Geographic and Taxonomic Occurrence R-Based Scrubbing

Streamlines downloading and cleaning biodiversity data from Integrated Digitized Biocollections (iDigBio) and the Global Biodiversity Information Facility (GBIF).

gatoRs: Geographic and Taxonomic Occurrence R-Based Scrubbing

Natalie N. Patten, Michelle L. Gaynor, Douglas E. Soltis, and Pamela S. Soltis

Update - June 2026

In 2026, iDigBio moved to a GBIF hosted portal due to the end of their funding. A small subset of data providers did not move their recordsets over to the new hosted portal. This includes about 1.7 million records. Therefore, we modified gators_download() to pull these records from a GitHub-hosted archived download of these recordsets (downloaded on June 28, 2026). The full archived data set can be found on mgaynor1/OccurrenceArchive.

We hope you can continue to use gatoRs.

Overview

gatoRs (Geographic and Taxonomic Occurrence R-Based Scrubbing) provides users with tools for downloading and processing biodiversity data. Click here for the full user guide.

Installation

install.packages("devtools")
devtools::install_github("nataliepatten/gatoRs")

**Thank you to the CoordinateCleaner team for updating their package! We no longer have a spatial error associated with our package! **

Quick Start

Our package aims to streamline downloading and processing of biodiversity specimen data. Here is a quick example of how to download and clean with our package.

Step 1: Download

library(gatoRs)
galaxdf <- gators_download(synonyms.list = c("Galax urceolata", "Galax aphylla"), 
                write.file = FALSE,
                gbif.match = "fuzzy",
                idigbio.filter = TRUE)

Step 2: Clean

We do not recommend jumping to our full clean function. See our extended introduction here!

clean_data <- full_clean(galaxdf,
                         synonyms.list = c("Galax urceolata", "Galax aphylla"), 
                         digits = 3,
                         basis.list = c("Preserved Specimen","Physical specimen"), 
                         accepted.name = "Galax urceolata")

The gatoRs logo was created using the hexSticker package (https://github.com/GuangchuangYu/hexSticker).

Reference

Patten N, Gaynor M, Soltis D, Soltis P (2024). “Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data.” Applications in Plant Sciences 12(2):e11575. doi:10.1002/aps3.11575.