks can be written in any language (and you can mix multiple languages).

The biggest difference (and, I would say, advantage) is that it separates code from output, making it work well with version control.

Pardon me for shooting from the hip here, but IMO if you're using R for something radically different than statistical analysis and data visualization, there might be another tool/language that's more purpose-suited.

> As someone who basically uses R as a nice LISP-y scripting language to orchestrate calling low-level compiled code from other languages

When I read this, I think, would `bash` or something equally portable/universally installed work?

R is a beautiful thing when limited to its core uses (I use it every day ([0]). But in my experience, the more we build away from those core uses, the more brittleness we introduce. I wish the Posit team would focus on the core R experience, resolve some of the hundreds of open issues on its core packages in a timely way, [1,2] and just generally play to R's strengths.

[0] https://github.com/hsflabstanford/vegan-meta

[1] https://github.com/rstudio/rmarkdown/issues

[2] https://github.com/tidyverse/ggplot2/issues

reminds me a lot of rmarkdown - which allows you to run many languages in a similar fashion https://rmarkdown.rstudio.com/

I'm surprised to see no one has pointed out [RMarkdown + RStudio](https://rmarkdown.rstudio.com) as one way to immediately interface with Pandoc.

I used to write papers and slides in LaTeX (using vim, because who needs render previews), then eventually switched to Pandoc (also vim). I eventually discovered RMarkdown+RStudio. I was looking for a nice way to format a simple table and discovered that rmarkdown had nice extensions of basic markdown (this was many years ago so maybe that is incorporated into vanilla markdown/pandoc).

The RMarkdown page claims:

> R Markdown supports dozens of static and dynamic output formats including HTML, PDF, MS Word, Beamer, HTML5 slides, Tufte-style handouts, books, dashboards, shiny applications, scientific articles, websites, and more.

...which I think is largely due to using pandoc as the core generator.

RStudio shows you the pandoc command it runs to generate your document, which I've used to figure out the pandoc command I want to run when I've switched to using pandoc directly.

This is a bit of a "lazy" way to interact with pandoc. Maybe the "laziest" aspect: when I get a new computer, I can install the entire stack by installing Rstudio, then opening a new rmarkdown document. Rstudio asks whether I'd like to install all the necessary libraries -- click "yes" and that's it. Maybe that sounds silly but it used to be a lot of work to manage your LaTeX install. These days I greatly favor things that save me time, which seems to get more precious every year.

Then, I worked on a Shiny project where I had to learn R Markdown. I was very excited about it because being paid to learn a new technology is something I have always preferred. I also worked with Highcharts graphs, which I didn’t do for years. It was also the first time I was being paid to design something. I didn’t enjoy that part as much as development, but I cannot say it was a bother either.

files/figure-latex/unnamed-chunk-2-1.pdf) Try to find the following text in midterm-question.Rmd: . See https://github.com/rstudio/rmarkdown/issues/385 for more info.

We used R Markdown for cleaning and analysis, creating updateable web pages we could share with everyone involved. Similarweb’s categories were useful, but too niche for us. So we spent a lot of time recategorizing and redefining the groupings. We used the token count for each website — how many words or phrases — to measure it’s importance in the overall training data.

In [R Markdown](https://rmarkdown.rstudio.com/) or [Quarto](https://quarto.org/), I can include inline code in a math equation, e.g.,

you probably want an rmd file with html output

If you want Markdown instead of Org Mode, Codebraid is great.

https://github.com/gpoore/codebraid

Fortunately, literate programming is a thing, so there are still tools for that. If you want PDF/HTML output facilities, it looks like CodeBraid is the way to go. It uses the Pandoc framework, so you can do all kinds of neat things with it.

For the Python in markdown case, you might be interested in one of my projects that allows executable Python code (including optional Jupyter kernel support) in Pandoc markdown: https://github.com/gpoore/codebraid. Pandoc does all the document parsing (there is no regex preprocessor for extracting code), so converting markdown to markdown often works particularly well.

A tool that really helped me was codebraid, it allows me to keep the code and output of said code in sync really easily.