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Process and map Naturalized Alien Plant Species (NAPS) data for the IASDT

Source: R/dwf_naps_process.R, R/dwf_naps_distribution.R, R/dwf_naps_plot.R, and 1 more
naps_data.Rd

Processes and visualises Naturalized Alien Plant Species (NAPS) 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

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

naps_distribution(
  species = NULL,
  env_file = ".env",
  verbose = FALSE,
  dist_citizen = 100L
)

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

naps_standardisation(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.

dist_citizen

Numeric. Distance in km for spatial filtering of citizen science data in GBIF or grid cells in countries at which species has not yet recognized as "naturalized". Default is 100L km.

Functions details

  • naps_standardisation(): Load pre-prepared standardisation information for NAPS verbatim names and prepare a unique ias_id for each standardised NAPS. This function should be called only once per workflow version. The ias_id is determined based on sorting the standardised species names alphabetically within their taxonomic hierarchy (in the order of: class, order, family, and taxon_name). If a new standardisation file is used, new ias_id values will be generated, which will break reproducibility and prevent consistent data linkage across analyses.

  • naps_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 naps_distribution() and naps_plot().

  • naps_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

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

Author

Ahmed El-Gabbas