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

Source: R/DWF_IAS_Process.R, R/DWF_IAS_Distribution.R, R/DWF_IAS_Plot.R
IAS_data.Rd

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

Usage

IAS_Process(EnvFile = ".env", NCores = 6L, Overwrite = TRUE)

IAS_Distribution(
  Species = NULL,
  EnvFile = ".env",
  Verbose = FALSE,
  Overwrite = FALSE
)

IAS_Plot(Species = NULL, EnvFile = ".env", Overwrite = FALSE)

Arguments

EnvFile

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

NCores

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

Overwrite

Logical. If TRUE, overwrites existing maps; otherwise, skips if maps exist. Default: FALSE.

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 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