Workflow

• Workflow is a system to make it easier on your brain to do your work
• Don’t waste time finding things or trying to remember that great idea you had
• We’ll work toward an organized and systematic workflow that ensures replicability and minimizes mistakes
• Keystone habit: a way to organize all other good habits

Getting organized

In the etiquette section, we talked about some very general tips for staying organized. This will be specific to research. Here, we’ll cover strategies to organize…

1. notes for your research project
2. your project folders
3. notes on papers you’ve read
4. papers you’re citing

Project notebooks

• Organize your projects into notebooks (or folders) of some kind
• Digital options: OneNote, Evernote, Notion, Google Keep, just text files in a folder
• Other options: Bullet journals (pen and paper, gasp!)

Project notebooks

Here’s my system:

• Three main research categories: 1) pending research; 2) ongoing research; and 3) completed research
• Pending research is for ideas
  • Google Keep note
  • After some thought, transition to individual notebook/folder (ReMarkable)
  • After more thought, transition to ongoing research (if viable)

Project notebooks

Here’s my system:

• Three main research categories: 1) pending research; 2) ongoing research; and 3) completed research
• Pending research is for ideas
• Ongoing research is for actual working projects
  • Section for each project
  • Subsections for “meeting notes” (if co-authored) and “ideas/thoughts”

Project notebooks

Here’s my system:

• Three main research categories: 1) pending research; 2) ongoing research; and 3) completed research
• Pending research is for ideas
• Ongoing research is for actual working projects
• Completed research is for, you guessed it, completed projects
  • After paper is officially accepted and all supporting documentation finalized

Project folders

Key is to have a system where files are named appropriately and everything is easily accessible. Basically it’s a closet for your research.

Project folders

project
|   README.md
|   paper.qmd (or .tex)
|   abstract.qmd
|   presentation.qmd
|   BibTeX.bib (symbolic link)
|
|---analysis
|   |   _analysis.R
|   |   1_sumstats.R
|   |   2_awesome-stuff.R
|
|---data-code
|   |   _build-data.R
|   |   1_data1.R
|   |   2_data2.R
|   |   final_dat1.csv
|   |   final_dat2.csv
|
|---data
|   |   input (symbolic links)
|   |   output (analytic data sets)
|
|---results
|   |   table1.tex
|   |   figure1.png

Project folders

• Project need not start out perfectly organized
• Think of the folder/file structure as your kitchen
  • It will get dirty
  • Don’t let it get so dirty that you forget stuff
  • Clean up regularly!

Reading papers

• We read lots of papers. That’s part of the job and critical to doing good work.
• Want to avoid losing our notes on papers we’ve already read
• Lots of ways to store PDFs and handwritten notes
  • OneNote “learning” notebook
  • Several Mac/iPad options
  • Research Rabbit
  • ReMarkable tablets (my strategy)
• AI tools can help you digest papers faster (Elicit, Semantic Scholar, Scholarcy)