taxize: taxonomic search and retrieval in R

By S. Chamberlain, Eduard Szöcs. F1000Research, 2013

666 citations recorded by the source corpus.

All species are hierarchically related to one another, and we use taxonomic names to label the nodes in this hierarchy. Taxonomic data is becoming increasingly available on the web, but scientists need a way to access it in a programmatic fashion that’s easy and reproducible. We have developed taxize, an open-source software package (freely available from http://cran.r-project.org/web/packages/taxize/index.html) for the R language. taxize provides simple, programmatic access to taxonomic data for 13 data sources around the web. We discuss the need for a taxonomic toolbelt in R, and outline a suite of use cases for which taxize is ideally suited (including a full workflow as an appendix). The taxize package facilitates open and reproducible science by allowing taxonomic data collection to be done in the open-source R platform.

Subfields: Artificial Intelligence, Ecological Modeling, Ecology

View Paper: https://www.semanticscholar.org/paper/445a2da03f1353f238f465e8722975bf572316b1

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Citations in the corpus

Assessing different components of diversity across a river network using eDNA (2019, methodology): “We used the R packages “taxize” (Chamberlain & Szöcs, 2013, version 0.9.7) and “rentrez” (Winter, 2017, version 1.2.2) to obtain taxonomic labels based on the ac‐ cession numbers.”
camtrapR: an R package for efficient camera trap data management (2016, methodology): “…them against the ITIS taxonomic database (www.itis.gov) and returns their matching counterparts (utilizing the R package taxize (Chamberlain & Sz € ocs 2013) internally), making sure species names and spelling are standardized and taxonomically sound, and thus making it easier to combine data…”
On the inconsistency of pollinator species traits for predicting either response to land-use change or functional contribution (2018, background): “R201120829, Chamberlain and Szöcs 2013) which defines relationships among higher plants (Webb et al.”