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R Markdown: The Definitive Guide

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Re: R Markdown: The Definitive Guide

#41

Post by clircle »

mespe wrote: post #4

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/deb…

I write my blog mostly in Rmarkdown from Emacs using ESS/polymode. Mostly works well accept for some markdown-mode induced bugginess.

I'm using it occasionally at work as well, but I still prefer R scripts with nice comments for work.

Re: R Markdown: The Definitive Guide

#42

Post by nojito »

mespe wrote: post #12
ska wrote: post #6

Earlier quoted context omitted.

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?

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.

You can avoid project related issues by using the here package.

https://github.com/jennybc/here_here

Re: R Markdown: The Definitive Guide

#43

Post by Tarq0n »

jdgoesmarching wrote: post #38
RobinL wrote: post #3

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 highlight…

Currently working on a DA masters with a background in markdown and was so happy to discover this. Then I was baffled to discover that there wasn’t an equivalent for Python. Jupyter is great, but I really love the simplicity of my text files and I’m surprised that there isn’t a major implementation given how popular both markdown and Python are. I guess notebooks are just too appealing.

Honestly jank and bad ergonomics pervade the Python data science ecosystem. The pandas API is kind of bad (multi-indexes anyone?) matplotlib is way too low level, tensorflow is a shitshow. I think the R community got lucky with a greater focus on user experience, even if it comes at the cost of explicitness sometimes (lots of DSL's with a lot of 'magic').

Re: R Markdown: The Definitive Guide

#44

Post by data_ders »

This is the first HN thread about R where I don’t see a commenter shitposting about how “terrible” R is. Maybe that’s a testament to all the great work done by the great Yihui Xie and the RStudio folks.

Currently using RStudio to write my masters papers in markdown and convert them to PDF. Love it!

Re: R Markdown: The Definitive Guide

#45

Post by reactspa »

jcheng wrote: post #33
mespe wrote: post #10

Earlier quoted context omitted.

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 specif…

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 exam…

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

Re: R Markdown: The Definitive Guide

#46

Post by cwyers »

runningmike wrote: post #20

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.

RMarkdown uses pandoc too, and it's on version 2.6, while Jupyter Book is pre-1.0.

Re: R Markdown: The Definitive Guide

#47

Post by AuthorizedCust »

phillc73 wrote: post #23
mespe wrote: post #10

Earlier quoted context omitted.

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 specif…

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…

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.

Re: R Markdown: The Definitive Guide

#48

Post by CornCobs »

Tarq0n wrote: post #43
jdgoesmarching wrote: post #38

Earlier quoted context omitted.

Currently working on a DA masters with a background in markdown and was so happy to discover this. Then I was baffled to discover that there wasn’t an equivalent for Python. Jupyter is great, but I really love the simplicity of my text files and I’m surprised that there isn’t a major implementation given how popular both markdown and Python are. I guess notebooks are just too appealing.

Honestly jank and bad ergonomics pervade the Python data science ecosystem. The pandas API is kind of bad (multi-indexes anyone?) matplotlib is way too low level, tensorflow is a shitshow. I think the R community got lucky with a greater focus on user experience, even if it comes at the cost of explicitness sometimes (lots of DSL's with a lot of 'magic').

Honestly, in my experience, R's DSLs are not a bad thing. When you are doing analytics day in and out you basically are speaking the DSL anyway, so what if you have to learn this slightly different language if it expresses what you want to accomplish clearly?

Re: R Markdown: The Definitive Guide

#49

Post by CornCobs »

minimaxir wrote: post #32
phillc73 wrote: post #23

Earlier quoted context omitted.

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…

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.

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

Re: R Markdown: The Definitive Guide

#50

Post by confounded »

mespe wrote: post #10
minimaxir wrote: post #5

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.c…

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 specif…

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).
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