Overview

Author

VLab Course Team

Estimated duration: 30 minutes

Format: lab notebook (Explainer video + real-time walkthrough incoming)

Prerequisites: Access to VLab5, completion of VLab5 platform orientation.

Course map (Pages)

  • Intro to RStudio in VLab5
    intro-rstudio.qmd - Launch options (D4Science vs Google Cloud), RStudio panes (Console, Terminal, Environment, Files/Plots/Packages/Help/Viewer), system checks (R/RStudio versions, RAM).

  • Project Organization
    project-organization.qmd - Pre-installed repositories in ~/GitHubRepos, stable vs dev structure, quick terminal command to list repos, README locations.

  • Running scripts in a loaded repository
    running-scripts-in-loaded-repo.qmd - Open .Rproj, run renv::restore(), render example Rmd (summary_catch.Rmd in geoflow-tunaatlas), pattern for Shiny apps (shiny::runApp()).

  • Deploy repos in your own VLab (Bonus)
    deploy-repos-in-vlab-rstudioserver.qmd - High-level notes for advanced users: RStudio Server image, preload script, global renv cache at image build-time, and optional per-project/per-user cache notes.

Learning objectives

By the end of this lesson, learners will be able to:

  • Navigate the VLab5 RStudio environment confidently.
  • Understand the structure of project repositories, including stable vs dev versions.
  • Use renv::restore() to initialize a reproducible R environment.
  • Execute a complete R script within VLab5.
  • (Bonus) Understand how the shared package cache works within the infrastructure.
  • (Bonus) Deploy a repo in their own VLab environment if needed.

What you will do

  • Launch RStudio (D4Science or Google Cloud) and inspect the environment.
  • Explore pre-installed repos in ~/GitHubRepos and locate main scripts.
  • Restore packages with renv::restore() and run a full workflow (Rmd or Shiny).
  • Inspect outputs in outputs/ and review logs.
  • (Bonus) Review how deployment works and how to configure a global cache.

Expected outcome

By the end of this lesson, learners will:

  • Identify and choose an appropriate repository.
  • Execute a full R workflow in VLab5.
  • (Bonus) Understand package dependencies and renv logic.