Skip to contents

Process EASIN data for the IAS-pDT

Source: R/DWF_EASIN_Process.R, R/DWF_EASIN_Taxonomy.R, R/DWF_EASIN_Down.R, and 1 more
EASIN_data.Rd

Extracts, processes, and visualizes data from the European Alien Species Information Network (EASIN) for the Invasive Alien Species prototype Digital Twin (IAS-pDT). Manages taxonomy, occurrence data, and plots, handling API pagination and server limits. Orchestrated by EASIN_Process() with helpers EASIN_Taxonomy(), EASIN_Down(), and EASIN_Plot().

Usage

EASIN_Process(
  ExtractTaxa = TRUE,
  ExtractData = TRUE,
  NDownTries = 10L,
  NCores = 6L,
  SleepTime = 10L,
  NSearch = 1000L,
  EnvFile = ".env",
  DeleteChunks = TRUE,
  StartYear = 1981L,
  Plot = TRUE
)

EASIN_Taxonomy(
  EnvFile = ".env",
  Kingdom = "Plantae",
  Phylum = "Tracheophyta",
  NSearch = 100
)

EASIN_Down(
  SpKey,
  Timeout = 200,
  Verbose = FALSE,
  EnvFile = ".env",
  NSearch = 1000,
  Attempts = 10,
  SleepTime = 5,
  DeleteChunks = TRUE,
  ReturnData = FALSE
)

EASIN_Plot(EnvFile = ".env")

Arguments

ExtractTaxa

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

ExtractData

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

NDownTries

Integer. Retry attempts for downloads. Default: 10.

NCores

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

SleepTime

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

NSearch

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

EnvFile

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

DeleteChunks

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

StartYear

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"

SpKey

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.

Attempts

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

ReturnData

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_Down(): Downloads occurrence data for a given EASIN ID, handling pagination and pauses. Returns a dataframe if ReturnData = 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