gatoRs: Geographic and Taxonomic Occurrence R-Based Scrubbing

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

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")

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")