Orchids

Orchids, Photo taken by Lyn Cook.

1 Introduction

This vignette demonstrates how to analyze occurrence data for Orchids 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.

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This is the glimpse of your data :

library(dplyr)
library(ecotourism)
data("orchids")
orchids |> glimpse()

Rows: 35,052
Columns: 14
$ obs_lat     <dbl> -35.20000, -35.20000, -35.20000, -35.20000, -35.20000, -35…
$ obs_lon     <dbl> 117.8000, 118.0000, 116.7000, 117.7000, 117.6000, 117.8073…
$ date        <date> 2017-09-11, 2019-08-02, 2016-10-06, 2017-09-07, 2022-08-0…
$ time        <chr> "18:08:00", "12:38:00", "17:32:00", "09:30:00", "09:21:09"…
$ year        <dbl> 2017, 2019, 2016, 2017, 2022, 2024, 2024, 2021, 2024, 2016…
$ month       <dbl> 9, 8, 10, 9, 8, 9, 8, 9, 10, 10, 9, 10, 9, 4, 10, 10, 7, 9…
$ day         <dbl> 11, 2, 6, 7, 6, 18, 23, 23, 19, 3, 30, 23, 25, 10, 9, 4, 3…
$ hour        <int> 18, 12, 17, 9, 9, 10, 9, 16, 11, 14, 13, 12, 12, 16, 16, 1…
$ weekday     <ord> Monday, Friday, Thursday, Thursday, Saturday, Wednesday, F…
$ dayofyear   <dbl> 254, 214, 280, 250, 218, 262, 236, 266, 293, 277, 273, 297…
$ sci_name    <chr> "Pterostylis heberlei", "Corybas limpidus", "Caladenia int…
$ record_type <chr> "HUMAN_OBSERVATION", "HUMAN_OBSERVATION", "HUMAN_OBSERVATI…
$ obs_state   <chr> "Western Australia", "Western Australia", "Western Austral…
$ ws_id       <chr> "948010-99999", "948010-99999", "956470-99999", "948010-99…

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2 Visualization

2.1 Spatial Distribution Map

Distribution of Occurrence Orchids Sightings in Australia

library(ggplot2)
library(ggthemes)

orchids |> 
  ggplot() +
    geom_sf(data = oz_lga) +
    geom_point(
      aes(x = obs_lon, y = obs_lat), color = "red", alpha = 0.5, size = 0.3) +
    theme_map()

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3 Weekly, Monthly, and Yearly Trends

Weekday Distribution of Orchids Sightings

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

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

Monthly Distribution of Orchids Sightings

library(lubridate)

orchids |>
    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 Orchids Sightings

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

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4 Relational visualization

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

Here’s a short R script that:

1. Joins orchids with weather using ws_id and date.

2. Counts daily occurrences.

3. Plots precipitation vs number of orchids sightings.

library(ggbeeswarm)

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

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

orchids_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 orchids occurrence",
    x = "Rainy",
    y = "Number of orchids records"
  ) +
  theme_minimal()

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


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