[mespe]

Funny thing is this has actually motivated me to move away from using rmarkdown. To the point that I went "backwards" and wrote several reports and an academic paper in Sweave after using rmarkdown for years. My primary motivation was that I needed to know the documents could be built by any R session, not just from within RStudio. I didn't want to be in a situation where my "reproducible" document relied on a specific IDE to build correctly.

[jcheng]

Hi, I’m with RStudio.

We generally treat “working in RStudio but not elsewhere” as serious bugs, especially in our open source R packages. Not only because we don’t want to artificially limit usage of other interactive environments, but because a lot of what people do with R is run their code in non-interactive settings like CI/CD pipelines or ETL jobs.

(Actually, an R Markdown compilation is a particularly good example of something people often do from Travis or GitHub Actions)

[JHonaker]

I actually use Emacs to author R Markdown and the exporting works pretty flawlessly.

Before anyone asks, I use Org Mode. I just don't feel like pushing that format on my co-workers. If it's for me only, I use Org. If it's for a collaboration or export into a report, it goes into an R Markdown file.

[valarauko]

Curious: how does Org-Mode compare with RMarkdown's use case? I'm only tangentially familiar with both. I've had the hardest time getting into Emacs (Doom-Emacs), and while Org-Mode seems great, the benefits seem to come entirely from Emacs, not the syntax.

I used markdown + pandoc to write my PhD thesis, but was forced to resort to latex for any formatting that was even slightly complicated (ie, multifigure plots, tables, etc).

[reactspa]

I have created portable (for Windows) versions of R and R-Studio that work fine for the most part. However I was unable to make Bookdown work on them.

An official portable version of R-Studio: one that lives off a folder in the computer, and can be moved to a new PC in a pinch with all settings and plugins intact, and works with all official packages... would be very sweet. (Reason: upgrading from one PC to a newer one is a pain if one has to install application software from scratch. Copying over the "portableApps" folder is so much easier.

Portable R available via PortableApps here: https://portableapps.com/node/32898

Portable RStudio via instructions here: https://rpubs.com/jsmccid/rportable

[phillc73]

I'm all for finding alternatives to RStudio's dominance in the R space. No doubt they do some excellent things, but I also have a vague uneasiness at the cultishness surrounding some of their products. It sometimes feels like if you're not using the 'tidyverse', you're viewed as doing it wrong.

Anyway, this feeling set me off on an exploration of alternative tools and packages. Instead of rmarkdown I'm now exploring the pander[1] package, which seems to do most of what I'm looking for, perhaps only a little limited in output formats.

Edit: The Pandoc.brew examples might be most interesting from a direct alternative to rmarkdown for document creation context.[2]

[1] http://rapporter.github.io/pander/

[2] http://rapporter.github.io/pander/#examples

[bigfudge]

For me part of the cultish ness is justified because I have to teach about 100 non programmers to use R and rmd every year. Tidyverse solves the big problem that R used to have was that there were hundreds of ways to do things, none of the functions had consistent naming or calling signatures and it was hard to Google sensible answers. Tidyvers is fast, consistent and has good docs. Pipes discourage lots of mutable state which is a major cause of errors in non programmers code. I think if you are going to be sharing your code with other researchers and are not using tidyverse then These days I think you basically are doing it wrong.

[stilisstuk]

Hmmm... I've always found tideverse syntax inelegant. Data.table syntax does more with fewer different words. But it can get a bit convoluted. Any ways: there are different ways to solveing problems and writing code. Should we not encourage this? Otherwise it's just cargo cult again and again.

[bigfudge]

To a point. I’m actually a data table user too, but it’s actually a pain at the moment (and a good example of why tidyverse quality matters) because they broke the integration with reshape and made me rewrite a bunch of guides a while ago. I don’t like to encourage cargo cutting, but to some extent it’s needed as a beginner. Heck, we’re all still cargo culting to some degree unless you also understand the machine code.

[AuthorizedCust]

I teach a graduate course on R every year. One of my points on the Tidyverse is that it does an excellent job of providing clean and sound extensions to core language functionality. I emphasize how thoughtfully designed it is. It is a refreshing change from other languages, which feel more like a collection of random parts.

[yihui]

To be honest, I can feel the "cultishness" you mentioned, but I'm curious if you also feel that for R Markdown products (which are mostly irrelevant to Tidyverse). If you do, I'd love to try my best to fix that, because that's something that I personally don't like. I want to make it clear that if you don't use R Markdown, you are definitely not doing anything wrong, e.g., LaTeX and HTML are totally legitimate and supported:

https://bookdown.org/yihui/rmarkdown-cookbook/latex-hardcore...

https://bookdown.org/yihui/rmarkdown-cookbook/html-hardcore....

[minimaxir]

As someone who learnt R before tidyverse was a thing, I would have quit R a long time ago without the tidyverse.

Base R is that much of a pain.

[valarauko]

I also learnt R before tidyverse was a thing (2007), and eventually abandoned it for Python & Pandas a year before tidyverse came out. I sorely missed ggplot, but I couldn't justify the ugliness of R to make up for it. Now when I look at R code, it's almost always tidyverse, and makes little sense to me.

I'll probably move to Julia at some point.

[CornCobs]

Agreed. Tidyverse is a totally different language, even. And it's one that is consistent, easy to use and most importantly, it feels designed

Huge props to Hadley Wickham and whoever helps bring programming niceties to R's otherwise mostly non-programmer userbase

[yihui]

I'm one of the main developers of R Markdown. As @jcheng said, it is definitely not our intention to lock you in RStudio for any of our R packages. You probably can't imagine how hard I have been trying to avoid relying on RStudio specifically for certain features. There are decisions that I can definitely make in favor of the RStudio IDE, but usually I don't do that, and hope things also work well with other editors. Pretty much everything you do in the RStudio IDE for R Markdown documents or projects can be done in command line. It's not possible that a document is no longer reproducible just because you stop using RStudio.

[vharuck]

Which parts don't work outside of R Studio for you? Is it something recent? I usually create my single-page and bookdown documents as one step in a separate R script, and haven't found any problems beyond the rmarkdown package's poor documentation (I really wish the R Studio developers would write in-package documentation with as much care as with their online documentation).

[mespe]

If I recall correctly, I had issues primarily with more complicated documents, and mostly due to some RStudio "project" and file path configuration issues - I would have to look to see what the specific issues were. Simple, one-file .Rmd docs are typically fine either way.

[confounded]

It's pretty easy to compile the documents; it's all just R functions (rmarkdown is a wrapper around knitr and pandoc). I've been writing Rmarkdown docs for many years in Emacs without hiccups (or without hiccups from rmarkdown::render, anyway).