Download - Download specimen data from both GBIF and the iDigBio archive

The gators_download() function downloads data from GBIF and iDigBio for your desired species. In June 2026, we modified this function to queries an archive of iDigBio that contains only recordsets that were not uploaded to GBIF by June 2026. Since funding ended for iDigBio in 2026, iDigBio no longer has the resources to host data. Though the vast majority of recordsets migrated to GBIF, we wanted to make sure we had information available for the remaining few who have not migrated.

Usage

gators_download(
  synonyms.list,
  write.file = FALSE,
  filename = NA,
  gbif.match = "fuzzy",
  gbif.prov = FALSE,
  idigbio.match = "fuzzy",
  idigbio.filter = TRUE,
  fuzzy.ratio = 50,
  limit = 1e+05
)

Arguments

synonyms.list: A list of scientific names including the accepted scientific name and any synonyms for your desired species. For example, synonyms.list = c("Asclepias curtissii","Asclepias aceratoides", "Asclepias arenicola", "Oxypteryx arenicola", "Oxypteryx curtissii"). This parameter is required.
write.file: A parameter to choose whether to produce a .csv file containing search results. This parameter is not required and is assigned FALSE by default.
filename: The path and file name for the retrieved data. Note that this parameter should include the ".csv" extension as well. For example, filename = "base_folder/other_folder/my_file.csv". The file path can be entered either as relative to the current working directory (example: "../my_file.csv") or as a full path. This parameter is required if write.file = TRUE.
gbif.match: A parameter to select either search by fuzzy matching of scientific name or to search by species code. For example, gbif.match = "fuzzy" will search by fuzzy match and gbif.match = "code" will search by code. This parameter is not required and is assigned "fuzzy" by default.
gbif.prov: A parameter to obtain the provider/verbatim columns from GBIF. This parameter is optional and is assigned FALSE by default.
idigbio.match: Default = "fuzzy". Options are "fuzzy" or "exact". The fuzzy match uses rapidfuzz to calculate a rapidfuzz_partial_token_set_ratio or similarity ratio between the two strings. This option is helpful when word order differs or our strings are partial matches.
idigbio.filter: A parameter to remove less relevant search results from iDigBio. Based on the search input, results may include data points for a different species that mention the desired species in the locality information, for example. Choosing idigbio.filter = TRUE will return the data frame with rows in which the name column fuzzy matches a name on the synonym list. This parameter is not required and is assigned TRUE by default.
fuzzy.ratio: Default = 50%. We let more match than probably are helpful, and return all ratios greater than 50%.
limit: Default = 100,000 (maximum). Set limit to the number of records requested for each element in synonyms.list from GBIF.

Value

Returns a data frame and writes a csv file as specified in the input. This csv file will contain search results for the desired species from the GBIF and iDigBio databases. The columns are as follows:

scientificName
genus
specificEpithet
infraspecificEpithet
ID (contains unique IDs defined from GBIF or iDigBio)
occurrenceID
basisOfRecord
eventDate
year
month
day
institutionCode
recordedBy
informationWithheld
country
county
stateProvince
locality
latitude
longitude
coordinateUncertaintyInMeters
habitat
aggregator (either GBIF or iDigBio)

Details

With gators_download() you can obtain biodiversity records for your species of interest from both GBIF and iDigBio. This function is innovative in how it searches iDigBio. Unlike spocc::occ(), we do not query the iDigBio API using the scientific name field, as this will only return exact matches. Instead, we designed a “pseudo-fuzzy match” to search all fields for partial matches to the supplied scientific names. This function uses the correct_class(), setupduckDB(), get_idigbio_arc(), get_gbif(), fix_columns(), fix_names(), and filter_fix_names(). This function requires the packages magrittr, dplyr, duckDB, arrow, DBI, rgbif, and stringr.

Examples

if(exists("crazy")){
  df <- gators_download(synonyms.list = c("Galax urceolata", "Galax aphylla"))
  df <- gators_download(synonyms.list = "Galax urceolata",
                        gbif.match = "code",
                        idigbio.filter = FALSE,
                        limit = 10)
}