General overview of my digital workflow setup.

Reference manager: Zotero

Open source citation management, paper PDF organization, integration with word processors (Microsoft Word, Google Docs).

Zotero 7 download

Zotero Connector Chrome extension: auto pull paper metadata and PDF from webpage into Zotero
Zotero only has 300 MB cloud storage on its free tier! I highly recommend using cloud storage for PDFs and using Linked Attachments.
- Base directory: set to path to directory in cloud storage
  - Ex. C:\Users\yliao\OneDrive - UBC\Zotero
- Data directory: leave as default!
  - Ex. C:\Users\yliao\Zotero

Filename Format template:

{{ firstCreator case="snake"}}{{ year suffix="_"prefix="_" }}{{ title truncate="80" case="snake"}}

Windows OS: If Zotero 7 doesn’t launch, turn on Windows 8 compatibility mode

Find zotero.exe (default is "C:\Program Files\Zotero\zotero.exe"), and right click into “Properties”
Go to “Compatibility” tab, check “Run this program in compatibility mode for:” and make sure “Windows 8” is selected in drop-down menu

Extensions

Zotero Attanger: auto-move and organize files
Better BibTeX for Zotero: bibliographic data management utilities, especially useful for citekey formulas
- Current citekey formula: auth.lower + '_' + shorttitle(1,1).lower + '_' + year

Guides

VSCode

VSCode download

Extensions

Remote - SSH
Gremlins tracker for Visual Studio Code: reveals invisible characters and non-standard characters
vscode-pdf: display PDF files

Running R in VSCode

R in Visual Studio Code - Set R path setting to R executable path (ex. /usr/local/bin/R)

R extension
radian: alternative R console with syntax highlighting and multiline editing
- Set bracketed paste to true
- Set R terminal to radian path (ex. /home/yliao/miniforge3/bin/radian)
- If CTRL+Enter keeps creating a new R Interactive session, can try turning “Always Use Active Terminal” off
R Debugger extension

vscode-R: Interacting with R terminals

For self-managed R terminals, add these lines to ~/.Rprofile:

if (interactive() && Sys.getenv("RSTUDIO") == "") {
  Sys.setenv(TERM_PROGRAM = "vscode")
  source(file.path(Sys.getenv(
    if (.Platform$OS.type == "windows") "USERPROFILE" else "HOME"
  ), ".vscode-R", "init.R"))
}

Snippet of R VSCode settings (JSON)

  "r.plot.useHttpgd": true,
  "r.lsp.diagnostics": false,
  "r.alwaysUseActiveTerminal": true,
  "r.rterm.windows": "C:\\Users\\yliao\\AppData\\Local\\Programs\\Python\\Python312\\Scripts\\radian.exe",
  "r.rpath.windows": "C:\\Program Files\\R\\R-4.3.2\\bin\\R.exe",
  "r.rpath.linux": "/usr/local/bin/R",
  "r.rterm.linux": "/home/yliao/miniforge3/bin/radian",
  "r.removeLeadingComments": true,
  "r.session.levelOfObjectDetail": "Normal",
  "r.bracketedPaste": true,

\(\LaTeX\) in VSCode

LaTeX Workshop

Digital brain: Obsidian

Obsidian download

Markdown-based note-taking.

My Obsidian vault is currently stored in 1TB UBC OneDrive and periodically backed up to GitHub repository.

Extensions

Highlights:

Obsidian Git: back up entire vault to a GitHub repository
Obsidian Zotero Integration
- Easily add cite-key & citations from Zotero, import notes & metadata as templated LitNotes
- Danny Hatcher: Zotero Obsidian Integration LitNotes overview
- Alexandra Phelan: An Updated Academic Workflow: Zotero & Obsidian
Obsidian Pandoc Reference List
Templater: template plugin that can execute JavaScript code, can automate creation of daily notes
- Dann Berg: My Obsidian Daily Note Template

Miscellaneous

To-do list: Todoist (free tier!)

PPspliT: PowerPoint add-in that splits animations steps into separate slides for ease of export to PDF