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Download occurrence records from SpeciesLink

Source: R/get_specieslink.R
get_specieslink.Rd

Retrieves occurrence data from the speciesLink network using user-defined filters. The function allows querying by taxonomic, geographic, and collection-related parameters.

Usage

get_specieslink(species = NULL, key = NULL, dir,
                       filename = "specieslink_output",save = FALSE,
                       basisOfRecord = NULL, family = NULL, institutionCode = NULL,
                       collectionID = NULL, catalogNumber = NULL,
                       kingdom = NULL, phylum = NULL, class = NULL,
                       order = NULL, genus = NULL, specificEpithet = NULL,
                       infraspecificEpithet = NULL, collectionCode = NULL,
                       identifiedBy = NULL, yearIdentified = NULL,
                       country = NULL, stateProvince = NULL, county = NULL,
                       typeStatus = NULL, recordedBy = NULL,
                       recordNumber = NULL, yearCollected = NULL,
                       locality = NULL, occurrenceRemarks = NULL,
                       barcode = NULL, bbox = NULL, landuse_1 = NULL,
                       landuse_year_1 = NULL, landuse_2 = NULL,
                       landuse_year_2 = NULL, phonetic = FALSE,
                       coordinates = NULL, scope = NULL, synonyms = NULL,
                       typus = FALSE, images = FALSE, redlist = NULL,
                       limit = NULL, file.format = "csv",
                       compress = FALSE, verbose = TRUE)

Arguments

species

(character) species name. Default is NULL.

key

(character) API key or authentication token if required. Default is NULL.

dir

(character) directory where files will be saved (if save = TRUE).

filename

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

save

(logical) whether to save the results to file. Default is FALSE.

basisOfRecord

(character) filter by basis of record. Default is NULL.

family

(character) family name. Default is NULL.

institutionCode

(character) code of the institution that holds the specimen. Default is NULL.

collectionID

(character) unique identifier for the collection. Default is NULL.

catalogNumber

(character) catalog number of the specimen or record. Default is NULL.

kingdom

(character) kingdom name. Default is NULL.

phylum

(character) phylum name. Default is NULL.

class

(character) class name. Default is NULL.

order

(character) order name. Default is NULL.

genus

(character) genus name. Default is NULL.

specificEpithet

(character) specific epithet of the species. Default is NULL.

infraspecificEpithet

(character) infraspecific epithet. Default is NULL.

collectionCode

(character) code identifying the collection within an institution. Default is NULL.

identifiedBy

(character) name of the person who identified the specimen. Default is NULL.

yearIdentified

(numeric) year of identification. Default is NULL.

country

(character) country name. Default is NULL.

stateProvince

(character) state or province name. Default is NULL.

county

(character) county or municipality name. Default is NULL.

typeStatus

(character) type status. Default is NULL.

recordedBy

(character) collector name. Default is NULL.

recordNumber

(numeric) collector’s record number. Default is NULL.

yearCollected

(numeric) year of collection. Default is NULL.

locality

(character) locality description. Default is NULL.

occurrenceRemarks

(character) text field for remarks about the occurrence. Default is NULL.

barcode

(character) barcode or unique specimen identifier. Default is NULL.

bbox

(character) bounding box coordinates in the format "lon_min+lat_min+lon_max+lat_max". Default is NULL.

landuse_1

(character) land use category for the first year. Default is NULL.

landuse_year_1

(numeric) year corresponding to landuse_1. Default is NULL.

landuse_2

(character) land use category for the second year. Default is NULL.

landuse_year_2

(numeric) year corresponding to landuse_2. Default is NULL.

phonetic

(logical) whether to use phonetic matching for taxon names. Default is FALSE.

coordinates

(character) whether to include only records with geographic coordinates ("yes", "no", "original", "automatic", "blocked", "consistent", "suspect")). Default is NULL.

scope

(character) scope of the query ("p", "a", "m", "f", "b"). Default is NULL.

synonyms

(chacarter) whether to include synonyms of the specified taxon ("sp2000", "flora2020", "MycoBank", "algaebase", "DSMZ", "moure"). Default is NULL.

typus

(logical) whether to filter only type specimens. Default is FALSE.

images

(logical) whether to restrict to records with associated images. Default is FALSE.

redlist

(character) filter by IUCN Red List category. Default is NULL.

limit

(numeric) maximum number of records to return. Default is NULL.

file.format

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

compress

(logical) whether to compress the output file into .zip. Default is FALSE.

verbose

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

#' @details The speciesLink API key can be set permanently using:


set_specieslink_credentials("your_api_key")

Value

A data.frame containing the occurrence data fields returned by speciesLink.

Examples

if (FALSE) { # \dontrun{
# Retrieve records for Arecaceae in São Paulo
res <- get_specieslink(
  family = "Arecaceae",
  country = "Brazil",
  stateProvince = "São Paulo",
  basisOfRecord = "PreservedSpecimen",
  limit = 10
)

# Save results as compressed CSV
get_specieslink(
  family = "Arecaceae",
  country = "Brazil",
  save = TRUE,
  dir = tempdir(),
  filename = "arecaceae_sp",
  compress = TRUE
)
} # }