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Download species distribution information from BIEN

Source: R/bien_here.R
bien_here.Rd

This function downloads distribution information from the BIEN database, required for filtering occurrence records using specialists' information via the flag_bien() function.

Usage

bien_here(
  data_dir,
  species,
  synonyms = NULL,
  overwrite = TRUE,
  progress_bar = FALSE,
  verbose = TRUE
)

Arguments

data_dir

(character) directory to save the data downloaded from BIEN.

species

(character) a vector of species names for which to retrieve distribution information.

synonyms

(data.frame) an optional data.frame containing synonyms of the target species. The first column must contain the target species names, and the second column their corresponding synonyms. Default is NULL. See details for more information.

overwrite

(logical) whether to overwrite existing files. Default is TRUE.

progress_bar

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

verbose

(logical) whether to display progress messages. Default is TRUE.

Value

A data frame indicating whether the polygon(s) representing the species range are available in BIEN. If the range is available, a GeoPackage file (.gpkg) is saved in data_dir/bien. The file name corresponds to the species name, with an underscore (“_”) replacing the space between the genus and the specific epithet.

Details

This function uses the BIEN::BIEN_ranges_load_species() function to retrieve polygons representing the distribution ranges of species available in the BIEN database.

Because taxonomic information in BIEN may be outdated, you can optionally provide a table of synonyms to broaden the search. The synonyms data.frame should have the accepted species in the first column and their synonyms in the second. See RuHere::synonys for an example.

Examples

# \donttest{
# Define a directory to save the data
data_dir <- tempdir() # Here, a temporary directory

# Download species distribution information from BIEN
bien_here(data_dir = data_dir, species = "Handroanthus serratifolius")
#>                       species range_available
#>                        <char>          <lgcl>
#> 1: Handroanthus serratifolius            TRUE
# }