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Manta Rays

Source: vignettes/manta_rays.qmd

Photograph by Di Cook.

1 Introduction

This vignette demonstrates how to analyze occurrence data for Manta Rays in Australia, using records from the Atlas of Living Australia (ALA).

The dataset has been prepared for you to explore, making it suitable for both study and practice with real-world ecological data. In this vignette we provide short examples of how to manipulate and visualize the dataset, but you are encouraged to develop your own creative approaches for analysis and visualization.

This is the glimpse of your data :

library(dplyr)
library(ecotourism)
data("manta_rays")
manta_rays |> glimpse()
Rows: 953
Columns: 14
$ obs_lat     <dbl> -33.93000, -33.93000, -33.93000, -33.80058, -33.80012, -33…
$ obs_lon     <dbl> 151.3500, 151.3500, 151.3500, 151.2955, 151.2969, 151.2948…
$ date        <date> 2014-01-04, 2015-07-28, 2014-08-07, 2024-12-22, 2024-12-2…
$ time        <chr> "00:00:00", "00:00:00", "00:00:00", "11:44:00", "12:50:25"…
$ year        <dbl> 2014, 2015, 2014, 2024, 2024, 2024, 2014, 2017, 2017, 2017…
$ month       <dbl> 1, 7, 8, 12, 12, 12, 4, 3, 3, 2, 2, 3, 2, 3, 11, 2, 2, 3, …
$ day         <dbl> 4, 28, 7, 22, 22, 22, 25, 3, 4, 27, 26, 3, 26, 2, 29, 26, …
$ hour        <int> 0, 0, 0, 11, 12, 8, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ weekday     <ord> Saturday, Tuesday, Thursday, Sunday, Sunday, Sunday, Frida…
$ dayofyear   <dbl> 4, 209, 219, 357, 357, 357, 115, 62, 63, 58, 57, 62, 57, 6…
$ sci_name    <chr> "Mobula alfredi", "Mobula alfredi", "Mobula alfredi", "Mob…
$ record_type <chr> "MACHINE_OBSERVATION", "MACHINE_OBSERVATION", "MACHINE_OBS…
$ obs_state   <chr> NA, NA, NA, "New South Wales", "New South Wales", "New Sou…
$ ws_id       <chr> "947800-99999", "947800-99999", "947800-99999", "957680-99…

2 Visualization

2.1 Spatial Distribution Map

Distribution of Occurrence Manta Rays Sightings in Australia

library(ggplot2)
library(ggthemes)

manta_rays |> 
  ggplot() +
    geom_sf(data = oz_lga) +
    geom_point(aes(x = obs_lon, y = obs_lat), color = "red") +
    theme_map()

Weekday Distribution of Manta Rays Sightings

week_order <- c("Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday", "Sunday")

manta_rays |> 
  ggplot(aes(x = factor(weekday, levels = week_order))) +
    geom_bar() +
    labs(x = "Weekday", y = "Number of Records") +
    theme_minimal()

Monthly Distribution of Manta Rays Sightings

library(lubridate)
manta_rays |>
    dplyr::mutate(month =month(month, label = TRUE, abbr = TRUE)) |>
    ggplot(aes(x = factor(month))) +
    geom_bar() +
    labs(x = "Month", y = "Number of Records") +
    theme_minimal()

Yearly Distribution of Manta Rays Sightings

manta_rays |>
    ggplot(aes(x = factor(year))) +
    geom_bar() +
    labs(x = "Year", y = "Number of Records") +
    theme_minimal()

4 Relational visualization

We want to see if manta_rays occurrences are related to precipitation on the same day from the weather dataset.

Here’s a short R script that:

  1. Joins manta_rays with weather using ws_id and date.

  2. Counts daily occurrences.

  3. Plots precipitation vs number of manta_rays sightings.

library(ggbeeswarm)

# Prepare manta_rays occurrence counts per day
manta_rays_daily <- manta_rays |>
  group_by(ws_id, date) |>
  summarise(occurrence = n(), .groups = "drop")

# Join with weather data for precipitation
manta_rays_weather <- manta_rays_daily |>
  left_join(weather |> select(ws_id, date, prcp), 
            by = c("ws_id", "date"))

# Simple plot: rainy day vs manta_rays occurrence
manta_rays_weather |>
  filter(!is.na(prcp)) |>
  mutate(rain = if_else(prcp > 5, "yes", "no")) |>
  ggplot(aes(x = rain, y = occurrence)) +
  geom_quasirandom(alpha = 0.6) +
  ylim(c(0, 15)) +
  labs(
    title = "Relationship between rainy day and Manta Rays occurrence",
    x = "Rainy",
    y = "Number of Manta Rays records"
  ) +
  theme_minimal()

manta_rays_weather <- manta_rays_daily |> 
  left_join(
    weather |> select(ws_id, date, temp, prcp),
    by = c("ws_id", "date")
  )


ggplot(manta_rays_weather, aes(temp, occurrence, color = prcp)) +
  geom_point(alpha = 0.5) +
  scale_color_viridis_c() +
  labs(
    title = "Manta Rays occurrence vs temperature, colored by precipitation",
    x = "Mean daily temperature (°C)",
    y = "Occurrences",
    color = "Precipitation (mm)"
  ) +
  theme_minimal()