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Identify records outside natural ranges according to BIEN

Source: R/flag_bien.R
flag_bien.Rd

Flags (validates) occurrence records based on known distribution data from the Botanical Information and Ecology Network (BIEN) 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 BIEN dataset.

Usage

flag_bien(
  data_dir,
  occ,
  species = "species",
  long = "decimalLongitude",
  lat = "decimalLatitude",
  buffer = 10,
  progress_bar = FALSE,
  verbose = TRUE
)

Arguments

data_dir

(character) Required directory path where the BIEN 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".

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 TRUE.

Value

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

Examples

# Load example data
data("occurrences", package = "RuHere")
# Filter occurrences for golden trumpet tree
occ <- occurrences[occurrences$species == "Handroanthus serratifolius", ]
# Set folder where distributional datasets were saved
# Here, just a sample provided in the package
# You must run 'bien_here()' beforehand to download the necessary data files
dataset_dir <- system.file("extdata/datasets", package = "RuHere")

# Flag records using BIEN specialist information
occ_bien <- flag_bien(data_dir = dataset_dir, occ = occ)
#> Checking the distribution from 1 of 1 species