Rocc package: management and analysis of species occurrence data

Installing and loading the package

devtools::install_github("liibre/Rocc")
library(Rocc)

Downloading and binding occurrence data from R

• rspeciesLink() downloads occurrences directly from speciesLink API

• rgbif2() downloads occurrences from GBIF, a wrapper function of rgbif() in the package rgbif

• bind_dwc() formats an output of occurrence data based on the current DarwinCore standard and bind data from the different sources such as GBIF and speciesLink

Basic taxonomic cleaning

• check_string() identifies open nomenclature, infraspecies categories, authorship, undetermined species, hybrid species, non-ascii characters in species name, digits in species name. Performs a check in the given name and returns a flag of the status and a string correction. For taxonomic check see suggest_flora() and check_flora()

• suggest_flora() trims and corrects typo of a given species name

• check_flora() makes a request to Brazilian Flora 2020 API and returns accepted name and synonyms

Direct query to Brazilian Flora 2020 database

• search_flora() searches in the List of Species of the Brazilian Flora 2020 database (by endemism, life form, habitat or vegetation type)

• update_flora() downloads, updates and formats the data from the ipt server of the List of Species of the Brazilian Flora

Additional functions

• getGADM() downloads shapefiles for administrative units for countries from https://gadm.org/data.html in either sf or sp formats

• getGAZ() downloads the corresponding DIVA-GIS gazetteer from http://www.diva-gis.org/gData

• getWDPA() downloads shapefiles from the the IUCN Global Database for Protected Areas for each country (https://www.protectedplanet.net)

Examples

For more details, see Articles section.