Package 'infinitylists'

Download Observations for Infinity List

Description

This function downloads observation data for the given taxon and year range from the "Infinity List" source, processes and cleans the data, adds additional columns (e.g., establishment status), and optionally saves the raw and processed data.

Usage

download_ala_obs(
  taxon,
  year_range = c(1923, as.numeric(format(Sys.Date(), "%Y"))),
  save_raw_data = FALSE,
  output_dir = file.path(system.file(package = "infinitylists"), "data/")
)

Arguments

taxon	A character vector or string specifying the taxon (e.g., species, genus) for which observations are to be downloaded.
year_range	A numeric vector of length 2 indicating the start and end years for data retrieval. Default is from 1923 to the current year
save_raw_data	A logical value indicating whether to save the raw data. By default, raw data is not saved (FALSE).
output_dir	A character string specifying the directory where any saved data (raw or processed) will be stored. Default is file.path(system.file(package = "infinitylists"), "data/").

Details

The function carries out the following steps:

1. Retrieve the data from the "Infinity List" source.

2. Process and clean the retrieved data to remove any inconsistencies.

3. Add additional columns to the cleaned data, such as the establishment status for the given taxon.

4. If save_raw_data is TRUE, save the processed data to the specified output_dir.

Value

This function saves the processed data and returns invisibly. The structure and content of the returned value (if any) is determined by the functions called within (e.g., retrieve_data, process_data).

---

Download and Process GBIF Observations

Description

This function retrieves, processes, and saves GBIF (Global Biodiversity Information Facility) observation data for a specified taxon.

Usage

download_gbif_obs(
  taxon,
  min_year = 1923,
  max_year = as.numeric(format(Sys.Date(), "%Y")),
  country_code = NULL,
  save_raw_data = FALSE,
  output_dir = file.path(system.file(package = "infinitylists"), "data/")
)

Arguments

taxon	Character. The taxon (species, genus, etc.) for which to retrieve GBIF data.
min_year	Numeric. The minimum year for the observations to be retrieved. Default is 1923.
max_year	Numeric. The maximum year for the observations to be retrieved. Default is the current year.
country_code	Character. The ISO 3166-1 alpha-2 country code to filter observations by country. Default is NULL (no country filter).
save_raw_data	Logical. Whether to save the raw data retrieved from GBIF. Default is FALSE.
output_dir	Character. The directory where the processed data will be saved. Default is a "data" directory within the "infinitylists" package.

Value

None. The function saves the processed data to the specified output directory.

---

Infinity List Server Function

Description

Initializes and sets up the server-side logic for the Infinity List Shiny application. This function manages the user interactions, data processing, and rendering of both UI elements and outputs (tables, maps, stats). It handles file uploads, data filtering, and interaction with map elements.

Usage

infinity_server(...)

Arguments

...	Additional arguments that might be passed to server functions. These could be passed from a Shiny UI function or another server function.

Details

The server function handles several main tasks:

• Observes and processes KML file uploads.

• Reactively creates polygons based on user inputs.

• Filters and processes ALA data based on user-selected polygons.

• Computes and displays statistics about observed species.

• Updates select input choices based on the available data.

• Renders and displays a data table with specific details.

• Provides a CSV download handler for the displayed data.

• Renders a Leaflet map with markers, polygons, and buffers.

Key internal functions include:

• load_place(): For processing KML files.

• create_circle_polygon(): To create polygons from user inputs.

• points_in_target(): To determine if points lie within a target polygon.

• points_in_buffer(): To determine if points lie within a buffer around a polygon.

• filter_by_taxon(): Filters the ALA data by selected taxa.

• add_buffer(): Adds a buffer around a given polygon.

Value

This function sets up and returns a server function for the Shiny app. It does not have a direct return value, but rather, it sets up reactive outputs, observers, and expressions that the Shiny app will utilize.

See Also

infinitylistApp: Main function that launches the Infinity List Shiny app.

---

Launch the Infinity List Application

Description

This function initializes and runs the "Infinity List" application using Shiny. Before launching, it checks for any available updates and downloads them if necessary. The app provides a user interface (ui) and server-side logic (server) to interactively work with the Infinity List.

Usage

infinitylistApp(...)

Arguments

...	Additional arguments passed to shinyApp(). This can include parameters like port, launch.browser, and others as described in the documentation for shinyApp().

Details

The function carries out the following steps:

1. Checks and downloads any available updates using check_and_download_update().

2. Initializes the user interface (ui) for the application.

3. Sets up the server-side logic (server) for the application.

4. Launches the Shiny application using shinyApp().

Value

This function launches the Shiny application and does not return until the app is terminated by the user.

Examples

## Not run: 
  # Launch the Infinity List App
  infinitylistApp()

## End(Not run)

---

Generate galah query for Global GBIF Node

Description

Generate galah query for Global GBIF Node

Usage

query_gbif_global(taxon, min_year, max_year, country_code = NULL)

Arguments

taxon	character, genus/family/kingdom
min_year	numeric, year cut off for query, only records where year >= min_year will be included
max_year	numeric, year cut off for query, only records where year <= max_year will be included
country_code	character, code for country

---