rspeciesLink: Gets occurrence data from speciesLink

In LimaRAF/plantR: Managing Species Records from Biological Collections

Gets occurrence data from speciesLink

Description

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

Usage

rspeciesLink(
  dir = "results/",
  filename = "output",
  save = FALSE,
  basisOfRecord = NULL,
  family = 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,
  file.format = "csv",
  compress = FALSE
)

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 FALSE
basisOfRecord	Character. Any in 'PreservedSpecimen', 'LivingSpecimen', 'FossilSpecimen', 'HumanObservation', 'MachineObservation' or 'MaterialSample'. Default is 'PreservedSpecimen' for museum and herbarium search
family	Family name. More than one name should be concatenated in a vector
species	Genus or genus and epithet separated by space. More than one species can be concatenated into a vector. The request cannot be done with more than 50 species at a time. Use lapply, or any sort of loop when dealing with multiple species.
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
file.format	Character. The file extension to be used for saving ('csv' or 'rds'). Default to 'csv'.
compress	Logical. Should the file be compressed? Default to FALSE.

Details

The time necessary to download records from the speciesLink API will depend on the number of records and species in the query and from the speed of the internet connection.

The speciesLink API does not allow the download of ~50 or more taxa at a time. So to download records from larger lists of species, you will probably need to make the queries in a loop (see Examples).

Value

A data.frame with the search result, which can also be saved on disk

Author(s)

Sara Mortara

Examples

## Not run: 
# Example for a single species, saving into a file called "ex01"
ex01 <-
 rspeciesLink(filename = "ex01",
                    species =  c("Eugenia platyphylla"),
                    Scope = "plants")
# Use lapply or similar for more than 50 species
# Making a request for multiple species
sp_list <- lapply(sp, function(x) rspeciesLink(species = x,
                                              Scope = "plants",
                                              basisOfRecord = "PreservedSpecimen",
                                              Synonyms = "flora2020"))
# Adding species names to each element of the list
names(sp_list) = sp
# Binding all searchs and keeping a column w/ the named used in the search
sp_df <- bind_rows(sp_list, .id = "original_search")

## End(Not run)

LimaRAF/plantR documentation built on Jan. 1, 2023, 10:18 a.m.