ecodive

Last update 5 November 2026

Copyright license MIT license, File License

Software version identifier PACKAGES.rds, 1.0.0, 2.0.0, 2.1.0, 2.2.0, 2.2.1, 2.2.2, 2.2.6, PACKAGES.rds, 2.3.1

Description

Computes alpha and beta diversity metrics in a parallel, memory-efficient manner using 'C' and 'pthreads'. Implements 51 classic, compositional, and phylogenetic indices including 'Shannon', 'Bray-Curtis', 'Faith', 'JSD', 'Hellinger', 'Robust Aitchison', and the 'UniFrac' family. Provides random sub-sampling for table rarefaction and parses 'Newick' trees into 'phylo' objects. Integrates with data structures from 'phyloseq', 'rbiom', and other common 'bioinformatics' packages. Algorithms are described in Smith 'et al.' (2026) <doi:10.21105/joss.09777>.

Cites work

ecodive: Parallel and Memory-Efficient R Package for Ecological Diversity Analysis

Cited in

(1)

rbiom

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