Quarto: A scientific and technical publishing system built on Pandoc
quarto.org
quarto.org
For replicable research, in uni I once built interactive visualizations from a R studio source that contained the data + the code but that resulted in multiple outputs (html embedding the R notebook and markdown files, Microsoft Word, PDF...)
Technically, it was quite simple, but it enabled interesting usecases: I could send my homework to my professor in an easily readable format, but if he wanted to dig deeper, he could also check I did everything right, and he could also alter the data to check if it kept working: using the html file, he just had to click to the source notebook at the bottom to start tweaking.
It would be wonderful if scientific publishing moved to something like that, where the publication would be a subset (ex: Word output) of a process that everyone could inspect and alter.
Of course, as datasets are becoming the most valuable ingredient in a big soup, I fear this will take a while to happen.
BTW op: your dynamic examples like https://htmlpreview.github.io/?https://github.com/quarto-dev... are not working in my browser (Edge)
> Of course, as datasets are becoming the most valuable ingredient in a big soup, I fear this will take a while to happen.
even though it would be wonderful, having worked in this industry i don't see it ever moving to such a system of communication (not on any significant level at least).
publishers are a middleman too deeply entrenched to simply cut out, and anything resembling a threat to their status will get bought out under the guise of 'look we're innovating here' and then die a slow silent death.
Require a viral license (like the GPL) for all published content, to ensure derivate work using either the data or the code must also be made available under similar conditions but for both the data and the code, with a clause allowing publication to non-open access journals provided that the data and the code of the preprint is published on a sister journal (let's call it "Replicable Science Reprints") say 1 month after the publication to the non-open access journal.
If you manage to reach an impact factor high enough to incentivize would-be author to submit to this journal, it would be quite hard to kill!
Also, the citations would increase the IF over time, by sheer virtue of being open access, and encouraging derivative work.
existing subscription journals would have no incentive to allow republication at all, even less so with a measly 1 month embargo period.
citations and high IFs don't depend on permissive licensing and openness -- they are more easily reached via established subscription publishers who already have the supply chain to serve their content to thousands of subscribing organizations and millions of academics.
i mean OA/OS itself is a good example here. it's been an ongoing project for some 20 years, and granted there has been change, it's also been ample time for the industry to adapt to and limit this change. so now you have read-and-publish agreements (=more expensive subscriptions basically), transformative agreements (=we'll go full OA once you've lined our pockets enough), etc.
meanwhile there are plenty of journals, initiatives, manifestos, platforms -- PLoS stable of journals, other publishers, all the various *rxivs popping up, COS and OSF -- advocating hard for OA/OS but they're ultimately limited to carving a niche for themselves with little effect on the wider system itself.
and achieving even that little effect has involved an ungodly amount of policy changes and introducing mandates that favor this one particular mode of communication.
so yeah i don't think this will catch on either, not in my lifetime at least.
You have already noticed some of the changes, but you're not thinking long term enough.
Look at what's happening in universities, not for existing researchers, as they will eventually be replaced.
I must admit I'm a bit disconnected as I left a couple of years before COVID, but already back then, students do their lit review using google. If something is not easily accessible, unless it's a must-known paper, they won't bother with even scihub (and I'm talking about scihub because even if the university provides access to most journals, most people don't bother with that as it requires being on campus or using a weird VPN)
In classes, there're a lot exercises based on replication: try to get the same results as this or that to learn about this method. For now, it's mostly done with books, but a new trend is using published datasets to level up.
I'm not saying you aren't partially right, but things are changing fast!
https://dave.autonoma.ca/blog/2019/05/22/typesetting-markdow...
I've been working on an editor that can interpolate string variables to replace those scripts:
https://github.com/DaveJarvis/keenwrite/blob/master/docs/scr...
Many Markdown publishing systems put YAML headers into Markdown documents, which feels like mixing presentation with content. With KeenWrite you can do:
keenwrite -i filename.Rmd -o filename.pdf -v variables.yaml
1. Inserting tables, and code is unreasonably difficult. Who wants to copy/paste numbers manually while inserting an opaque set of pipes ampersands and other arcane symbols.
2. Editor plugins for latex are pretty lackluster. In markdown I can use my existing text editors plugin infrastructure including premium grammar checking tools.
Since it is programatically generated, I don't have to manually fiddle with the numbers when the report has to be refreshed.
TODO
README
typesetting
Etc ad nausea
The common thread seems to be emacs. Mostly.
need to write and export to different formats--> need for task management system --> need for small excel sheet (org mode tables --> need for http request/response aka postman/insomnia --> continuing
It's worth noting that, in RStudio + RMarkdown, you can already mix different languages in chunks.
But for those who would rather not work in RStudio, maybe this will be appealing.
The "native" format is MyST, which is markdown with extra things added in to customize behaviour of code blocks: https://jupyterbook.org/reference/cheatsheet.html
I've been writing some stuff in MyST and I found it very productive. The ability to also support jupyter notebooks is also interesting.
I use R Markdown extensively. I am wondering if R Markdown is retiring? Should I begin to switch to Quarto? And is there a way to change the default code font to ligatures fonts (for example Fira Code)?
It seems like since this is a standalone executable it should play nicely with different environments as long as those environments have the components needed for that engine. I'm thinking about how this would integrate with multiple different Conda environments.
/* * project-index.ts * * Copyright (C) 2020 by RStudio, PBC * */
So, it is the next generation of that.