orgmode instead of RMarkdown/Bookdown/Blogdown

[removed]

While I am not using org-babel with R I guess following might be as good a start as any: [https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html](https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html) At least that's what I assume you are looking for based on your description

I'm a bioinformatics researcher who programs in R using Emacs. My advice would be stick to RMarkdown. It's possible to do everything you mentioned in org files, but the learning curve is steeper. More importantly, you can't share org files with collaborators - they won't know what to do with it. Check out the poly-R package, it gives great support for RMarkdown in Emacs: https://github.com/polymode/poly-R

The "most visible" differences with org-mode is the fact that org is an outliner, so manage variable length chunk of text is abruptly easier than md* markup, the second one is in term of feature richness. On the other side: R is an ecosystem, org-mode is a glue for anything, so while can embed R as pretty anything else, is not specially crafted for R, so you might loose "integration benefit" of a markup crafted to be a companion of a programming language and language ecosystem. Org-mode offer the ability to store and retrieve a bit of anything covering most desktop usage needs, from email to agenda, but for instance it does very little about diagrams, in that case if you daily produce diagrams trying them in org-mode might be not better than a non-Emacs, non-integrated-with-anything-else diagram tool. For R I see no difference in such terms...

[removed]

[removed]

[removed]

Yes to reports, no to publications. That's because my collaborators prefer writing in Word though. If your coauthors are cool with it you could definitely use RMarkdown/Emacs to that end

[removed]

Well, there is no "correct", I mean, try. There is a tread-off: on one side benefit from integration and org mode, on the over benefit from the dedicated development. Personally I use org-mode for nearly anything, I access most of my files via org-mode links to org-attach relevant files, selected via org-roam managed notes. It works beautifully well. On contrary after many test I'm almost give up on the accounting side: plain-text accounting it's too time consuming for me. I do keep track of *selected* transactions in org, the rest in GNUCash, with an unconformable UI, no integration etc but importing is quick enough to be sustainable and reporting suffice. Similarly in the past I've kept Zotero for a while since importing to Zotero is far simpler than org-mode based setup but after a certain time I slowly drop Zotero because it's hyper-limited integration while there is too limited for my taste and for that the tread-off "easy import vs integration" fall a bit more in the integration side... That's my suggestion: I suppose, without proof, that keeping R ecosystem for certain aspects of your work would be better than seeking integration at actual Emacs status, but that's ad idea, you can only try to discover if it's correct or not :-)

[removed]

I sent you a chat message with the link

> Configuring and learning emacs just to replace my IDE seems to be enough work for now Completely agree, for me the path was (is) EXWM: I realize that classic floating WM are a waste of time and the tiling WM I've tried was (are) too rigid for my taste, Emacs on contrary work beautifully well (free splitting, resizing, "flipping" (`mode-line-other-buffer`) and `windmov`ing around are easy, once used a bit and bound to single meaningful keystrokes, so EXWM seems to be the best solution. It's far from perfect due to issues with certain X11 apps/floating windows but works enough for me to be a daily driver. A thing after another my usage of Emacs goes up and so the desire of integration. Looking for "a replacement for X" never really worked too much alone, it can be just an element to make a decision, a catalyst but not much more than that, not enough alone :-)