#rmarkdown — Public Fediverse posts

Interactive resizing of picture and table content in Rmd and Quarto: https://r2resize.obi.obianom.com/index.html #rstats #quarto #rmarkdown

Interactive resizing of picture and table content in Rmd and Quarto: https://r2resize.obi.obianom.com/index.html #rstats #quarto #rmarkdown

Interactive resizing of picture and table content in Rmd and Quarto: https://r2resize.obi.obianom.com/index.html #rstats #quarto #rmarkdown

#AcademicChatter Hello, fellow academic chatters. I'm an experimental scientist. And I regularly have the problem of how to organize acquired data by different participants to a same experiment. I'd like to have some feedback of how other people do this. Not necessarily specific computer programmes (such as digital labbooks), but rather how-tos based on robust, basic things, such as text and csv files, folder structures etc. I'm often battling with the workflow which is including handwritten measurements, their digital counterparts, metadata for the measurements, codes for samples, all of these done by different people, but all will have to end in one final dataset, where I would like to be able to trace data back to the paper files, and their metadata. And all of this with not too much additional effort by everybody ;-) Have done this usually with some shared server space, but usually it ends up as something a bit difficult to get through. I'm now rather thinking about a system involving perhaps something based on #MarkDown or even #RMarkdown or #knitr etc. Any feedback much welcome 😁
#ReproducibleResearch

To the people analysing research data out there with R... I see #Quarto popping up everywhere and I am trying to figure out how it differs from #RMarkdown and why people are switching. So, have you used it? What are you using it for?

I don't like that it seems to add another layer of software and whenever a company tells me I should be using their format, that makes me suspicious... Please help!

rOpenSci | All the Ways to Programmatically Edit or Parse R Markdown / Quarto Documents

Argh only just seeing this doc now, wish I'd found it a couple of months ago 🤣 I was generating static Rmd from one with dynamically generated chunks. I ended up using whisker pulling in external R code templates supplemented with knitr hooks to do some extra customisation during chunk processing.

https://ropensci.org/blog/2025/09/18/markdown-programmatic-parsing/

#RStats #RMarkdown #Quarto

Interactive resizing of picture and table content in Rmd and Quarto: https://r2resize.obi.obianom.com/index.html #rstats #quarto #rmarkdown

Performing some quick statistical analyses in classic #RStats and neatly “knitting” them into a PDF using #RMarkdown, #knitr, and #MacTeX #texLaTeX.

Call me old-fashioned, but I really enjoy this workflow. :awesome:

#OpenSource #FOSS #statistics

Performing some quick statistical analyses in classic #RStats and neatly “knitting” them into a PDF using #RMarkdown, #knitr, and #MacTeX #texLaTeX.

Call me old-fashioned, but I really enjoy this workflow. :awesome:

#OpenSource #FOSS #statistics

Performing some quick statistical analyses in classic #RStats and neatly “knitting” them into a PDF using #RMarkdown, #knitr, and #MacTeX #texLaTeX.

Call me old-fashioned, but I really enjoy this workflow. :awesome:

#OpenSource #FOSS #statistics

Performing some quick statistical analyses in classic #RStats and neatly “knitting” them into a PDF using #RMarkdown, #knitr, and #MacTeX #texLaTeX.

Call me old-fashioned, but I really enjoy this workflow. :awesome:

#OpenSource #FOSS #statistics

Performing some quick statistical analyses in classic #RStats and neatly “knitting” them into a PDF using #RMarkdown, #knitr, and #MacTeX #texLaTeX.

Call me old-fashioned, but I really enjoy this workflow. :awesome:

#OpenSource #FOSS #statistics

R is wonderful: Creating a Supplement PDF full of summary & regression results tables, and estimated marginal mean plots, all completely auto-generated by the R Markdown code itself with no need for any manual post-modifications. 'gtsummary', 'ggplot2' rock! #Rstats #RMarkdown

Next week I get to present an #RStats talk on writing code to be run by people with no programming experience that requires some interactivity.

Have some examples of parameterised #RMarkdown documents; of #Shiny and using source to call more complex code without overwhelming them.

I also plan on concentrating on the importance of training these staff on the differences between errors, warnings and messages (which are unhelpfully similar in appearance in R).

Any other suggestions? (1/2?)

Interactive resizing of picture and table content in Rmd and Quarto: https://r2resize.obi.obianom.com/index.html #rstats #quarto #rmarkdown

@robyn If I stop videos and go back to a website or blog, I’ll get your advice on #Hugo through #RMarkdown as that seems like a fun route. I take all the advice I can get from people with actual #skillz. My two coworkers with PhDs in ML have me using PyCharm for my air quality project and another good coworker got me to dual boot my desktop into #Mint running on a USB. Wish I used a bigger USB as Mint is nice in my limited use so far

@tinyspheresof @rkward Sorry for the late response. Currently, there is no such functionality in #rkward, except that one in the screenshot.
But let me tell you about an upcoming feature called “Code navigation”. It is enabled in the latest AppImage (https://cdn.kde.org/ci-builds/education/rkward/master/linux/)
It helps you to very quickly navigate the R and #RMarkdown scripts. It will address your problem directly.

A first today: I changed the citation style in my #rstats #Rmarkdown doc, and it was easy and it worked! Thanks to Nicolas Tierney's "Rmarkdown for scientists" rmd4sci.njtierney.com/citing-artic... and github.com/citation-sty.... Save the csl code in a file in your R project and add a YAML line. 😎

13 Citing Articles & Bibliogra...

I'm trying out #Rkward on my new #KDEneon install. Is there any way in an #Rmarkdown script to highlight the code blocks/chunks in the script editor? They now have the same background as the rest of the script, and don't really stand out.

The three backticks / graves at the start and end of the code block do have a different background colour, but not the code in between.

@rkward
#rstats

Interactive resizing of picture and table content in Rmd and Quarto: https://r2resize.obi.obianom.com/index.html #rstats #quarto #rmarkdown

Как я за год написал шесть больших научных статей и несколько маленьких

Без «литературных негров» и чатГПТ — личный рассказ об инструментах, технологиях и приёмах, которые помогли мне не вылететь из аспирантуры и догнать коллег. Открытые данные, Python, R, RMarkdown, Quarto, git и немного ИИ в помощь исследователю.

https://habr.com/ru/articles/898038/

#научные_исследования #научная_работа #научные_статьи #открытые_данные #публикации #rmarkdown #deepl #rstudio #git #r_lang

Как я за год написал шесть больших научных статей и несколько маленьких

Без «литературных негров» и чатГПТ — личный рассказ об инструментах, технологиях и приёмах, которые помогли мне не вылететь из аспирантуры и догнать коллег. Открытые данные, Python, R, RMarkdown, Quarto, git и немного ИИ в помощь исследователю.

https://habr.com/ru/articles/898038/

#научные_исследования #научная_работа #научные_статьи #открытые_данные #публикации #rmarkdown #deepl #rstudio #git #r_lang

Как я за год написал шесть больших научных статей и несколько маленьких

Без «литературных негров» и чатГПТ — личный рассказ об инструментах, технологиях и приёмах, которые помогли мне не вылететь из аспирантуры и догнать коллег. Открытые данные, Python, R, RMarkdown, Quarto, git и немного ИИ в помощь исследователю.

https://habr.com/ru/articles/898038/

#научные_исследования #научная_работа #научные_статьи #открытые_данные #публикации #rmarkdown #deepl #rstudio #git #r_lang

Как я за год написал шесть больших научных статей и несколько маленьких

Без «литературных негров» и чатГПТ — личный рассказ об инструментах, технологиях и приёмах, которые помогли мне не вылететь из аспирантуры и догнать коллег. Открытые данные, Python, R, RMarkdown, Quarto, git и немного ИИ в помощь исследователю.

https://habr.com/ru/articles/898038/

#научные_исследования #научная_работа #научные_статьи #открытые_данные #публикации #rmarkdown #deepl #rstudio #git #r_lang

Looking for tips on how to love #julialang Pluto.jl. So many people enjoy it and I just don't get it. Likely just me as I also dislike #Jupyter notebooks and prefer the "see all and be reproducible" style of #RMarkdown and #Quarto. Why F1 to see keyboard shortcuts. Why clunky Path/URL navigation?

3/ And this is an example #Rmarkdown document and the output

Template available here: https://github.com/Pakillo/grateful/blob/master/Rmd_Quarto/separate_bibliographies/grateful-Rmarkdown-separatebib.Rmd

Writing manuscripts in #Quarto or #Rmarkdown?

Here's how to easily generate an appendix citing the #rstats packages used with {grateful}

https://pakillo.github.io/grateful

1/

Interactive resizing of picture and table content in Rmd and Quarto: https://r2resize.obi.obianom.com/index.html #rstats #quarto #rmarkdown

@kupac I have all these same concerns about notebooks and more. I find #rmarkdown and #quarto much better than Jupyter, but they still suffer from similar problems.

Unless I am explicitly planning on compiling an HTML report, I tend to stay away from these literate programming tools.

I’m only just starting using #RMarkdown. Writing a #GIS lab has been enjoyable so far. If my life situation was different at graduation, I would have asked @paezha for a #postdoc. I think he uses it and #GitHub to collaborate with his students. There’s also all the cool urban #spatial #accessibility research he does.

@djnavarro

I hadn't heard of that, it sounds very interesting.

I'm a regular #RMarkdown user, and haven't found the time or motivation to jump to #Quarto. It looks like a combination of removing the rough spots of RMarkdown, but also expanding the features in a way that adds to my mental overhead.

We have a *really* hard time embracing the elegance of a truly minimal system for writing. At this point I'd love to have the absolute minimum set of features beyond basic markdown for academic writing. Maybe #litedown is that?

📄 New blog post on embedding #rexams exercises in #rmarkdown or #quarto documents

Joint work with @retostauffer

Generate quizzes for self-paced #elearning in #rstats

https://www.r-exams.org/tutorials/exams2forms/

I just discovered a tool that might be quite useful for others while working with #rstats and #rmarkdown

Occasionally, I just add #bibtem|s in my #Rmd instead of #bibtex in an extra file. Here is a tool to make bibitems easily.

Online Bibtex Converter

https://asouqi.github.io/bibtex-converter/

Update: I have added in example (screenshot) using #RWKard as #IDE.

#LaTeX #RKWard

I just discovered a tool that might be quite useful for others while working with #rstats and #rmarkdown

Occasionally, I just add #bibtem|s in my #Rmd instead of #bibtex in an extra file. Here is a tool to make bibitems easily.

Online Bibtex Converter

https://asouqi.github.io/bibtex-converter/

Update: I have added in example (screenshot) using #RWKard as #IDE.

#LaTeX #RKWard

I just discovered a tool that might be quite useful for others while working with #rstats and #rmarkdown

Occasionally, I just add #bibtem|s in my #Rmd instead of #bibtex in an extra file. Here is a tool to make bibitems easily.

Online Bibtex Converter

https://asouqi.github.io/bibtex-converter/

Update: I have added in example (screenshot) using #RWKard as #IDE.

#LaTeX #RKWard

I just discovered a tool that might be quite useful for others while working with #rstats and #rmarkdown

Occasionally, I just add #bibtem|s in my #Rmd instead of #bibtex in an extra file. Here is a tool to make bibitems easily.

Online Bibtex Converter

https://asouqi.github.io/bibtex-converter/

Update: I have added in example (screenshot) using #RWKard as #IDE.

#LaTeX #RKWard

I just discovered a tool that might be quite useful for others while working with #rstats and #rmarkdown

Occasionally, I just add #bibtem|s in my #Rmd instead of #bibtex in an extra file. Here is a tool to make bibitems easily.

Online Bibtex Converter

https://asouqi.github.io/bibtex-converter/

Update: I have added in example (screenshot) using #RWKard as #IDE.

#LaTeX #RKWard

Starting with #RMarkdown is a great way to introduce students to the world of #rstats. It's not just about teaching programming skills, but also about explaining other technologies like #LaTeX, #YAML, #Rnw, #markdown & #Rscript! 💻 And I'm convinced that we should focus on building a small solid foundation (#smallR 🙂 ). Think of base R (aggregate, subset, …), #rdatatable and graphics (#tinyplot) instead of diving straight into popular packages like #tidyverse. Let's keep it simple! Who's with me?

Starting with #RMarkdown is a great way to introduce students to the world of #rstats. It's not just about teaching programming skills, but also about explaining other technologies like #LaTeX, #YAML, #Rnw, #markdown & #Rscript! 💻 And I'm convinced that we should focus on building a small solid foundation (#smallR 🙂 ). Think of base R (aggregate, subset, …), #rdatatable and graphics (#tinyplot) instead of diving straight into popular packages like #tidyverse. Let's keep it simple! Who's with me?

Starting with #RMarkdown is a great way to introduce students to the world of #rstats. It's not just about teaching programming skills, but also about explaining other technologies like #LaTeX, #YAML, #Rnw, #markdown & #Rscript! 💻 And I'm convinced that we should focus on building a small solid foundation (#smallR 🙂 ). Think of base R (aggregate, subset, …), #rdatatable and graphics (#tinyplot) instead of diving straight into popular packages like #tidyverse. Let's keep it simple! Who's with me?

Starting with #RMarkdown is a great way to introduce students to the world of #rstats. It's not just about teaching programming skills, but also about explaining other technologies like #LaTeX, #YAML, #Rnw, #markdown & #Rscript! 💻 And I'm convinced that we should focus on building a small solid foundation (#smallR 🙂 ). Think of base R (aggregate, subset, …), #rdatatable and graphics (#tinyplot) instead of diving straight into popular packages like #tidyverse. Let's keep it simple! Who's with me?

Starting with #RMarkdown is a great way to introduce students to the world of #rstats. It's not just about teaching programming skills, but also about explaining other technologies like #LaTeX, #YAML, #Rnw, #markdown & #Rscript! 💻 And I'm convinced that we should focus on building a small solid foundation (#smallR 🙂 ). Think of base R (aggregate, subset, …), #rdatatable and graphics (#tinyplot) instead of diving straight into popular packages like #tidyverse. Let's keep it simple! Who's with me?

@coatless UI elements to set chunk options is one of the reasons. Three or four times after first learning of #Quarto, I’ve started a new research paper project. Each time, I’ve thought that this time I’m switching to Quarto. And each time I’ve ended up doing it in #RMarkdown with the #papaja package anyway, like I’m used to. A few times I have given up because I couldn’t (immediately) figure out how to use/switch to/implement an APA template, and I felt like I didn’t have time to spare to figure it out, so I switched back to what I knew and got along with analyses and writing. One time I got the template running, although I remember I didn’t quite understand what I did or how it worked. I just noticed that it did after copy/pasting some files to the folder I was working in. But then I switched to #RMarkdown and #papaja anyway after a while because I missed some of the functions of the papaja package, other than the template. So all this boils down to inertia for me as well, I suppose. I just submitted a paper written in papaja again, last week. But the next one I’ll write in Quarto, definitely. Maybe.

@hsorlie I wrote tutorials and other content in both #rmarkdown using the #bookdown package and #quarto. They are very similar.

The newer Quarto took a lot of good stuff from Bookdown, but it also offers convenient extra's and i.m.h.o. a more streamlined experience. Dealing with figures and page layout is much easier, for example.

Converting from one to the other isn't that difficult, I actually just migrated one of my older tutorials from Bookdown to Quarto.

Hive mind, do you employ (unit) testing in data analysis scripts? If so, how and what are your best practices?

We frequently develop packages with unit testing. But equally often write "run-once" analysis scripts/notebooks. Those often contain functions and (more often) assumptions on loaded data but we rarely test/check these. This is something to improve but I wonder how others handle this.

#RStats #rmarkdown #testthat #assertthat #python #jupyter #unittesting #datascience #bioinformatics

I (think I) would like to write my article based #PhD #thesis in #rstudio. The finished articles are written with #RMarkdown and #papaja, so I’m sort of used to the format, but now I need to write a compilation or synopsis. I’ve heard of the #bookdown package, but I’m also looking at finally going #quarto. Any advice? Packages, or tips and tricks? #rstats

After making my first simple #Remarkjs #presentation, I think I see the landscape a little clearer:

👉 @jmlilly's Liminal is a "minor extension" that provides a scientific theme for Remark.js http://www.jmlilly.net/talks/liminal-v2/

👉 @yihui's #Xaringan is an #Rpackage that translates #Rmarkdown into Remark-readable #markdown; using the #RStudio #IDE it supports theming & live previews of your slides https://slides.yihui.org/xaringan/

👉 @grrrck's added some serious extra bling to Xaringan https://pkg.garrickadenbuie.com/xaringanExtra/

🙏 I'm trying to get rid of an ugly hack that I used because of my #rmarkdown / #knitr / #quarto tech debt. Can you help ? https://github.com/tadascience/link/issues/3

Using #RMarkdown and #knitr after a long break. When did everything become so buggy? Several commands from the official R Markdown cheat sheet and R Markdown reference produce errors. 😒