Workflow

There’s a famous blog post about workflows in R1 about a talk Jenny Bryan gave that included this slide:

If the first line of your R script is

setwd("C:\Users\jenny\path\that\only\I\have")

I will come into your office and SET YOUR COMPUTER ON FIRE 🔥.

If the first line of your R script is

rm(list = ls())

I will come into your office and SET YOUR COMPUTER ON FIRE 🔥.

The problem with setwd()

  • setwd() changes the working directory, leading to potential issues in collaboration and reproducibility
    • You and I don’t have the same file structure!
    • For example, my current working directory is
    getwd()
  • It’s also really annoying to move around files and folders, even if it’s just you using them

R Projects

  • R projects provide a structured and organized way to work on projects in R
  • R projects encapsulate all project-related files and settings into a single directory
  • RStudio makes it easy to work with R projects

R Projects

my-project/
├─ my-project.Rproj
├─ README
├─ data/
│   ├── raw/
│   └── processed/
├─ R/
├─ results/
│   ├── tables/
│   ├── figures/
│   └── output/
└─ docs/

  • An .Rproj file is mostly just a placeholder. It remembers various options, and makes it easy to open a new RStudio session that starts up in the correct working directory. You never need to edit it directly.

  • A README file can just be a text file that includes notes for yourself or future users.

  • I like to have a folder for raw data – which I never touch – and a folder(s) for datasets that I create along the way.

Benefits of R Projects

  1. Isolation: Each project has its own workspace, separate from other projects
  2. Reproducibility: Projects ensure that code and data are self-contained and portable
  3. Collaboration: Projects facilitate collaboration by sharing the entire project directory

Creating an R Project

  1. Open RStudio and go to File > New Project, or click on the projects button in the upper-right corner of RStudeio.
  2. Choose a project location (New Directory, Version Control, Existing Directory).
  3. Specify the project directory and create the project.
  4. Choose the project type (e.g., regular project, Quarto website, Bookdown book)

The {here} Package

  • The {here} package simplifies file path management within R projects.
  • It provides a consistent and reliable way to reference files within the project directory.

Benefits of the {here} Package

  1. Simplicity : Avoids the need for manual file path manipulation with setwd() and paste() functions
  2. Flexibility : Works seamlessly even when scripts are run from different locations
  3. Portability : Ensures that file paths work consistently across different systems

Using {here} in your project

  1. Install the {here} package: install.packages("here").
  2. Load the {here} package in your R script: library(here).
  3. Use the here() function to reference files within your project directory.

I actually like to use here::here() rather than loading the package with library(here) every time.

Using {here} in your project

  • Construct file paths with reference to the top directory holding your .Rproj file.

  • here::here("data", "raw", "data.csv") for me, here, becomes "/Users/l.smith/Documents/Presentations/reproducible-epi-SER/data/raw/data.csv"

  • But if I send you my code to run, it will become whatever file path you need it to be, as long as you’re running it within the R Project.

Start fresh

  • rm(list = ls()) removes objects from your environment, but it doesn’t unload the packages

  • You can easily create errors of the type Error in... could not find function... because your code runs just fine until you restart R and realize you never included the right library() calls

  • Restart your R session early and often as you write code!

Conclusion

  • Embrace the project-oriented workflow in R for better organization, reproducibility, and collaboration
  • Use R projects to encapsulate project-related files and settings
  • The {here} package helps with reliable and portable file path management

Additional Resources