Research project template

This is a template repository that aims to codify my workflow and incorporates best practices for research code.

Goals:

• clear documentation
• consistent structure
• version control
• explicit wrt inputs, outputs and methods
• reproducibility
• testing (liberal assertions at a minimum)

Aspirational goals:

• continuous integration
• formal testing

Useful resources:

• SKHiggins R_guide
• Good Research Code Handbook
• Science as Amateur Software Development by R McElreath

Key components of R workflow

• Git and Github
• Virtual environments {renv::init(), add renv/library to .gitignore}
• Folder and file structure as laid out below
• Number scripts to make sequence explicit
• Highlight and resolve any non linear sequences
• Liberal use of assertions for testing {assertthat}
• Data manipulation:
  • tidyverse for dataframes
  • data.table for big data {DT}
  • If it's a matrix, use a matrix

Files and folder structure

TEMPLATE
|-- data/ # gitignored
|  `-- example.csv
|-- docs/
|  |-- README.md
|  `--project.drawio
|-- renv/
|  |-- library/ # gitignored
|  |-- .gitignore
|  |-- activate.R
|  `-- settings.json
|-- results/ # gitignored
|   |-- plots
|   |-- rdata
|   |   `-- example.rds
|   |-- reports
|   `-- tables
|-- scripts/
|   |-- 01_cleaning.r
|   |-- 02_analysis.r
|   `-- 03_reporting.r
|-- src/
|   |-- functions
|   |   `-- project_function.r
|   |-- run_better.r
|   `-- run_quick.r
|-- tests/
|-- .gitignore
|-- .Rprofile
`-- renv.lock