My setup as a researcher. How to write, run statistics, and work seamlessly with R, Obsidian, Linux, and Zotero, and collaborate with senior professors who only accept MS Word files!

1. txt-as-md-obsidian

   1 5 87 0.0 JavaScript

   Discontinued Edit txt files in Obsidian.md as if they were markdown

   One problem is that Obsidian cannot view Rmarkdown files (.Rmd), and RStudio does not recognize markdown files (.md) as Rmardown, even though it may contain have R code blocks. A solution I found is I modified the Obsidian plugin 'txt as md' (https://github.com/deathau/txt-as-md-obsidian) to also add more filetypes, including Rmd. Once you do that, Obsidian can easily open and work with .Rmd files as if they are native md files.

2. SurveyJS

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3. obsidian-zotero-integration

   2 12 1,243 7.1 TypeScript

   Insert and import citations, bibliographies, notes, and PDF annotations from Zotero into Obsidian.

   

   Another problem is that no matter how much I tried, the two available Zotero plugins for Obsidian do not work for me (this https://github.com/mgmeyers/obsidian-zotero-integration and this https://github.com/hans/obsidian-citation-plugin). I am not sure if that is because I'm on Linux, but they just don't work. However, RStudio on Linux works great with Zotero, and I can easily add citations using the Better BibTeX for Zotero plugin (https://github.com/retorquere/zotero-better-bibtex) to create citation keys. That way, I can simply copy/paste the citation key (e.g. '@lastname2020') in the text and have it render into the citation when I render the file in Rstudio. I sometimes write documents with > 300 references, and Zotero running in a Windows VM, trying to refresh a huge word document would take a long time, and would lead to corrupt citations. That's no problem with a markdown/Rmarkdown document.

4. obsidian-citation-plugin

   3 23 1,194 0.0 TypeScript

   Obsidian plugin which integrates your academic reference manager with the Obsidian editor. Search your references from within Obsidian and automatically create and reference literature notes for papers and books.

   

   Another problem is that no matter how much I tried, the two available Zotero plugins for Obsidian do not work for me (this https://github.com/mgmeyers/obsidian-zotero-integration and this https://github.com/hans/obsidian-citation-plugin). I am not sure if that is because I'm on Linux, but they just don't work. However, RStudio on Linux works great with Zotero, and I can easily add citations using the Better BibTeX for Zotero plugin (https://github.com/retorquere/zotero-better-bibtex) to create citation keys. That way, I can simply copy/paste the citation key (e.g. '@lastname2020') in the text and have it render into the citation when I render the file in Rstudio. I sometimes write documents with > 300 references, and Zotero running in a Windows VM, trying to refresh a huge word document would take a long time, and would lead to corrupt citations. That's no problem with a markdown/Rmarkdown document.

5. zotero-better-bibtex

   4 33 5,822 9.9 TypeScript

   Make Zotero effective for us LaTeX holdouts

   

   Another problem is that no matter how much I tried, the two available Zotero plugins for Obsidian do not work for me (this https://github.com/mgmeyers/obsidian-zotero-integration and this https://github.com/hans/obsidian-citation-plugin). I am not sure if that is because I'm on Linux, but they just don't work. However, RStudio on Linux works great with Zotero, and I can easily add citations using the Better BibTeX for Zotero plugin (https://github.com/retorquere/zotero-better-bibtex) to create citation keys. That way, I can simply copy/paste the citation key (e.g. '@lastname2020') in the text and have it render into the citation when I render the file in Rstudio. I sometimes write documents with > 300 references, and Zotero running in a Windows VM, trying to refresh a huge word document would take a long time, and would lead to corrupt citations. That's no problem with a markdown/Rmarkdown document.

6. papaja

   5 2 669 7.2 HTML

   papaja (Preparing APA Journal Articles) is an R package that provides document formats to produce complete APA manuscripts from RMarkdown-files (PDF and Word documents) and helper functions that facilitate reporting statistics, tables, and plots.

   

   When I want to submit the paper to a journal, I render again to docx, change the formatting according to what the journal wants, and submit. Rstudio also has packages like papaja (https://github.com/crsh/papaja) which allow you to format an Rmarkdown easily for journal articles.

7. pandocomatic

   6 1 165 6.1 Ruby

   Automate the use of pandoc

   

8. obsidian-custom-file-extensions-plugin

   7 3 49 6.5 TypeScript

   An obsidian plugin allowing you to register and view different file extensions in a modular manner.

   

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