The Taxonomic and Biodiversity Software Stack in R

By

Chamberlain, Scott

Type

Article

Date of Publication

2017-8-12

Original Publication

Metabarcoding and metagenomics

Volume

1

Pages

1--1

Subjects

r , rstats , software , taxonomy

Contributed by

Pensoft Publishers

Language

English

Published by

Bulgaria Pensoft Publishers 2017-

Identifiers

DOI: https://doi.org/10.3897/tdwgproceedings.1.20219

 

Abstract

High quality R software for taxonomy and biodiversity occurrence data are important, both because there are a large number of biologists who use R, and because R allows reproducible and open science. I will do an overview of the software that our non-profit organization rOpenSci (https://ropensci.org) produces for both taxonomy and biodiversity work, their use cases, and future improvements. In addition, I will provide details about our latest work on software that defines taxonomic classes for consistent and powerful manipulations of taxonomic data (for example, select certain taxonomic names, and associated data are selected for those taxa). Finally, I will discuss new R software (pegax (https://github.com/ropenscilabs/pegax)) for high performance taxonomic name parsing, which will allow fast and operating system independent parsing of taxonomic names.