Reproducible epidemiology in R

What is `{renv}`?

{renv} is an R package for managing project dependencies and creating reproducible environments

Benefits of using `{renv}`

Isolation: Creates project-specific environments separate from the global R library.
Reproducibility: Ensures consistent package versions for code reproducibility.
Collaboration: Facilitates sharing and collaborating on projects with others.

Getting Started with `{renv}`

Install {renv}

install.packages("renv")

Initialize a project

renv::init()

Install packages

install.packages("other_package")
# only an option when using renv!
install.packages("github_user/github_package")

Track dependencies via a lockfile

renv::snapshot()

Behind the scenes

Your project .Rprofile is updated to include:
```
source("renv/activate.R")
```
This is run every time R starts, and does some management of the library paths to make sure when you call install.packges("package") or library(package) it does to the right place (renv/library/R-{version}/{computer-specifics})

A renv.lock file (really just a text file) is created to store the names and versions of the packages.

`renv.lock`

{
  "R": {
    "Version": "4.3.0",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://cran.rstudio.com"
      }
    ]
  },
  "Packages": {
    "R6": {
      "Package": "R6",
      "Version": "2.5.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
    },
    base64enc": {
      "Package": "base64enc",
      "Version": "0.1-3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "543776ae6848fde2f48ff3816d0628bc"
    },

Using `{renv}` later

Restore an environment

renv::restore()

Install new packages

install.packages("other_package")

Update the lockfile

renv::snapshot()

Collaboration with `{renv}`

Share the project’s renv.lock file with collaborators to ensure consistent environments
When they run renv::restore(), the correct versions of the packages will be installed on their computer

renv::restore()

Other helpful functions

Remove packages that are no longer used:

renv::clean()

Check the status of the project library with respect to the lockfile:

renv::status()

This will tell you to renv::snapshot() to add packages you’ve installed but haven’t snapshotted, or renv::restore() if you’re missing packages you need but which aren’t installed

Conclusion

{renv} benefits:

Isolation, reproducibility, and collaboration

Getting started with {renv}

Initialize a project using renv::init()
Install packages and store with renv::snapshot()
Restore later or elsewhere with renv::restore()

Additional resources