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Francisco Rodriguez-Sanchez3/ And this is an example <a href="https://ecoevo.social/tags/Rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Rmarkdown</a> document and the output Template available here: <a href="https://github.com/Pakillo/grateful/blob/master/Rmd_Quarto/separate_bibliographies/grateful-Rmarkdown-separatebib.Rmd" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/Pakillo/grateful/blob/master/Rmd_Quarto/separate_bibliographies/grateful-Rmarkdown-separatebib.Rmd</a>

Francisco Rodriguez-SanchezWriting manuscripts in <a href="https://ecoevo.social/tags/Quarto" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Quarto</a> or <a href="https://ecoevo.social/tags/Rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Rmarkdown</a>?Here's how to easily generate an appendix citing the <a href="https://ecoevo.social/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> packages used with {grateful} <a href="https://pakillo.github.io/grateful" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://pakillo.github.io/grateful</a>1/

Data ScienceInteractive resizing of picture and table content in Rmd and Quarto: <a href="https://r2resize.obi.obianom.com/index.html" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://r2resize.obi.obianom.com/index.html</a> <a href="https://genomic.social/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> <a href="https://genomic.social/tags/quarto" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#quarto</a> <a href="https://genomic.social/tags/rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rmarkdown</a>

James Hawley, PhD<a href="https://functional.cafe/@kupac" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@kupac</a> I have all these same concerns about notebooks and more. I find <a href="https://scholar.social/tags/rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rmarkdown</a> and <a href="https://scholar.social/tags/quarto" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#quarto</a> 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.

Still Mad About CD PricesHey, <a href="https://infosec.exchange/tags/Rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Rstats</a> people: I'm always behind the curve on these things. Should I start using Quarto instead of <a href="https://infosec.exchange/tags/rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rmarkdown</a>? Is <a href="https://infosec.exchange/tags/Quarto" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Quarto</a> open, accessible, etc.? Is it locked into Rstudio's little world, or is it enshittification-resistant? I'm searching on these topics as well, but if anyone has the straight dope, I'd love to hear it.

Pete JonesI threw together a quick R package for executing the R code up to a specified point in a .Rmd/.qmd notebook. It's very much work-in-progress: <a href="https://codeberg.org/pjphd/catchup" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://codeberg.org/pjphd/catchup</a>I explain the idea behind it in the README, but the short version is I wanted the package to offer something similar to what the "run all chunks" family of features in RStudio does. As far as I can tell, nothing exists for this purpose, so maybe I'm the only person that wants to be able to do this (or maybe there's just not a lot of people left who work interactively but don't use RStudio or something VSCode-based). If I'm not and you decide to try it out, please bear in mind the note of caution in the README, and let me know if you run into any problems or if it's missing something useful. This really is a first draft and I'm sure it can be better. 😄<a href="https://hcommons.social/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> <a href="https://hcommons.social/tags/quarto" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#quarto</a> <a href="https://hcommons.social/tags/quartopub" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#quartopub</a> <a href="https://hcommons.social/tags/rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rmarkdown</a>

kupac^ESC:wq<a href="https://fosstodon.org/@brodriguesco" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@brodriguesco</a> I commend you for pointing this out. I am no fool anymore. (Just made a report template using params yeeey \o/ ) <a href="https://functional.cafe/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> <a href="https://functional.cafe/tags/rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rmarkdown</a>

Yann Büchau :nixos:Holy cow is <a href="https://fosstodon.org/tags/Rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Rmarkdown</a> <a href="https://fosstodon.org/tags/RStats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RStats</a> <a href="https://fosstodon.org/tags/knitr" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#knitr</a> inferior to <a href="https://fosstodon.org/tags/Jupyter" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Jupyter</a>. 😠- WHY does it need to rerun EVERYTHING for hours when making a HTML/PDF? - WHY is the apparent solution (caching) so weird? No clear instructions, only blog posts with broken formatting everywhere. - WHY don't you at least see where it hangs during the process? No indication which line is currently executed? - WHY does making a PDF silently fail after hours?[/rant]

Tyler Smith<a href="https://hachyderm.io/@djnavarro" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@djnavarro</a> I hadn't heard of that, it sounds very interesting. I'm a regular <a href="https://ottawa.place/tags/RMarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RMarkdown</a> user, and haven't found the time or motivation to jump to <a href="https://ottawa.place/tags/Quarto" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Quarto</a>. 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 <a href="https://ottawa.place/tags/litedown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#litedown</a> is that?

Achim Zeileis📄 New blog post on embedding <a href="https://fosstodon.org/tags/rexams" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rexams</a> exercises in <a href="https://fosstodon.org/tags/rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rmarkdown</a> or <a href="https://fosstodon.org/tags/quarto" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#quarto</a> documentsJoint work with <a href="https://fosstodon.org/@retostauffer" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@retostauffer</a> Generate quizzes for self-paced <a href="https://fosstodon.org/tags/elearning" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#elearning</a> in <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> <a href="https://www.r-exams.org/tutorials/exams2forms/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.r-exams.org/tutorials/exams2forms/</a>

Achim ZeileisThis is enabled by the new "exams2forms" <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> pkg.Can be used more generally to embed interactive exercises into <a href="https://fosstodon.org/tags/rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rmarkdown</a> or <a href="https://fosstodon.org/tags/quarto" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#quarto</a> documents, online books, etc.Already submitted to CRAN but for the moment at:<a href="https://zeileis.R-universe.dev/exams2forms" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://zeileis.R-universe.dev/exams2forms</a>

Kelly SovacoolI'm so desperate I actually posted a question on stack overflow about this 😅 <a href="https://stackoverflow.com/questions/79143394/improving-the-r-traceback-when-rendering-r-markdown-non-interactively" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://stackoverflow.com/questions/79143394/improving-the-r-traceback-when-rendering-r-markdown-non-interactively</a><a href="https://mastodon.social/tags/rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rmarkdown</a> <a href="https://mastodon.social/tags/rlang" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rlang</a> <a href="https://mastodon.social/tags/posit" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#posit</a> <a href="https://mastodon.social/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a>

René Dario 🇺🇲🇲🇽🐧🎮💻🕵🏽🏋️Sometimes, when working with <a href="https://fosstodon.org/tags/RStats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RStats</a>, I wish to output a knitr::kable() object. I don't want to have to go through the trouble of creating an entire <a href="https://fosstodon.org/tags/RMarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RMarkdown</a> document just for the one table. Thankfully, I found a solution: <a href="https://stackoverflow.com/questions/50257488/save-knitrkable-output-to-html-file-r" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://stackoverflow.com/questions/50257488/save-knitrkable-output-to-html-file-r</a>

Alex HolcombeUsing RMarkdown Quarto to make lecture slides now, have worked out most of the problems I had initially, and quite happy with using it now. I particularly like the background-image feature , with opacity, making it easy to have a nice unobtrusive background on all one's slides, and that image positioning is now quite easy. Example <a href="https://alexholcombe.github.io/PSYC2016lectures/lecture5distraction.html#/title-slide" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://alexholcombe.github.io/PSYC2016lectures/lecture5distraction.html#/title-slide</a> and code: <a href="https://github.com/alexholcombe/PSYC2016lectures" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/alexholcombe/PSYC2016lectures</a> <a href="https://fediscience.org/tags/Rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Rstats</a> <a href="https://fediscience.org/tags/Rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Rmarkdown</a>

James Hawley, PhD<a href="https://fediscience.org/@giuseppebilotta" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@giuseppebilotta</a> <a href="https://genomic.social/@mdziemann" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@mdziemann</a> I haven't heard that "offline"/"online" terminology before, but I think that's what I mean.I think of workflow tools like <a href="https://scholar.social/tags/snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#snakemake</a> or <a href="https://scholar.social/tags/nextflow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nextflow</a> as a kind of "offline" executor, and individual scripts are heavily documented to make them more literate-like. But if I want to collate everything into a legible report of some kind, then I'll reach for <a href="https://scholar.social/tags/rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rmarkdown</a> or <a href="https://scholar.social/tags/QuartoPub" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#QuartoPub</a> to show and explain the results.

Jon HarmonCharlotte Wickham is talking about <a href="https://fosstodon.org/tags/Quarto" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Quarto</a> I was skeptical ("isn't it just <a href="https://fosstodon.org/tags/rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rmarkdown</a> rebranded for python users?") but it has really grown on me. Quarto dashboards via card layouts look really easy, I should play with those more. <a href="https://fosstodon.org/tags/PositConf2024" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PositConf2024</a> <a href="https://fosstodon.org/tags/RStats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RStats</a> <a href="https://fosstodon.org/tags/PyData" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PyData</a> 🧵 8/17

Francisco Rodriguez-SanchezThis new <a href="https://ecoevo.social/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> package makes it very easy to monitor outputs for unexpected changes e.g. due to changes in data files or packages used: <a href="https://github.com/brandmaier/reproducibleRchunks" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/brandmaier/reproducibleRchunks</a> Just replace r by reproducibleR in <a href="https://ecoevo.social/tags/Rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Rmarkdown</a> or <a href="https://ecoevo.social/tags/Quarto" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Quarto</a> chunks. When rendering you'll get a note if output has changed

RKWardRKWard is getting a very useful feature: the live preview of <a href="https://fosstodon.org/tags/RMarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RMarkdown</a> files, that previously was limited to HTML documents, can now render any output format, including package vignettes, but also PDF formats like beamer presentations or even custom formats. formats that RKWard can't show itself are offered to be opened in the system defined application. <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a>

MiguelI introduce you to taxnames, inserting taxonomic names in Markdown (and LaTeX) documents: <a href="https://github.com/kamapu/taxnames" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/kamapu/taxnames</a> <a href="https://social.cologne/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> <a href="https://social.cologne/tags/rmarkdown" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rmarkdown</a> <a href="https://social.cologne/tags/quarto" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#quarto</a> <a href="https://social.cologne/tags/taxonomy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#taxonomy</a> <a href="https://social.cologne/tags/biodiversity" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#biodiversity</a> <a href="https://social.cologne/tags/taxlist" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#taxlist</a> <a href="https://social.cologne/tags/ropensci" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ropensci</a>

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