[HN Gopher] R Markdown: The Definitive Guide ___________________________________________________________________ R Markdown: The Definitive Guide Author : Koshkin Score : 82 points Date : 2021-02-03 18:26 UTC (4 hours ago) (HTM) web link (bookdown.org) (TXT) w3m dump (bookdown.org) | melling wrote: | I recently discovered R Markdown. Started doing the ISLR examples | with it. | | https://github.com/melling/ISLR/blob/main/chapter08/08_Lab02... | | https://github.com/melling/ISLR/blob/main/chapter08/08_Lab02... | | I need to figure out how to better fit images so I don't have | pages with large gaps | | Also, you can now embed executable Python in the files. | bnj wrote: | Tangentially: Reading [0] from Stephen Wolfram yesterday got me | digging into Wolfram notebooks. Does anyone have experience or | reflections on using R Notebooks as the main way to keep track of | notes? | | I don't see the Wolfram products talked about very much here | | [0]: https://writings.stephenwolfram.com/2019/02/seeking-the- | prod... | mespe wrote: | I've been using Rmarkdown and knitr for a long while, and have | watched its evolution over the years (roughly 8 years now). As | someone who does not use RStudio, it's become a bit of a pain for | me to use. The authors seem to expect it is being used from | RStudio, and using it in a different environment has become a bit | fragile. | | It's also a bit telling that this "definitive guide" does not | include any troubleshooting/debugging sections - the expectation | seems to be that it "just works" so long as you use it in | RStudio, but otherwise you are on your own. | | Not sure that I am aware of many other R packages with this | mentality, but I am personally not a fan. | ska wrote: | I haven't used it for a few years, but I have previously set up | some purely command line tooling for this (autogenerated | verification reports) which worked well. Is this getting harder | to do? | mespe wrote: | Some functionality has been tied to RStudio's concept of a | "project" (https://support.rstudio.com/hc/en- | us/articles/200526207-Usin...). I have had several documents | authored by others which would not build on my system without | some intervention due to this. | ska wrote: | Interesting. Thanks. | runningmike wrote: | Jupyter Book is more flexible, simpler and tested to death since | it is build upon Sphinx and docstrings. Since jupyter uses pandoc | for converting notebooks, pandoc is the power tool for | publication creations nowadays. | spinningslate wrote: | Jupyter has downsides too, e.g. version control. An R Markdown | document "in the raw" is just a text file. | | For info, Rmd also uses pandoc under the covers. Agree it's the | power tool, quite a wonderful thing. | qbasic_forever wrote: | Jupyter Book (and the larger jupyter ecosystem now) are | starting to standardize on MyST notebooks as a version- | control friendly all text notebook format. It's similar to r | markdown and uses fenced code blocks to represent code cells. | You can diff them, edit in any text editor, etc. See: | https://myst-nb.readthedocs.io/en/latest/ | closed wrote: | I'm familiar with both Rmarkdown and Jupyter Book. Rmarkdown | also uses pandoc. Both are very flexible. | minimaxir wrote: | R Markdown/Notebooks, IMO, has evolved to be the key value | proposition of RStudio over the years. From a productivity | standpoint when both working with R and publishing pretty | reports/PDFs it has been incredible. (that said, if VS Code gets | more robust R Markdown support, I may consider switching from | RStudio) | | I wrote a blog post a few years ago comparing R | Markdown/Notebooks to Jupyter Notebooks: | https://minimaxir.com/2017/06/r-notebooks/ | mespe wrote: | 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. | phillc73 wrote: | 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 | vharuck wrote: | 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 wrote: | 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. | [deleted] | halfeatenpie wrote: | I've always been a big fan of R Markdown. For me and my work, | there's always been a fine line between R Markdown and R Shiny, | with certain limitations (or something I felt was a limitation) | in R Markdown could be overcome by building it in R Shiny. | andylynch wrote: | Very nice to see this here. R Markdown is a great tool on is own | and working with it in RStudio is a superpower, plus the clean | format is really nice in version control. | kasperset wrote: | This has been discussed before but I am watching the development | of https://github.com/fonsp/Pluto.jl so that it can provide some | solid alternative. | phillc73 wrote: | If you're interested in Pluto.jl, I recently saw an | announcement about Neptune.jl[1], which appears to remove some | of the reactive nature of Pluto. It's a fork of Pluto and | executes code sequentially one cell at a time instead. An | interesting read anyway and maybe worth trying. | | [1] https://github.com/compleathorseplayer/Neptune.jl | tfehring wrote: | Huh. I wonder what the impetus for that was and what the | purported advantages over Jupyter are, since reactivity seems | like the main value add of Pluto.jl - and a significant one | at that. | nojito wrote: | Using RMarkdown effectively pretty much tripled my salary. It's | an amazing tool that is wholly underappreciated in the "data" | space. | quantstats wrote: | Could you expand on what you mean by using it effectively? I've | just started using RStudio and any tips/ways to use it more | efficiently are welcome! Thanks. | ct0 wrote: | I could imagine the time invested on making the same report | in another language takes 3x. | randomfool wrote: | Plug that if you're a Jupyter user to chime in on the survey at | https://www.surveymonkey.com/r/LCB7GBF. | | Background: https://blog.jupyter.org/survey-jupyterlab-and- | beyond-88c7fb... | RobinL wrote: | As an occasional R user, I think R markdown one of the things | that R does really well. For data scientists who want to output | reports (mix of text and calculations), I haven't come across | anything as mature or easy to use in the Python ecosystem. I'm a | big user of Jupyter notebooks, but version control issues put me | off, and I've never got to grips customising the formatting of | jupyter nbconvert. | | It's worth highlighting that R Markdown actually supports a | number of languages including Python - for instance see here: | https://bookdown.org/yihui/rmarkdown/language-engines.html | | For example, I am currently considering using R markdown to | author the documentation for one of my Python packages. Currently | my documentation is written in markdown, but I keep having to | copy and paste calculations and tables into the markdown. When | things change, it would be nice to just be able to re-run the R | markdown, converting Rmd -> md and thereby interpolating the | latest version of all calculations into the final markdown doc. | spinningslate wrote: | I'd strongly agree with this. I use R Markdown with Python in | the Rstudio IDE, and prefer it to Jupyter. The publishing | pipeline is really flexible, e.g. with one-click deployment to | RStudio Server [0] (which is a paid product). | | No affiliation to RStudio, just a happy customer. | | [0]: https://rstudio.com/products/rstudio/download-server/ | gpoore wrote: | 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. | [deleted] ___________________________________________________________________ (page generated 2021-02-03 23:00 UTC)