Pre-workshop checklist

Here are the main steps needed to set up your environment so that you’re ready to use asar and stockplotr to create a stock assessment report.

If you have any questions, please contact the workshop organizers.

1. Ensure that you can run R code with a platform like RStudio, VS Code, Positron, etc.
2. Ensure you have downloaded Quarto, version 1.6+ and can create Quarto documents.
3. Create a new Github repo for the workshop.
4. Clone your repo and set up an RStudio Project.
5. Run the following code to get two essential files from the workflows-workshop github repo:

• input data file “Report.sso” will save to a “example_output” folder in your home directory
• example plot file “landings_fig_png.png” will save to a “example_plots” folder in your home directory

# Function to obtain two files used during workshop
get_workshop_files <- function(dest_folder,
                               dest_file,
                               url){
  if (!file.exists(dest_folder)) {
    dir.create(dest_folder)
  }
  if (!file.exists(dest_file)) {
    cli::cli_alert_info("📥 Downloading {dest_file}...")
    download.file(url, dest_file, mode = "wb")
    message("✅ Download complete.")
  } else {
    cli::cli_alert_info("✅ File already exists: {dest_file}")
  }
}

# Obtain example output file
get_workshop_files(
  dest_folder = file.path(here::here("example_output")),
  dest_file = file.path(here::here("example_output", "Report.sso")),
  url = "https://github.com/nmfs-ost/workflows-workshop/blob/main/example_output/Report.sso"
  )

# Obtain example figure file
get_workshop_files(
  dest_folder = file.path(here::here("example_plots")),
  dest_file = file.path(here::here("example_plots", "landings_fig_png.png")),
  url = "https://github.com/nmfs-ost/workflows-workshop/blob/main/example_plots/landings_fig_png.png"
  )

6. Install important R packages {#sec-install_pkgs}

TipTip

The following packages are already installed in the asar workspace on JupyterHub, so if you are using that space, you can skip this section.

We recommend using the pak R package to install R packages where possible, since it avoids re-downloading files if they’re already present.

install.packages("pak")

• asar

pak::pak("nmfs-ost/asar")

Please see the asar README for more installation options.

• stockplotr

pak::pak("nmfs-ost/stockplotr")

Please see the stockplotr README for more installation options.

• tinytex

We recommend installing the full tinytex bundle to ensure that all LaTeX packages will be present when you need them. This will take ~30 minutes to complete.

pak::pkg_install("rstudio/tinytex")
tinytex::install_tinytex(bundle = "TinyTeX-2")