ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations]
Gaurav S. Kandlikar,
Zachary J. Gold,
Madeline C. Cowen,
Rachel S. Meyer,
Amanda C. Freise,
Nathan J.B. Kraft,
Jordan Moberg-Parker,
Joshua Sprague,
David J. Kushner,
Emily E. Curd
Affiliations
Gaurav S. Kandlikar
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
Zachary J. Gold
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
Madeline C. Cowen
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
Rachel S. Meyer
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
Amanda C. Freise
Department of Microbiology and Microbial Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
Nathan J.B. Kraft
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
Jordan Moberg-Parker
Department of Microbiology and Microbial Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
Joshua Sprague
Channel Islands National Park, National Park Service, Ventura, CA, USA
David J. Kushner
Channel Islands National Park, National Park Service, Ventura, CA, USA
Emily E. Curd
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results.
