Running Rscripts in a loaded project

Author

VLab Course Team

Before running any code in a repository, make sure you are inside the correct R project (.Rproj). This activates project-specific settings (including renv) and sets the working directory properly.

Step 1 - Open the project (`.Rproj`)

Open a project using one of these options:

From the Files pane (bottom-right): navigate to the repository folder and click the .Rproj file.
Programmatically (requires rstudioapi):

if (!requireNamespace("rstudioapi", quietly = TRUE)) install.packages("rstudioapi")
rstudioapi::openProject("~/GitHubRepos/geoflow-tunaatlas/stable")

Opening the .Rproj ensures that renv is activated via the project’s .Rprofile and that your working directory is correct.

Step 2 - Restore the Project environment with `renv`

The renv package manages project-specific R environments to guarantee reproducibility. It records exact package versions in renv.lock and restores them on any machine.

Run this once per project:

renv::restore()

What this does:

Installs missing packages or links them from VLab’s shared cache (fast).
Aligns your session’s packages with the versions expected by the project.

Useful tips:

# Check environment status (optional)
renv::status()

# If prompted after updates, restart your R session
if (requireNamespace("rstudioapi", quietly = TRUE)) rstudioapi::restartSession()

✅ Always run renv::restore() when you open a new repository.
ℹ️ A later section of this course dives deeper into renv, shared caches in VLab, and linking multiple repos to a common cache directory.

If you want to use the cache renv with your own projects or within your Vlab feel free to follow this tutorial renv cache path.

Example with geoflow-tunaatlas project

Step 3: Explore the `.Rmd` report

The file summary_catch.Rmd is an R Markdown document that allows you to explore catch datasets and generate visual outputs like maps and plots. A similar file is also available for effort data.

You can render the entire report at once using:

rmarkdown::render("summary_catch.Rmd")

However, for learning purposes, we recommend exploring the file chunk-by-chunk to understand each step in the workflow.

Open the file in the RStudio editor and review each code block, which typically includes: - Data loading from zenodo, or in the VLab from existing folder (to avoid re-downloading data) - Data transformation and filtering - Visualization with maps and plots - Output generation

Outputs

Executing the full .Rmd will generate an HTML report and may also create visual outputs or data files, often saved in the same directory or an outputs/ subfolder.

Note: geoflow-tunaatlas is the most complex repository used in this course. It contains several scripts, workflows, and Docker-related files beyond the .Rmd example shown here.

Other repositories

For all of the other repositories in this course:

tunaatlas_pie_map_shiny
shiny_compare_tunaatlas_datasets
darwin_core_viewer the usage is much simpler. You typically only need two commands to get started:

renv::restore()
shiny::runApp()

These repositories are Shiny apps that can be launched directly after restoring the environment.

You’re now ready to explore and execute workflows and Shiny apps across all repositories in VLab!

Step 1 - Open the project (.Rproj)

Step 2 - Restore the Project environment with renv