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!

This page summarizes the projects mentioned and recommended in the original post on /r/ObsidianMD

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  • txt-as-md-obsidian

    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.

  • InfluxDB

    Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

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  • obsidian-zotero-integration

    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.

  • obsidian-citation-plugin

    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.

  • zotero-better-bibtex

    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.

  • papaja

    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.

  • pandocomatic

    Automate the use of pandoc

  • obsidian-custom-file-extensions-plugin

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

  • SaaSHub

    SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

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NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a more popular project.

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