fundiversity: a modular R package to compute functional diversity indices

This is a Preprint and has not been peer reviewed. The published version of this Preprint is available: https://doi.org/10.1111/ecog.06585. This is version 6 of this Preprint.

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Authors

Matthias Grenié , Hugo Gruson

Abstract

1. Functional diversity is widely used and widespread. However, the main package used to compute functional diversity indices FD is not flexible and not adapted to the volume of data used in modern ecological analyses.

2. We here present fundiversity, an R package that eases the computation of classical functional diversity indices. It leverages parallelization and memoization (caching results in memory) to maximize efficiency with data with thousands of columns and rows.

3. We also did a performance comparison with packages that provide analog functions. In addition to being more flexible, fundiversity was always an order of magnitude quicker than alternatives.

4. fundiversity aims to be a lightweight efficient tool to compute functional diversity indices, that can be used in a variety of contexts. Because it has been designed following clear principles, it is easy to extend. We hope the wider community will adopt it and we welcome all contributions.

DOI

https://doi.org/10.32942/osf.io/dg7hw

Subjects

Biodiversity, Ecology and Evolutionary Biology, Life Sciences, Other Ecology and Evolutionary Biology, Research Methods in Life Sciences

Keywords

biodiversity, community ecology, diversity facet, diversity index, functional biogeography, functional ecology, R package

Dates

Published: 2022-07-18 05:27

Last Updated: 2023-02-15 17:46

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License

CC-By Attribution-ShareAlike 4.0 International