rspeciesLink: Gets occurrence data from speciesLink
In saramortara/rocc: Workflows for biodiversity data download and cleaning

rspeciesLink

R Documentation

Gets occurrence data from speciesLink

Description

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

Usage

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(s)

Sara Mortara & Andrea Sánchez-Tapia

Examples

## Not run: 
ex01 <- rspeciesLink(filename = "ex01",
                    species =  c("Eugenia platyphylla", "Chaetocalyx acutifolia"),
                    Scope = "plants")

## End(Not run)

saramortara/rocc documentation built on April 3, 2022, 3:41 p.m.