get_idigbio

Downloads species occurrence records from the iDigBio (Integrated Digitized Biocollections) database with flexible taxonomic and geographic filtering options.

Usage

get_idigbio(species = NULL, fields = "all", genus = NULL,
family = NULL, order = NULL, phylum = NULL, kingdom = NULL, country = NULL,
county = NULL, limit = NULL, offset = NULL, dir, filename = "idigbio_output",
save = FALSE, compress = FALSE, file.format = "csv", verbose = TRUE, ...)

Arguments

species

(character) scientific name(s) of species to search for. Default is NULL.

fields

(character) fields to retrieve from iDigBio. Default is "all".

genus

(character) genus name for filtering results. Default is NULL.

family

(character) family name for filtering results. Default is NULL.

order

(character) order name for filtering results. Default is NULL.

phylum

(character) phylum name for filtering results. Default is NULL.

kingdom

(character) kingdom name for filtering results. Default is NULL.

country

(character) country name for geographic filtering. Default is NULL.

county

(character) county name for geographic filtering. Default is NULL.

limit

(numeric) maximum number of records to retrieve. Default is NULL (no limit).

offset

(numeric) number of records to skip before starting retrieval. Default is NULL (starts at 0).

dir

(character) directory path where the file will be saved. Required if save = TRUE.

filename

(character) name of the output file without extension. Default is "idigbio_output".

save

(logical) if TRUE, saves the results to a CSV file. Default is FALSE.

compress

(logical) if TRUE and save = TRUE, compresses the output file as .csv.zip. Default is FALSE.

file.format

(character) file format for saving output ("csv", "rds"). Default is "csv"

verbose

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

...

additional arguments passed to ridigbio::idig_search_records().

Value

A data.frame containing occurrence records from iDigBio with the requested fields.

Examples

# \donttest{
## search for a single species
records_basic <- get_idigbio(species = "Arecaceae")

## search for multiple species
records_multiple <- get_idigbio(
  species = c("Araucaria angustifolia"),
  limit = 100)

## save results as a compressed RDS file
records_saved_rds <- get_idigbio(
  species = "Anacardiaceae",
  limit = 50,
  dir = tempdir(),
  filename = "anacardiaceae_records",
  save = TRUE,
  compress = TRUE,
  file.format = "rds")
#> Writing /tmp/RtmplOA5kz/anacardiaceae_records.rds on disk.
# }