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Identify records outside natural ranges according to the IUCN

Source: R/flag_iucn.R
flag_iucn.Rd

Flags (validates) occurrence records based on known distribution data from the International Union for Conservation of Nature (IUCN) data. This function checks if an occurrence point for a given species falls within its documented distribution, allowing for user-defined buffers around the region. Records are flagged as valid (TRUE) if they fall inside the documented distribution (plus optional buffer) for the species in the IUCN dataset.

Usage

flag_iucn(
  data_dir,
  occ,
  species = "species",
  long = "decimalLongitude",
  lat = "decimalLatitude",
  origin = "native",
  presence = "all",
  buffer = 20,
  progress_bar = FALSE,
  verbose = FALSE
)

Arguments

data_dir

(character) Required directory path where the IUCN data is saved

occ

(data.frame or data.table) a data frame containing the occurrence records to be flagged. Must contain columns for species, longitude, and latitude.

species

(character) the name of the column in occ that contains the species scientific names. Default is "species".

long

(character) the name of the column in occ that contains the longitude values. Default is "decimalLongitude".

lat

(character) the name of the column in occ that contains the latitude values. Default is "decimalLatitude".

origin

(character) vector specifying which origin categories should be considered as part of the species' range. Options are: "native", "introduced", "reintroduced", "vagrant", "origin uncertain", "assisted colonisation", and "all". For example, if origin = "introduced", only regions where the species is considered introduced will be used to validate records. Default is "native".

presence

(character) vector specifying which presence type should be considered as part of the species' range. Options are: "extant", "probably extant", "possibly extant", "extinct", "possibly extinct", "presence uncertain", and "all". For example, if presence = "extinct", only regions where the species is considered extinct will be used to validate records. Default is "all", meaning all regions will be considered.

buffer

(numeric) buffer distance (in kilometers) to be applied around the region of distribution. Default is 20 km.

progress_bar

(logical) whether to display a progress bar during processing. If TRUE, the 'pbapply' package must be installed. Default is FALSE.

verbose

(logical) if TRUE, prints messages about the progress and the number of species being checked. Default is FALSE.

Value

A data.frame that is the original occ data frame augmented with a new column named iucn_flag. This column is logical (TRUE/FALSE) indicating whether the record falls within the expected distribution (plus buffer) based on the IUCN data. Records for species not found in the IUCN data will have NA in the iucn_flag column.

Examples

# Load example data
data("occurrences", package = "RuHere")
# Get only occurrences from Araucaria
occ <- occurrences[occurrences$species == "Araucaria angustifolia", ]
# Set folder where distributional datasets were saved
# Here, just a sample provided in tha package
# You must run 'iucn_here()' beforehand to download the necessary data files
dataset_dir <- system.file("extdata/datasets", package = "RuHere")

# Flag records using IUCN specialist information
occ_iucn <- flag_iucn(data_dir = dataset_dir, occ = occ)