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.

Coding environment = your local machine

Ensure that you can run R code with a platform like RStudio, VS Code, Positron, etc.
Ensure you have downloaded Quarto, version 1.6+, the quarto R package, and can create Quarto documents.

pak::pak("quarto")
quarto::quarto_version()

Optional: Create a new Github repo for the workshop. Do not complete the last step (“12.7 Clean up”). First, install Git if you don’t have it.
Optional: Clone your repo and set up an RStudio Project.
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 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("example_output"),
  dest_file = file.path("example_output", "Report.sso"),
  url = "https://raw.githubusercontent.com/nmfs-ost/workflows-workshop/main/example_output/Report.sso"
  )

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

Install important R packages

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")

Tip

To test your TinyTeX setup, you can save the following code in a Quarto file (“test.qmd”) and hit Render. If it renders, that’s a good sign! If you get an error, you may have an issue with your TinyTeX installation:

---
title: "TinyTeX Test"
format: pdf
---

Sample text to test if your Quarto file rendered into a PDF.

Explore {asar} and {stockplotr} websites

Browse the {asar} and {stockplotr} websites- especially the cheatsheets and articles.