The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.