liibre / Rocc

Get species occurrence data from speciesLink and GBIF, and species lists from the Brazilian Flora 2020. Perform basic taxonomic checks based on Brazilian Flora 2020. Download GADM, WDPA and DIVA-GIS gazetteer shapefiles.

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.