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Process and map Invasive Alien Species (IAS) data for the IASDT

Source: R/DWF_IAS_process.R, R/DWF_IAS_distribution.R, R/DWF_IAS_plot.R
IAS_data.Rd

Processes and visualises Invasive Alien Species (IAS) distribution data from GBIF, EASIN, and eLTER for the Invasive Alien Species Digital Twin (IASDT). Merges pre-processed data, creates presence-absence rasters, summarises distributions, and generates maps using helper functions.

Usage

IAS_process(env_file = ".env", n_cores = 6L, strategy = "multisession")

IAS_distribution(species = NULL, env_file = ".env", verbose = FALSE)

IAS_plot(species = NULL, env_file = ".env")

Arguments

env_file

Character. Path to the environment file containing paths to data sources. Defaults to .env.

n_cores

Integer. Number of CPU cores to use for parallel processing. Default: 6.

strategy

Character. The parallel processing strategy to use. Valid options are "sequential", "multisession" (default), "multicore", and "cluster". See future::plan() and ecokit::set_parallel() for details.

species

Character. Species name for distribution mapping.

verbose

Logical. If TRUE, prints progress messages. Default: FALSE.

Functions details

  • IAS_process(): Merges pre-processed GBIF (GBIF_process), EASIN (EASIN_process), and eLTER (eLTER_process) data (run these first). Outputs SpatRaster distribution rasters, summary tables, and JPEG maps using IAS_distribution() and IAS_plot().

  • IAS_distribution(): Generates presence-absence maps (.RData, .tif) for a species, including all grid cells in the study area and a set excluding cultivated/casual-only countries. Returns a file path to a tibble with presence counts (total, by source) and summary statistics for biogeographical regions

  • IAS_plot(): Creates JPEG distribution maps from GBIF, EASIN, and eLTER data using ggplot2.

Author

Ahmed El-Gabbas