02:00
OST-HS23: Open Science Tools
authoring and publishing workflows for collaborative scientific writing
October 17, 2023
While we are getting ready, please check for this email from GitHub and accept the invitation to join the GitHub organisation for the course.
Who has a LinkedIn account?
Who already had ORCID iD?
Who already had a GitHub account?
Who already uses a reference management system? (e.g. Mendeley, EndNote, Zotero)
Who has a personal homepage?
Who has published a report, scientific article, or similar?
Think about the last time you published a written document:
Take some written notes on the provided paper.
02:00
Take notes for 1 minute:
What does the item you have picked have to do with the reason for you being here?
01:00
authoring and publishing workflows for collaborative scientific writing
Every student will have a personal, published, free website that links to their (academic) profiles, shows slides, and has the potential to be used as a (scientific) blog.
Quarto
RStudio IDE
Zotero
Git
GitHub
Matrix / Element
My turn: Lecture segments + live coding
Our turn: Live coding + follow along
Your turn: Exercises
During my turn and our turn segments – raise your hand
During your turn segments – also feel free to raise your hand for questions but use the yellow sticky to signal: I’m done
I’ll assume you
know do not have R or git experience
have not worked in an IDE before (e.g. RStudio IDE)
want to learn about Quarto
want to learn about project management with GitHub
I’ll teach you
Quarto syntax and formats
Markdown
GitHub issues, project management, and publishing
Reference managemen with Zotero
Some R along the way!
Sit back and enjoy!
05:00
hello-penguins.qmd
in RStudio and in visual editing mode10:00
Quarto comes “batteries included” straight out of the box
revealjs
)Feature | R Markdown | Quarto |
---|---|---|
Basic Formats | ||
Beamer | beamer_presentation | beamer |
PowerPoint | powerpoint_presentation | pptx |
HTML Slides | revealjs | |
Advanced Layout | Quarto Article Layout |
Feature | R Markdown | Quarto |
---|---|---|
Cross References | Quarto Crossrefs | |
Websites & Blogs | ||
Books | bookdown | Quarto Books |
Interactivity | Shiny Documents | Quarto Interactive Documents |
Journal Articles | rticles | Journal Articles |
Dashboards | flexdashboard | Coming soon! |
In your exercises project in RStudio on Posit Cloud, go to File > New File > Quarto document to create a Quarto document with HTML output. Render the document, which will ask you to give it a name – you can use my-first-document.qmd
.
Use the visual editor for the next steps.
Add a title and your name as the author.
With reference to writing and publishing: Create three sections,
Add a table of contents.
Stretch goal: Change the html theme to sketchy
. Tipp: Check quarto.org and use search function with “HTML theming”
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