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Process EASIN data for the IASDT

Source: R/dwf_easin_process.R, R/dwf_easin_taxonomy.R, R/dwf_easin_download.R, and 1 more
EASIN_data.Rd

Extracts, processes, and visualises data from the European Alien Species Information Network (EASIN) for the Invasive Alien Species Digital Twin (IASDT). Manages taxonomy, occurrence data, and plots, handling API pagination and server limits. Orchestrated by easin_process() with helpers easin_taxonomy(), easin_download(), and easin_plot().

Usage

easin_process(
  extract_taxa = TRUE,
  extract_data = TRUE,
  n_download_attempts = 10L,
  n_cores = 6L,
  strategy = "multisession",
  sleep_time = 10L,
  n_search = 1000L,
  env_file = ".env",
  delete_chunks = TRUE,
  start_year = 1981L,
  plot = TRUE
)

easin_taxonomy(
  env_file = ".env",
  kingdom = "Plantae",
  phylum = "Tracheophyta",
  n_search = 100L
)

easin_download(
  species_key,
  timeout = 200,
  verbose = FALSE,
  env_file = ".env",
  n_search = 1000,
  n_attempts = 10,
  sleep_time = 5,
  delete_chunks = TRUE,
  return_data = FALSE
)

easin_plot(env_file = ".env")

Arguments

extract_taxa

Logical. If TRUE, extracts taxonomy using easin_taxonomy(). Default: TRUE.

extract_data

Logical.If TRUE, downloads occurrence data with easin_download(). Default: TRUE.

n_download_attempts

Integer. Retry attempts for downloads. Default: 10.

n_cores

Integer. Number of CPU cores to use for parallel processing. Default: 6. The maximum number of allowed cores are 8.

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.

sleep_time

Integer. Number of seconds to pause between each data retrieval request to prevent overloading the server. Default: 5 second.

Integer. Number of records to attempt to retrieve per request. Default: 1000, which is the current maximum allowed by the API.

env_file

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

delete_chunks

Logical. Whether to delete temporary files for data chunks from the file_parts subdirectory. Defaults to TRUE.

start_year

Integer. Earliest year for occurrence data (excludes earlier records). Default: 1981 (aligned with CHELSA climate data).

plot

Logical. If TRUE, generates plots via easin_plot(). Default: TRUE.

kingdom

Character. Taxonomic kingdom to query. Default: "Plantae".

phylum

Character. Taxonomic phylum within kingdom. Default: "Tracheophyta"

species_key

Character. EASIN taxon ID for which data is to be retrieved. This parameter cannot be NULL.

timeout

Integer. Download timeout in seconds. Default: 200.

verbose

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

n_attempts

Integer. Max download attempts per chunk. Default: 10.

return_data

Logical. If TRUE, returns data as a dataframe; otherwise, saves to disk and returns invisible(NULL). Default: FALSE.

Note

Uses a static RDS file with EASIN-GBIF taxonomic standardization, prepared by Marina Golivets (Feb 2024).

Functions details

  • easin_process(): Orchestrates taxonomy extraction, data downloads, and plotting for EASIN species data.

  • easin_taxonomy(): Fetches taxonomy data in chunks via the easin API, filtered by kingdom and phylum. Returns a tibble.

  • easin_download(): Downloads occurrence data for a given easin ID, handling pagination and pauses. Returns a dataframe if return_data = TRUE, else invisible(NULL).

  • easin_plot(): Creates summary plots (observations count, species count, distribution by partner) as JPEGs. Returns invisible(NULL).

Author

Ahmed El-Gabbas