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Create Zotero tutorial #1

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NeuroShepherd opened this issue Apr 7, 2024 · 2 comments
Open

Create Zotero tutorial #1

NeuroShepherd opened this issue Apr 7, 2024 · 2 comments
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@NeuroShepherd
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Create a version 1.0 Zotero walk-through tutorial for LMU community and beyond. Include the following:

  1. General citation info including some notes on .csl and BibTex
  2. Downloading Zotero and the web browser extensions
  3. Integrations with Word
  4. Integrations with RStudio and RMarkdown/Quarto
@NeuroShepherd NeuroShepherd self-assigned this Apr 7, 2024
@FlorianPargent
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FlorianPargent commented Apr 12, 2024

I have a project with some colleagues where we collaborate on a paper project over github with RMarkdown / Quarto. We use the following setup:

  1. We have created a Zotero group (https://www.zotero.org/groups/) where everybody can add references remotely (personally, I always add new papers to zotero via doi by using the "add by identifier" magic wand button in the zotero app)
  2. We use the Better BibTeX for Zotero plugin (https://retorque.re/zotero-better-bibtex/) and agree to always use the default citation keys used by the plugin (so that everybody can add references in Rmarkdown / Quarto that will work for everybody even if the bibfile is not synced at the moment)
  3. As an author that wants to knit the final paper, I locally export the zotero bibliography of the shared Zotero group. I can either manually update the bibfile frequently or chose the "Keep updated" option (https://retorque.re/zotero-better-bibtex/exporting/auto/) to avoid having to redo the export whenever references are added to the zotero group.
  4. We add the bibfile to git and commit new versions whenever changes are triggered by adding new references to the zotero group bibliography.

@NeuroShepherd
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Additional notes:

  • clarify why people need to download *.csl files and declare to use them in the yaml header of Quarto/Rmd documents. (e.g. over 10,000 *.csl formats found on Zotero: https://www.zotero.org/styles)
  • There is an easy Insert -> Citation button in the Visual editor for RStudio (but this does not exist for the Source editor, oddly.). This will automatically create/update references.bib
  • explain that users can, but don't need to, add custom tags to content they cite. this is mostly for convenience
  • can search by DOI, PubMed, and some other sources directly within the Insert pane
  • Need at least RStudio v1.4 for the above features
  • Include some highlights on Pandoc citation syntax: https://pandoc.org/MANUAL.html#citation-syntax
  • also use Pandoc info on citations in general: https://pandoc.org/MANUAL.html#citations
  • Potentially explain how to remove unused references from the bibliography.bib file automatically, but this isn't so important as it just ends up being a bit of unused text.
  • link out to the Posit blogpost: https://posit.co/blog/rstudio-1-4-preview-citations/

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