Gets occurrence data from speciesLink

Source: R/rspeciesLink.R

This function access version beta 0.1 of speciesLink API (https://api.splink.org.br/) and returns occurrence data of species.

rspeciesLink(
  dir = "results/",
  filename = "output",
  save = TRUE,
  basisOfRecord = NULL,
  species = NULL,
  collectionCode = NULL,
  country = NULL,
  stateProvince = NULL,
  county = NULL,
  Coordinates = NULL,
  CoordinatesQuality = NULL,
  Scope = NULL,
  Synonyms = "no synomyms",
  Typus = FALSE,
  Images = NULL,
  RedList = FALSE,
  MaxRecords = NULL
)

Arguments

dir

Path to directory where the file will be saved. Default is to create a "results/" directory
filename

Name of the output file
save

Logical. Save output to filename? Defaults to TRUE
basisOfRecord

Character. Any in 'PreservedSpecimen', 'LivingSpecimen', 'FossilSpecimen', 'HumanObservation', 'MachineObservation' or 'MaterialSample'. Default is 'PreservedSpecimen' for museum and herbarium search
species

Genus and epithet separated by space. More than one should be concatenated in a vector
collectionCode

Any collection available at speciesLink. Example: ALCB, E, INPA, MOBOT_BR. Accepts a vector of names
country

Any country name. No ASCII characters allowed. Accepts a vector of names
stateProvince

Any state or province. No ASCII characters allowed. Accepts a vector of names
county

Any municipality name. No ASCII characters allowed. Accepts a vector of names
Coordinates

Specify if records should have coordinates. Default is "no check" but it also accepts "Yes", No", "Original", "Automatic", "Blocked" or "no check"
CoordinatesQuality

Any character in "Good" or "Bad" to select specific type of coordinates
Scope

Group to be required. If NULL searches all groups. Any in "plants", "animals", "microrganisms" or "fossils"
Synonyms

If species names should be checked for synonyms in a specific dictionary. Set to "species2000" for search in Catálogo da Vida species2000, "flora2020" for Flora do Brasil 2020, "MycoBank" for MycoBank, "AlgaeBase" for AlgaeBase, "DSMZ" for DSMZ Prokaryotic Nomenclature Up-to-Date, "Moure" for Catálogo de Abelhas Moure or "no synonyms".
Typus

Logic. If TRUE select only typus
Images

If select only records with images. Default is NULL. It accepts: "Yes", "Live", "Polen", "Wood"
RedList

Logic. If TRUE only species in the IUCN Red List are returned
MaxRecords

Numeric. Maximum number of records to be required

Value

A list of two elements. The first element is a character string containing the url search and the second element is a data.frame with the search result. It also saves the output on disk

Author

Sara Mortara & Andrea Sánchez-Tapia

Examples

if (FALSE) {
ex01 <- rspeciesLink(filename = "ex01",
                    species =  c("Eugenia platyphylla", "Chaetocalyx acutifolia"),
                    Scope = "plants")
}