Using renv with reproducibleRchunks
In reproducibleRchunks: Automated Reproducibility Checks for R Markdown Documents

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(reproducibleRchunks)

Introduction

This vignette demonstrates how to create a small project using renv for dependency management. We will initialize a project, install the psych package, and run a simple factor analysis on one of the datasets that ships with that package, all while using reproducibleRchunks.

Creating a project

First, inside your R project, initialize renv to track and manage package dependencies:

# Initialize renv
renv::init()

renv creates a project-specific library and writes a lock file to record package versions. Your R session will be restarted (if running inside RStudio). Next we install the psych package as well as the reproducibleRchunks in the managed environment:

renv::install("psych")
renv::install("reproducibleRchunks")

After installation, snapshot the project state so the lock file is updated:

renv::snapshot(prompt = FALSE)

Running a factor analysis

With the packages installed and recorded, we can load psych and run a quick factor analysis on the bfi dataset that comes with that package. The following code chunk could now be a part of an R Markdown document inside your project:

library(psych)

# Use the first 200 cases of the bfi dataset for speed
bfi_subset <- head(bfi, 200)

fa_result <- fa(bfi_subset[, 1:10], nfactors = 3)
fa_result

This chunk is executed with reproducibleR, so fingerprints of bfi_subset and fa_result are stored for later reproducibility checks.

Note that if you operate inside RStudio, RStudio will ask your permission to install all packages necessary to render Markdown files inside your managed environment.

Restoring the environment

If you share your project, others can reproduce the same setup by calling renv::restore() in the project directory. This will install the recorded package versions and allow them to re-run the analyses above with verified reproducibility.

renv::restore()

GitHub actions

If you host your project on GitHub, you can add a github action that automatically verifies reproduction in the GitHub cloud:

reproducibleRchunks::use_github_action()

Depending on whether reproduction succeeded of failed, a badge is generated and added and committed to your repository. This is how the badges look like depending on the status: