ENVS 193DS Spring 2023 week 6 coding workshop

Since the midterm is due on Thursday, this coding workshop focuses on niche but potentially useful skills to have. By the end, you'll be able to:

• use color palette packages in R (examples include {NatParksPalettes} and {wesanderson})
• make an interactive plot using {plotly}
• insert images into ggplot objects using {magick}
• do some more advanced data cleaning using functions from {stringr} and {forcats} (both {tidyverse} packages)
• organize your Quarto/RMarkdown documents to better understand how they render/knit (useful for troubleshooting errors!)
• set up a repository with GitHub pages

Required packages

This workshop is going to be more fun if you have the following packages installed:

Things you should already have

• {tidyverse}
• {here}
• {naniar} (or equivalent)

Things that you don't have to have but would make this more fun for you:

• {skimr}: to quickly summarize data (documentation)
• {plotly}: to make interactive plots using Javascript (documentation)
• {magick}: to put images into plots (documentation)
• {NatParksPalettes}: a color palette package (documentation)
• {wesanderson}: another color palette package (documentation)
• {patchwork}: to put plots together (documentation)

New or new-ish functions

Not an exhaustive list!

• lubridate::year() (in {tidyverse})
• lubridate::month() (also in {tidyverse})
• forcats::fct_relevel() (also in {tidyverse})
• stringr::str_detect() (also in {tidyverse})
• paste/paste0
• skimr::skim()

Rendered output

In this workshop, we'll talk about how to use GitHub pages. The rendered output is here.

When using GitHub pages, the URL for any rendered/knitted output is "your github username.github.io"/ "repository name"/"file path". So, for example, the url for the rendered output (linked above) is: an-bui.github.io/ENVS-193DS_week-06/key/workshop-06_2023-05-09_key.html.

Data sources

The gray whale count data is from the Environmental Data Initiative's data portal. Source: SBC Marine Biodiversity Observation Network, M. Smith, and L. Kui. 2020. Santa Barbara Channel Marine BON: Gray Whales Count ver 2. Environmental Data Initiative. https://doi.org/10.6073/pasta/5ebbc61168c4e0fcd0546f4f68c70a11 (Accessed 2023-05-10).

The gray whale count happens every year off of Coal Oil Point! Read more about those efforts here.

Image sources

The object whale_image1 comes from NOAA Fisheries. The object whale_image2 is read in using magick::image_read() from this URL (current as of 2023-05-09).