AE 11: Multinomial classification


Go to the course GitHub organization and locate the repo titled ae-11-volcanoes-YOUR_GITHUB_USERNAME to get started.




For this application exercise we will work with a dataset of on volcanoes. The data come from The Smithsonian Institution via TidyTuesday.

volcano <- read_csv(here::here("ae", "data/volcano.csv"))
Rows: 958 Columns: 26
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (18): volcano_name, primary_volcano_type, last_eruption_year, country, r...
dbl  (8): volcano_number, latitude, longitude, elevation, population_within_...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

First, a bit of data prep:

volcano <- volcano %>%
    volcano_type = case_when(
      str_detect(primary_volcano_type, "Stratovolcano") ~ "Stratovolcano",
      str_detect(primary_volcano_type, "Shield") ~ "Shield",
      TRUE ~ "Other"
    volcano_type = fct_relevel(volcano_type, "Stratovolcano", "Shield", "Other")
  ) %>%
    volcano_type, latitude, longitude, 
    elevation, tectonic_settings, major_rock_1
    ) %>%
  mutate(across(where(is.character), as_factor))

Exploratory data analysis

  1. Create a map of volcanoes that is faceted by volcano_type. First, we create a map here.
world <- map_data("world")

world_map <- ggplot() +
    data = world, 
      x = long, y = lat, group = group),
      color = "white", fill = "gray50", 
      size = 0.05, alpha = 0.2
    ) +
  theme_minimal() +
  coord_quickmap() +
  labs(x = NULL, y = NULL)

Then you need to add a layer to the map using geom_point, and reproduce the following plot.

Build a new model

  1. Build a new model that uses a recipe that includes geographic information (latitude and longitude). How does this model compare to the original one presented on slides? Note:
    Use the same test/train split as well as same cross validation folds. Use seed 1234 for data splitting, and 9876 for cv.

New recipe, including geographic information:

Combine the original model specification as the one on slides and new recipe to obtain new workflow:

Fit resamples, and save it to volcano\_fit\_rs2

Collect metrics:

Draw ROC curves:

Compare these with the ones on slides. Comments on it. Which model do you prefer?


This exercise was inspired by