Rocc
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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 g...
Rocc package: management and analysis of species occurrence data
![](https://raw.githubusercontent.com/liibre/Rocc_logo/master/figs/Rocc_logo.png)
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 ofrgbif()
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 seesuggest_flora()
andcheck_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.